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Non-denaturating isoelectric focusing gel electrophoresis for uranium-protein complexes quantitative analysis with LA-ICP MS.
Xu, Ming; Frelon, Sandrine; Simon, Olivier; Lobinski, Ryszard; Mounicou, Sandra
A non-denaturating isoelectric focusing (ND-IEF) gel electrophoresis protocol has been developed to study and identify uranium (U)-protein complexes with laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS) and electrospray ionization mass spectrometry (ESI-MS). The ND-IEF-LA-ICP MS methodology set-up was initiated using in vitro U-protein complex standards (i.e., U-bovine serum albumin and U-transferrin) allowing the assessment of U recovery to 64.4?▒?0.4 %. This methodology enabled the quantification of U-protein complexes at 9.03?▒?0.23, 15.27?▒?0.36, and 177.31?▒?25.51 nmol U L(-1) in digestive gland cytosols of the crayfish, Procambarus clarkii, exposed respectively to 0, 0.12, and 2.5 ?mol of waterborne depleted U L(-1) during 10 days. ND-IEF-LA-ICP MS limit of detection was 19.3 pmol U L(-1). Elemental ICP MS signals obtained both in ND-IEF electropherograms and in size exclusion chromatograms of in vivo U-protein complexes revealed interactions between U- and Fe- and Cu-proteins. Moreover, three proteins (hemocyanin, pseudohemocyanin-2, and arginine kinase) out of 42 were identified as potential uranium targets in waterborne-exposed crayfish cytosols by microbore reversed phase chromatography coupled to molecular mass spectrometry (ĄRPC-ESI-MS/MS) after ND-IEF separation. PMID:23665639
Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNA populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.
Quantitation of Caseins and Whey Proteins of Processed Milks and Whey Protein Concentrates, Application of Gel Electrophoresis, and Comparison with Harland-Ashworth Procedure
Jay J. Basch; Frederic W. Douglas Jr.; Lisa G. Procino; V. H. Holsinger; Harold M. Farrell Jr.
Alternate methods for quantitation of caseins and whey proteins in milk pro- ducts were investigated. The Harland- Ashworth and Leighton procedures, which are used for routine determinations of soluble whey proteins in milk, could not be adapted satisfactorily to quantitation of whey protein in blends of nonfat dry milk solids and whey protein concentrates because of problems of precipitation techniques.
Electronic imaging systems for quantitative electrophoresis of DNA
Sutherland, J.C.
Gel electrophoresis is one of the most powerful and widely used methods for the separation of DNA. During the last decade, instruments have been developed that accurately quantitate in digital form the distribution of materials in a gel or on a blot prepared from a gel. In this paper, I review the various physical properties that can be used to quantitate the distribution of DNA on gels or blots and the instrumentation that has been developed to perform these tasks. The emphasis here is on DNA, but much of what is said also applies to RNA, proteins and other molecules. 36 refs.
Quantitation of Serum Free Light Chains in Combination with Protein Electrophoresis and Clinical Information for Diagnosing Multiple Myeloma in a General Hospital Population
Armin P. Piehler; Nina Gulbrandsen; Peter Kierulf; Petter Urdal
BACKGROUND: Serum free light chain (SFLC) measure- ments have recently come into use as an aid for diag- nosing monoclonal gammopathy. We evaluated SFLC measurements in combination with serum protein electrophoresis (SPE) and clinical information for di- agnosing multiple myeloma (MM) in a hospital population.
Protein Charge Ladders, Capillary Electrophoresis, and
Prentiss, Mara
Protein Charge Ladders, Capillary Electrophoresis, and the Role of Electrostatics in Biomolecular Introduction Life rests on a web of molecular recognition;1,2 the folding of proteins, the hybridization the recognition site of the protein. Hydrophobic interactions, although still a challenge to describe
SDS capillary gel electrophoresis of proteins in microfabricated channels
Yao, Shao; Anex, Deon S.; Caldwell, W. Brett; Arnold, Don W.; Smith, Katherine B.; Schultz, Peter G.
Analysis of variations in the concentrations or structures of biomolecules (e.g., mRNAs, proteins, peptides, natural products) that occur either naturally or in response to environmental or genetic perturbations can provide important insight into complex biological processes. Many biological samples are mixtures that require a separation step before quantitation of variations in the individual components. Two-dimensional denaturing gel electrophoresis has been used very effectively to separate complex mixtures of proteins, but it is time consuming and requires considerable amounts of sample. Microchannel-based separations have proven very effective in rapidly separating small amounts of nucleic acids; more recently, isoelectric focusing of proteins also has been adapted to the microchannel format. Here, we describe microchannel-based SDS capillary gel electrophoresis of proteins and demonstrate the speed and high resolution it provides. This development is an important step toward the miniaturization and integration of multidimensional and array separation methods for complex protein mixtures. PMID:10318890
Quantitative Proteomics Using Ultralow Flow Capillary Electrophoresis¢Mass Spectrometry
In this work, we evaluate the incorporation of an ultralow flow interface for coupling capillary electrophoresis (CE) and mass spectrometry (MS), in combination with reversed-phase high-pressure liquid chromatography (HPLC) fractionation as an alternate workflow for quantitative proteomics. Proteins, extracted from a SILAC (stable isotope labeling by amino acids in cell culture) labeled and an unlabeled yeast strain were mixed and digested enzymatically in solution. The resulting peptides were fractionated using RP-HPLC and analyzed by CE¢MS yielding a total of 28?538 quantified peptides that correspond to 3?272 quantified proteins. CE¢MS analysis was performed using a neutral capillary coating, providing the highest separation efficiency at ultralow flow conditions (<10 nL/min). Moreover, we were able to demonstrate that CE¢MS is a powerful method for the identification of low-abundance modified peptides within the same sample. Without any further enrichment strategies, we succeeded in quantifying 1?371 phosphopeptides present in the CE¢MS data set and found 49 phosphopeptides to be differentially regulated in the two yeast strains. Including acetylation, phosphorylation, deamidation, and oxidized forms, a total of 8?106 modified peptides could be identified in addition to 33?854 unique peptide sequences found. The work presented here shows the first quantitative proteomics approach that combines SILAC labeling with CE¢MS analysis. PMID:25839223
Noncovalent Polycationic Coatings for Capillaries in Capillary Electrophoresis of Proteins
Gao, Jinming
Noncovalent Polycationic Coatings for Capillaries in Capillary Electrophoresis of Proteins Emilio-silica capillaries is a common problem in the analysis of proteins by capillary electrophoresis.1-3 The walls is important in extending the utility of capillary electrophoresis to a broader range of proteins
1997 Oxford University Press850860 Nucleic Acids Research, 1997, Vol. 25, No. 4 Quantitative analysis of electrophoresis data: novel
Tullius, Thomas D.
® 1997 Oxford University Press850Ł860 Nucleic Acids Research, 1997, Vol. 25, No. 4 Quantitative is employed for the separation of proteins and nucleic acids. Methods available for quantitation analysis of electrophoresis data: novel curve fitting methodology and its application to the determination
Viral quantitative capillary electrophoresis for counting intact viruses.
Mironov, Gleb G; Chechik, Alexey V; Ozer, Rachel; Bell, John C; Berezovski, Maxim V
The quantification of a virus plays an important role in vaccine development, clinical diagnostics, and environmental contamination assays. In all these cases, it is essential to calculate the concentration or number of intact virus particles (ivp) and estimate the degree of degradation and contamination of virus samples. In this work, we propose a cost-efficient, robust method for the quantification and characterization of intact viruses based on capillary zone electrophoresis. This separation method is demonstrated on vaccinia virus (VV) with oncolytic properties. After virus sample preparation, the solution contains intact VV as well as broken viruses and residual DNA from the host cell used for preparation. Regulatory requirements limit the amount of the host cell DNA that can be present in vaccines or human therapeutics. We apply capillary electrophoresis to separate intact virus particles and the residual DNA and to measure the level of virus contamination with DNA impurities. Intercalating YOYO-1 dye is used to detect the encapsulated and free DNA by laser-induced fluorescence. After soft lysis of VV with proteinase K, all encapsulated DNA is dissolved to the free DNA. The change in peak areas and a DNA calibration curve help determine the initial concentration of intact viruses. This viral quantitative capillary electrophoresis (Viral qCE) is able to quantify the oncolytic vaccinia virus in the range of 10(6) to 10(12) ivp/mL. PMID:21599011
Quantitative assay for epinephrine in dental anesthetic solutions by capillary electrophoresis
Chen, David D.Y.
Quantitative assay for epinephrine in dental anesthetic solutions by capillary electrophoresis in capillary electrophoresis. The concentration detection limit for epinephrine is about 5.0 3 1027 M (90 ng ml, linearity, accuracy and specificity. Keywords: Capillary electrophoresis; epinephrine; dental anesthetic
Differences in protein fractions of avian plasma among three commercial electrophoresis systems.
Cray, Carolyn; King, Ed; Rodriguez, Marilyn; Decker, Lilli S; Arheart, Kristopher L
Previous studies have defined the presence of 6 protein fractions in plasma from many psittaciform species. Additionally, extensive reference intervals have been published for many of these species with the Beckman Paragon electrophoresis system, which had been commonly used in clinical laboratories to analyze the protein fractions of avian plasma. In mid-2009, Beckman discontinued the Paragon product line, leaving 2 primary alternative systems: Helena and Sebia. To compare electrophoresis results from the 3 commercial protein electrophoresis systems, specimens from 40 African grey parrots (Psittacus erithacus) were analyzed with the electrophoresis systems from Beckman, Helena, and Sebia. Marked differences in fraction migration were found between the Beckman/Helena and Sebia systems, which manifested as a large decrease in prealbumin and an increase in alpha1 globulins in the latter system. Both proportional and constant errors were observed among the fraction quantitation data of both the Helena and Sebia systems compared with the Beckman system. Based on Bland-Altman plot data and imprecision studies, the Helena system appears more similar with the Beckman system, although neither the Helena nor the Sebia systems are identical to the Beckman system. Because of the differences in electrophoresis methods, clinicians should be careful to consistently use particular clinical laboratories. For best application, reference intervals should be established based on both species and electrophoresis system. PMID:21877447
Analysis of bovine whey proteins in soybean dairy-like products by capillary electrophoresis
C Garc??a-Ruiz; M Torre; M. L Marina
The simultaneous separation of bovine whey proteins [?-lactalbumin and ?-lactoglobulin (A+B)] and soybean proteins was performed, for the first time, by capillary electrophoresis. Different experimental conditions were tested. The most suitable consisted of 0.050 M phosphate buffer (pH 8) with 1 M urea and 1.2 mg\\/ml methylhydroxyethylcellulose, UV detection at 280 nm, 15 kV applied voltage, and 30░C temperature. Quantitation
Quantification of protein complexes by blue native electrophoresis.
Heidler, Juliana; Strecker, Valentina; Csintalan, Florian; Bleier, Lea; Wittig, Ilka
Blue native electrophoresis (BNE) is a long established method for the analysis of native protein complexes. Applications of BNE range from investigating subunit composition, stoichiometry, and assembly of single protein complexes to profiling of whole complexomes. BNE is an indispensible tool to diagnostically analyze cells and tissues from patients with mitochondrial disorders or model organisms. Since functional proteomic studies often require quantification of protein complexes, we describe here different quantification methods subsequent to protein complex separation by BNE. PMID:23996189
Developmental appearance of proteins identified by two-dimensional gel electrophoresis in mouse gonadal tissue.
Durbin, E J; Erickson, R P; Van Keuren, M L; Iacob, R A; Kurnit, D M
Gonadal protein patterns of the mouse were studied during fetal development by two-dimensional gel electrophoresis. Fetal mice at days 8.5, 10.5, 12.5, and 14.5 post-coitum were analyzed for male or female specific proteins. Although no sex specific proteins were found, several proteins were found which were expressed in significantly different amounts in the two sexes at about the time of gonadal differentiation. Hence, quantitative differences, rather than qualitative ones, could be related to the initiation of testis or ovary development. PMID:2015082
Fractionation of Serum Proteins by Zone Electrophoresis in Glass Powder
C. J. Bradish; Nan V. Smart
IN connexion with recent electrophoretic studies of ox serum1, it became necessary to establish a reliable method for the fractionation of serum proteins which would allow numerous samples to be separated into distinct fractions of sufficient volume and concentration for subsequent physico-chemical and biological characterization. Zone electrophoresis2 appeared to be the method of choice, and the apparatus here described is
Electrophoresis. Author manuscript Improvement of the solubilization of proteins in two-dimensional
Paris-Sud XI, Universitķ de
Electrophoresis. Author manuscript Page /1 10 Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients Rabilloud Thierry 1 * , Adessi C. 3 , Giraudel A. 2 , Lunardi J. 1 of sparingly-soluble (membrane and nuclear) proteins by high resolution two-dimensional electrophoresis. IEF
Protein Separation by Capillary Gel Electrophoresis: A Review
Zhu, Zaifang; Lu, Joann J.; Liu, Shaorong
Capillary gel electrophoresis (CGE) has been used for protein separation for more than two decades. Due to the technology advancement, current CGE methods are becoming more and more robust and reliable for protein analysis, and some of the methods have been routinely used for the analysis of protein-based pharmaceuticals and quality controls. In light of this progress, we survey 147 papers related to CGE separations of proteins and present an overview of this technology. We first introduce briefly the early development of CGE. We then review the methodology, in which we specifically describe the matrices, coatings, and detection strategies used in CGE. CGE using microfabricated channels and incorporation of CGE with two-dimensional protein separations are also discussed in this section. We finally present a few representative applications of CGE for separating proteins in real-world samples. PMID:22122927
Protein Quantitation Using Mass Spectrometry
Zhang, Guoan; Ueberheide, Beatrix M.; Waldemarson, Sofia; Myung, Sunnie; Molloy, Kelly; Eriksson, Jan; Chait, Brian T.; Neubert, Thomas A.; Feny÷, David
Mass spectrometry is a method of choice for quantifying low-abundance proteins and peptides in many biological studies. Here, we describe a range of computational aspects of protein and peptide quantitation, including methods for finding and integrating mass spectrometric peptide peaks, and detecting interference to obtain a robust measure of the amount of proteins present in samples. PMID:20835801
Procedures for two-dimensional electrophoresis of proteins
Tollaksen, S.L.; Giometti, C.S.
High-resolution two-dimensional gel electrophoresis (2DE) of proteins, using isoelectric focusing in the first dimension and sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) in the second, was first described in 1975. In the 20 years since those publications, numerous modifications of the original method have evolved. The ISO-DALT system of 2DE is a high-throughput approach that has stood the test of time. The problem of casting many isoelectric focusing gels and SDS-PAGE slab gels (up to 20) in a reproducible manner has been solved by the use of the techniques and equipment described in this manual. The ISO-DALT system of two-dimensional gel electrophoresis originated in the late 1970s and has been modified many times to improve its high-resolution, high-throughput capabilities. This report provides the detailed procedures used with the current ISO-DALT system to prepare, run, stain, and photograph two-dimensional gels for protein analysis.
A rapid quantitative determination of phenolic acids in Brassica oleracea by capillary zone electrophoresis
Iris S. L. Lee; Mary C. Boyce; Michael C. Breadmore
A simple and rapid capillary zone electrophoresis method to quantitatively determine the phenolic acid contents in brassica vegetables is described. Phenolic compounds were extracted from broccoli, broccolini, Brussels sprouts, cabbage and cauliflower and the main hydroxycinnamic acids (sinapic, ferulic, p-coumaric and caffeic acids) were isolated by solid phase extraction with C18 cartridges. Using an optimised method, the four analytes were
Study of quantitative structure¢mobility relationship of carboxylic and sulphonic acids in capillary electrophoresis
Chunxia Xue; Huanxiang Liu; Xiaojun Yao; Mancang Liu; Zhide Hu; Botao Fan
A quantitative structure¢mobility relationship (QSMR) was developed for the absolute mobilities of 115 carboxylic and sulphonic acids in capillary electrophoresis based on the descriptors calculated from the structure alone. The heuristic method (HM) and radial basis function neural networks (RBFNN) were utilized to construct the linear and nonlinear prediction models, respectively. The prediction results were in agreement with the experimental
Capillary zone electrophoresis and capillary electrophoresis-mass spectrometry for analyzing qualitative and quantitative variations in therapeutic albumin.
Marie, Anne-Lise; Przybylski, Cķdric; Gonnet, Florence; Daniel, Rķgis; Urbain, Rķmi; Chevreux, Guillaume; Jorieux, Sylvie; Taverna, Myriam
The present study describes a reproducible and quantitative capillary zone electrophoresis (CZE) method, which leads to the separation of nine forms (native, oxidized and glycated) of human serum albumin (HSA). In an attempt to identify the different species separated by this CZE method, the capillary electrophoresis was coupled to mass spectrometry using a sheath liquid interface, an optimized capillary coating and a suitable CE running buffer. CE-MS analyses confirmed the heterogeneity of albumin preparation and revealed new truncated and modified forms such as Advanced Glycation End products (AGEs). Assignment of the CZE peaks was carried out using specific antibodies, carboxypeptidase A or sample reduction before or during the CE separation. Thus, five HSA forms were unambiguously identified. Using this CZE method several albumin batches produced by slightly different fractionation ways could be discriminated. Furthermore, analyses of HSA preparations marketed by five pharmaceutical industries revealed that two therapeutic albumins, including that marketed by LFB, contained the highest proportion of native form and lower levels of oxidized forms. PMID:24120174
Rapid electrophoresis and quantitation of haemoglobins on cellulose acetate
Marengo-Rowe, A. J.
A rapid and reproducible electrophoretic method for the separation and quantitation of haemoglobins on cellulose acetate is described. The accuracy of the method and its possible sources of error are discussed. The normal range for haemoglobin A2 by this method is 1% to 3% of the total haemoglobin concentration. Blood samples from 32 thalassaemic patients showed haemoglobin A2 values of 3Ę5% to 7%. Images PMID:5844210
Quantitative analysis of sugar constituents of glycoproteins by capillary electrophoresis
Fu-Tai A. Chen; Thomas S. Dobashi; Ramon A. Evangelista
A method for quantitative analysis of monosaccharides including N-acetylneuraminic acid derived from sialic acid- containing oligosaccharides and glycoproteins is presented. The analysis is based on the combination of chemical and enzymatic methods coupled with capillary electrophoretic (CE) separation and laser-induced fluorescence (LIF) detection. The present method utilizes a simplified acid hydrolysis procedure consisting of mild hydrolysis (0.1 M TFA) to
Maturation of Norway maple (Acer platanoides L.) seeds produces deep physiological dormancy and resistance to desiccation. This study used two-dimensional electrophoresis to investigate the protein products of genes activated during the complex developmental process of maturation. Qualitative and quantitative changes in protein composition during maturation were tracked in this species. The most intensive changes in protein content appeared at the
PhosphorImager enhancement of sedimentation equilibrium-quantitative polyacrylamide gel electrophoresis: a highly sensitive technique for quantitation of equilibrium gradients of individual components in mixtures.
Darawshe, S; Merezhinskaya, N; Minton, A P
The technique called sedimentation equilibrium-quantitative polyacrylamide gel electrophoresis (Darawshe et al. (1993) Anal. Biochem. 215, 236-242) has been extended to permit the quantitation and analysis of gradients of individual radiolabeled components in a mixture of radiolabeled solutes centrifuged to sedimentation equilibrium. Immediately following centrifugation, the contents of a sample tube are fractionated into aliquots corresponding to laminae of solution at different radial positions in the centrifuge. Following treatment with sodium dodecyl sulfate-containing buffer, a portion of each fraction is subjected to electrophoresis on a polyacrylamide gel. The gel is then incubated with a strong phosphor plate and subsequently scanned with a Molecular Dynamics PhosphorImage. The concentration of an individual radiolabeled component at a particular radial distance is proportional to the integrated intensity of the image of the radiolabeled band of that component in the fraction corresponding to that radial distance. Concentration gradients reconstructed in this fashion are interpreted in the context of conventional sedimentation equilibrium theory. The results of control experiments carried out with purified proteins of known molar mass and the measurement of the molar mass of a new, partially purified protein are reported. PMID:8533898
Quantitative bioanalysis of enantiomeric drugs using capillary electrophoresis and electrospray mass spectrometry
Erick K Kindt; Stephen Kurzyniec; Shau-Chun Wang; Gregory Kilby; David T Rossi
A novel assay method for an enantiomeric pair of drugs has been developed using a combination of capillary electrophoresis and electrospray tandem mass spectrometry connected with a homemade interface. Accurate quantification was demonstrated in plasma from 0.25 to 50 ?g\\/ml. A liquid¢liquid sample preparation technique allowed improvement in the quantitation limit to 10 ng\\/ml. Variables for the enantiomeric separation, including
Protein Electrophoresis in the Biology Classroom Using "Safe" Gels.
ERIC Educational Resources Information Center
Atkins, Thomas
Describes the use of electrophoresis in the high school utilizing two new gels that are easy to pour, do not require degassing, can be used on a horizontal gel electrophoresis, and are not neurotoxic or carcinogenic health hazards. Large diagrams and written instructions are used to present the protocol of setting up the electrophoresis. (PR)
Detection of Ā and Ā Light Chain Monoclonal Proteins in Human Serum: Automated Immunoassay versus Immunofixation Electrophoresis
Troy D. Jaskowski; Christine M. Litwin; Harry R. Hill
Recently, turbidimetric immunoassays for detecting and quantifying and free light chains (FLC) have become available and are promoted as being more sensitive than immunofixation electrophoresis (IFE) in detecting FLC monoclonal proteins. In this study, we assessed the ability of these turbidimetric assays to detect serum monoclonal proteins involving both free and heavy-chain-bound and light chains compared to standard immunofixation electrophoresis.
Quantitative aspects of rare earth metal determinations using capillary electrophoresis with indirect absorbance detection
Colburn, B.A.; Starnes, S.D.; Sepaniak, M.J. [Univ. of Tennessee, Knoxville, TN (United States)] [and others
The practical utility of capillary zone electrophoresis with indirect absorbance detection is examined for the separation and quantitation of rare earth metals. Various imidazole derivatives are investigated as to their suitability as running buffer (displaceable) detection ions with {alpha}-hydroxyisobutyric acid functioning as a chelating agent to enhance separations. Parameters important for quantitative analysis, such as limits of detection, relative standard deviation of peak areas, efficiency, resolution, peak shape and linear dynamic range are presented. The influence of sample matrix, method of injection, and background ion identity on these parameters are investigated and discussed.
MP 33200 EZQ Protein Quantitation Kit
Lebendiker, Mario
quantitation kit is ideal for determining protein concentra- tions of samples prior to polyacrylamide gelMP 33200 EZQ« Protein Quantitation Kit Product Information Storage upon receipt: Ę Room temperature Introduction The EZQ« Protein Quantitation Kit provides a fast and simple assay for proteins in solution
Quantitative determination of alginic acid in pharmaceutical formulations using capillary electrophoresis.
Moore, Douglas E; Miao, William G; Benikos, Con
A capillary electrophoresis (CE) method has been developed and validated for the quantitative determination of alginic acid, which is used as a rafting agent in complex antacid formulations. The method involves a preliminary separation of the alginic acid from the formulation by washing the sample matrix with methanol, diluted HCl and water. This is followed by electrophoresis within a fused silica capillary using borate/boric acid buffer as the electrolyte, and the quantification is performed by a UV detector monitoring at 200 nm, where the intrinsic absorption of alginic acid is measured. An assay precision of better than 3% was achieved in intra- and interday determinations. No interference was found from the matrix of the antacid formulations. PMID:14738939
Capillary electrophoresis methods for the determination of covalent polyphenol-protein complexes.
Trombley, John D; Loegel, Thomas N; Danielson, Neil D; Hagerman, Ann E
The bioactivities and bioavailability of plant polyphenols including proanthocyanidins and other catechin derivatives may be affected by covalent reaction between polyphenol and proteins. Both processing conditions and gastrointestinal conditions may promote formation of covalent complexes for polyphenol-rich foods and beverages such as wine. Little is known about covalent reactions between proteins and tannin, because suitable methods for quantitating covalent complexes have not been developed. We established capillary electrophoresis methods that can be used to distinguish free protein from covalently bound protein-polyphenol complexes and to monitor polyphenol oxidation products. The methods are developed using the model protein bovine serum albumin and the representative polyphenol (-)epigallocatechin gallate. By pairing capillaries with different diameters with appropriate alkaline borate buffers, we are able to optimize resolution of either the protein-polyphenol complexes or the polyphenol oxidation products. This analytical method, coupled with purification of the covalent complexes by diethylaminoethyl cellulose chromatography, should facilitate characterization of covalent complexes in polyphenol-rich foods and beverages such as wine. PMID:21400190
Quantitative determination of vitexin-2-O-rhamnoside in common oats using HPLC and capillary electrophoresis
M. V. Gavrilin; S. P. Senchenko; R. M. Gusov
Methods for quantitative determination of active substances in common oats were developed. The marker constituent was vitexin-2-O-rhamnoside.\\u000a HPLC and capillary electrophoresis were used to develop the analytical methods. HPLC over a reversed-phase column (4.6 ū 150\\u000a mm) with gradient elution detected over 40 constituents. Vitexin-2-O-rhamnoside had a content from 0.04 to 0.18% and accumulated\\u000a in leaves and stems much more
Quantitative bioanalysis of enantiomeric drugs using capillary electrophoresis and electrospray mass spectrometry.
Kindt, Erick K; Kurzyniec, Stephen; Wang, Shau-Chun; Kilby, Gregory; Rossi, David T
A novel assay method for an enantiomeric pair of drugs has been developed using a combination of capillary electrophoresis and electrospray tandem mass spectrometry connected with a homemade interface. Accurate quantification was demonstrated in plasma from 0.25 to 50 microg/ml. A liquid-liquid sample preparation technique allowed improvement in the quantitation limit to 10 ng/ml. Variables for the enantiomeric separation, including chiral selective reagent, organic solvents, buffer and acid concentration as well as injection technique, were optimized. This assay proved adequate for analysis of neat, spiked plasma, and plasma from a pharmacological study of the drug enantiomers. PMID:12684102
Studies on middle silkgland proteins of cocoon colour sex-limited silkworm ( Bombyx mori L.) using two-dimensional polyacrylamide gel electrophoresis
Yuan-Xiang Jin; Yu-Yin Chen; Meng-Kui Xu; Yong-Huang Jiang
Qualitative and quantitative differences in proteins expressed in the middle silkglands of male and female silkworm larvae\\u000a that differ in silk colour were investigated by high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE),\\u000a followed by computer assisted image analysis. About 1000 protein spots were resolved in both the sexes and most proteins were\\u000a shown to be distributed in the area
Comparison of capillary electrophoresis with traditional methods to analyse bovine whey proteins
Nicki M. Kinghorn; Carmen S. Norris; Geoff R. Paterson; Don E. Otter
The separation of the four major whey proteins by sodium dodecyl sulphate (SDS)-capillary gel electrophoresis (CGE) is described. Whilst commercially purified whey proteins could be analysed using the recommended protocol, the more complex nature of an acid whey and a reconstituted whey protein concentrate (WPC) powder necessitated considerable refinement of the CGE sample buffer. Individual whey proteins in the acid
Buxbaum, Engelbert
Denaturing, discontinuous electrophoresis in the presence of SDS has become a standard method for the protein scientist. However, there are situations where this method produces suboptimal results. In these cases, electrophoresis in the presence of positively charged detergents such as cetyltrimethylammonium bromide (CTAB) may work considerably better. Methods for electrophoresis and staining of such gels are presented. PMID:22585477
Technology Transfer Automated Retrieval System (TEKTRAN)
Most research concerning grain proteins has concentrated upon the gluten storage proteins. The albumins and globulins are the water and salt soluble proteins that contain biologically active enzymes and enzyme inhibitors. A Free Zone Capillary electrophoresis method was developed to separate these p...
Charge Shift Electrophoresis: Simple Method for Distinguishing between Amphiphilic and Hydrophilic Proteins in Detergent Solution
Ari Helenius; Kai Simons
Seventeen hydrophilic proteins and five amphiphilic membrane proteins were subjected to agarose gel electrophoresis in the presence of a nonionic detergent (Triton X-100), a mixture of a nonionic and an anionic detergent (Triton X-100 and sodium deoxycholate), and a mixture of a nonionic and a cationic detergent (Triton X-100 and cetyltrimethylammonium bromide). The electrophoretic mobility of the hydrophilic proteins was
[Quantitative study of multimolecular forms of serum gamma glutamyl transferase by polyacrylamide gel electrophoresis].
Staeffen, J; Ballan, P; Ferrer, J; Beylot, J; Series, C; Terme, R
The quantitative distribution of the multimolecular forms of serum gamma-glutamyl-transferase is studied in 286 sera by acrylamide gel electrophoresis, incubation, coloration in situ, photography, slide reading and integration. In 43 normal sera, the fast fraction represents 66% of the total activity; the ratio of the mean fast fraction to the medium and slow fraction was 2. During pregnancy (53 cases), in cord blood (54 cases), in hepatic cytolysis or cholestasis (55 cases), and in secondary liver carcinoma (21 cases), this ratio is considerably lower, demonstrating the predominance of medium and slow fractions. A similar decrease in the ratio, with predominance of the medium and slow fractions was seen in 22 cases of advanced cancer without metastases in the liver. PMID:241044
The qualitative and quantitative determination of quinolones of first and second generation by capillary electrophoresis.
Fierens, C; Hillaert, S; Van den Bossche, W
Capillary electrophoresis (CE) was applied to the study of 10 quinolones of first and second generation--nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, ciprofloxacin, ofloxacin, pefloxacin, fleroxacin, and flumequine. Separation was performed on a fused silica capillary (75 microm-60 cm) using a phosphate buffer (pH 7.0, 125 mM). Detection was at 214 nm. Only norfloxacin and ciprofloxacin cannot be separated in this way. Because of the specificity of the method, the identification of the individual quinolones by their migration time was possible. The same system has been applied for the quantitative determination of quinolones in tablets and capsules. Excipients do not adversely affect the results. Some parameters (linearity, precision, accuracy) were validated. Especially the possibility of simultaneous quantification and identification of the active ingredient in the finished product is very attractive. PMID:10815719
Pollen proteins after two-dimensional gel electrophoresis and pollen morphology of the amphiploids Aegilops kotschyi and Ae. variabilis with Secale cereale
A. Kalinowski; K. Winiarczyk; B. Wojciechowska
Proteins from pollen of parent forms and amphiploids Aegilops\\u000a variabilis ūSecale cereale and Ae. kotschyiūS. cereale, obtained by in vitro propagation or colchicine treatment of F1 hybrids, were subjected to a study by two-dimensional (2-D) electrophoresis. Qualitative and quantitative diversities of\\u000a protein patterns were revealed for the amphiploid pollen. The majority of peptides found in the parent forms were also
Resolving Acetylated and Phosphorylated Proteins by Neutral Urea Triton-Polyacrylamide Gel Electrophoresis, NUT-PAGE
Buehl, Christopher J.; Deng, Xiexiong; Liu, Mengyu; Hovde, Stacy; Xu, Xinjing; Kuo, Min-Hao
Protein acetylation and phosphorylation can be key modifications that regulate both normal and pathological protein functions. Current gel systems used to analyze modified proteins require either expensive reagents or time¢consuming second dimension electrophoresis. In this manuscript, we present a neutral pH gel system that allows the analysis of acetylated and phosphorylated proteins. This neutral pH urea Triton-polyacrylamide gel electrophoresis system, or NUT-PAGE, separates proteins based on their charge at pH 7 and generates discrete bands from each acetylated and phosphorylated species. In addition, the gel is composed of common and inexpensive laboratory reagents, and requires only a single dimension of electrophoresis. We are able to demonstrate the effectiveness of this system by analyzing phosphorylated species of an acidic protein, ?-synuclein, and both acetylated and phosphorylated species of a basic protein, histone H3. NUT-PAGE thus provides a cost-effective alternative to resolving acetylated and phosphorylated proteins, and potentially proteins with other post-translational modifications that alter net charge. Method Summary Here we present a single-dimension neutral pH urea Triton-polyacrylamide gel electrophoresis (NUT-PAGE) system affording high-resolution separation of acetylated and phosphorylated proteins. PMID:25109292
Technology Transfer Automated Retrieval System (TEKTRAN)
High performance capillary electrophoresis (HPCE) is an analytical method that uses a voltage differential to accurately move solvents and solutes through a capillary. HPCE is a relative newcomer to the field of cereal chemistry, it utilizes small inner diameter capillaries as an anti-convective med...
Application of electrophoresis and related methods, such as western blotting and zymography to the study of some proteins and enzymes
Maurice Pagano
Electrophoresis and related methods are currently used by laboratories working on proteins. This review focuses on four different applications of acrylamide electrophoresis related to protein study:1.Polyacrylamide gel electrophoresis with or without SDS (PAGE or SDS-PAGE).2.Polyacrylamide gels electrofocusing, western blotting and zymography.Basic principles and usual applications to proteins are discussed, then examples selected in different areas of biochemistry and cell biology
Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis Thierry RABILLOUD*,
Paris-Sud XI, Universitķ de
Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis Thierry mainly with chaotropes and new detergents, which are both able to enhance protein solubility. The input. Chaotropes. Detergents. Zwitterionic detergents. hal-00373287,version1-3Apr2009 Author manuscript, published
The sieving of spheres during agarose gel electrophoresis: quantitation and modeling.
Griess, G A; Moreno, E T; Easom, R A; Serwer, P
By use of agarose gel electrophoresis, the sieving of spherical particles in agarose gels has been quantitated and modeled for spheres with a radius (R) between 13.3 and 149 nm. For quantitation, the electrophoretic mobility has been determined as a function of agarose percentage (A). Because a previously used model of sieving [D. Rodbard and A. Chrambach (1970) Proc. Natl. Acad. Sci. USA 65, 970-977] was found incompatible with some of these data, alternative models have been tested. By use of an underivatized agarose, two models, both based on the assumption of a single effective pore radius (PE) for each A, were found to yield PE values that were independent of R and that were in agreement with values of PE obtained independently (PE = 118 nm X A-0.74): sieving by altered hydrodynamics in a cylindrical tube of radius, PE, and sieving by steric exclusion from a circular hole of radius, PE. The same analysis applied to a 6.5% hydroxyethylated commercial agarose yielded a steeper PE vs A plot and also agreement of the above two models with the data. The PE vs A plot was significantly altered by both further hydroxyethylation and factors that cause variation in the electro-osmosis found in commercial agarose. PMID:2752101
Viral quantitative capillary electrophoresis for counting and quality control of RNA viruses.
Azizi, Afnan; Mironov, Gleb G; Muharemagic, Darija; Wehbe, Mohamed; Bell, John C; Berezovski, Maxim V
The world of health care has witnessed an explosive boost to its capacity within the past few decades due to the introduction of viral therapeutics to its medicinal arsenal. As a result, a need for new methods of viral quantification has arisen to accommodate this rapid advancement in virology and associated requirements for efficiency, speed, and quality control. In this work, we apply viral quantitative capillary electrophoresis (viral qCE) to determine (i) the number of intact virus particles (ivp) in viral samples, (ii) the amount of DNA contamination, and (iii) the degree of viral degradation after sonication, vortexing, and freeze-thaw cycles. This quantification method is demonstrated on an RNA-based vesicular stomatitis virus (VSV) with oncolytic properties. A virus sample contains intact VSV particles as well as residual DNA from host cells, which is regulated by WHO guidelines, and may include some carried-over RNA. We use capillary zone electrophoresis with laser-induced fluorescent detection to separate intact virus particles from DNA and RNA impurities. YOYO-1 dye is used to stain all DNA and RNA in the sample. After soft lysis of VSV with proteinase K digestion of viral capsid and ribonucleoproteins, viral RNA is released. Therefore, the initial concentration of intact virus is calculated based on the gain of a nucleic acid peak and an RNA calibration curve. After additional NaOH treatment of the virus sample, RNA is hydrolyzed leaving residual DNA only, which is also calculated by a DNA calibration curve made by the same CE instrument. Viral qCE works in a wide dynamic range of virus concentrations from 10(8) to 10(13) ivp/mL. It can be completed in a few hours and requires minimum optimization of CE separation. PMID:23046075
Protein electrophoresis as a diagnostic and prognostic tool in raptor medicine.
Tatum, L M; Zaias, J; Mealey, B K; Cray, C; Bossart, G D
Plasma proteins of 139 healthy adult birds of prey from 10 species were separated by electrophoresis to characterize and document normal reference ranges and species-specific electrophoretic patternsand to evaluate the value of this technique for health screening, disease diagnosis, and prognostic indication. Species studied included bald eagle (Haliaeetus leucocephalus), red-tailed hawk (Buteo jamaicensis), barn owl (Tyto alba), great horned owl (Bubo virginianus), turkey vulture (Cathartes aura), Harris' hawk (Parabuteo unicinctus), Stellar's sea eagle (Haliaeetus pelagicus), barred owl (Strix varia), screech owl (Otus asio), and black vulture (Coragyps atratus). Several clinical cases show the diagnostic/therapeutic value of protein electrophoresis in raptors. This study establishes species-specific reference ranges for several birds of prey and discusses the benefit of electrophoresis as a diagnostic technique in health screens, as a diagnostic aid in conjunction with other tests, and as a prognostic indicator in clinical evaluation of raptors. PMID:11428396
Internal amino acid sequence analysis of proteins separated by gel electrophoresis after tryptic digestion in polyacrylamide matrix
Ch. Eckerskorn; F. Lottspeich
SummaryĀĀA method is described for obtaining peptide fragments for sequence analysis from microquantities of proteins separated by 1- or 2-dimensional polyacrylamide gel electrophoresis. After separation by electrophoresis, the proteins were stained with Coomassie Blue and excised. Proteolytic digestion with trypsin was performed directly in the polyacrylamide matrix. The resulting peptide fragments were eluted, separated by reversed phase HPLC, collected and
Determination of free L- and D-alanine in hydrolysed protein fertilisers by capillary electrophoresis.
Cavani, Luciano; Ciavatta, Claudio; Gessa, Carlo
of racemisation of hydrolysed protein fertilisers (HPFs) using an The objective of this study was to determine the degree inexpensive and easy to handle analytical method for qualitative control of the products. Using a polyacrylamide coated capillary and a run buffer containing 0.1 M Tris-borate+2.5 mM EDTA-Na2+0.1% sodium dodecylsulfate+10 mM beta-cyclodextrin a quantitative separation of D- and L-alanine (Ala) was made from an not treated HPF sample derivatised with dansyl chlorine by capillary electrophoresis. The D-Ala:[D-Ala+L-Ala] ratio, called degree of racemisation (RD), was calculated. The analysis of ten commercial HPFs has shown that more than 60% of HPFs have an RD > or = 40%. while only one product has shown an RD <5%. These results showed that most of the HPFs on the market are obtained with strong hydrolytic processes and high contents of D-amino acids are probably less effective as plant nutrients or even potentially dangerous to plants. PMID:12580515
Targeted Quantitation of Proteins by Mass Spectrometry
Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332
Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins
ERIC Educational Resources Information Center
Kim, Thomas D.; Craig, Paul A.
Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparationģ
Can You Solve the Crime? Using Agarose Electrophoresis To Identify an Unknown Colored Protein.
ERIC Educational Resources Information Center
Wiltfong, Cynthia L.; Chester, Emily; Albertin, Faith; Smith, Julia; Hall, Judith C.; Arth, Emily C.; Martin, Stephanie
Describes a lab that introduces agarose electrophoresis techniques and basic information on proteins to middle school and high school students. Insists that, built around a scenario in which students must solve a crime, the lab has real-world applications that should spark student interest. (KHR)
Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye.
Fujii, Kazuyasu; Kondo, Tadashi; Yokoo, Hideki; Okano, Tetsuya; Yamada, Masayo; Yamada, Tesshi; Iwatsuki, Keiji; Hirohashi, Setsuo
CyDye DIGE Fluor saturation dye (saturation dye, GE Healthcare Amersham Biosciences) enables highly sensitive 2-D PAGE. As the dye reacts with all reduced cysteine thiols, 2-D PAGE can be performed with a lower amount of protein, compared with CyDye DIGE Fluor minimal dye (GE Healthcare Amersham Biosciences), the sensitivity of which is equivalent to that of silver staining. We constructed a 2-D map of the saturation dye-labeled proteins of a liver cancer cell line (HepG2) and identified by MS 92 proteins corresponding to 123 protein spots. Functional classification revealed that the identified proteins had chaperone, protein binding, nucleotide binding, metal ion binding, isomerase activity, and motor activity. The functional distribution and the cysteine contents of the proteins were similar to those in the most comprehensive 2-D database of hepatoma cells (Seow et al.., Electrophoresis 2000, 21, 1787-1813), where silver staining was used for protein visualization. Hierarchical clustering on the basis of the quantitative expression profiles of the 123 characterized spots labeled with two charge- and mass-matched saturation dyes (Cy3 and Cy5) discriminated between nine hepatocellular carcinoma cell lines and primary cultured hepatocytes from five individuals, suggesting the utility of saturation dye and our database for proteomic studies of liver cancer. PMID:16429455
Increase in local protein concentration by field-inversion gel electrophoresis
Tsai, Henghang; Low, Teck Yew; Freeby, Steve; Paulus, Aran; Ramnarayanan, Kalpana; Cheng, Chung-pui Paul; Leung, Hon-chiu Eastwood
Background Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE). Results Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE) in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE) showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS), which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. Conclusion The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein separation tool. PMID:17897441
Changes in the actinomycetal communities during continuous thermophilic composting as revealed by denaturing gradient gel electrophoresis and quantitative PCR
Yong Xiao; Guang-Ming Zeng; Zhao-Hui Yang; Yan-He Ma; Cui Huang; Zheng-Yong Xu; Jing Huang; Chang-Zheng Fan
Actinomycetes degrade cellulose and solubilize lignin during composting. Changes in the diversity of the actinomycetal communities and the 16S rDNA copy numbers of actinomycetes were monitored by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR), respectively, during continuous thermophilic composting (CTC) and traditional composting (TC). qPCR indicated that the copy numbers from the CTC samples were 25¢80% higher than
Monitoring Equilibria and Kinetics of Protein Folding\\/Unfolding Reactions by Capillary Zone Electrophoresis
Barbara Verzola; Fabrizio Chiti; Giampaolo Manao; Pier Giorgio Righetti
A method is described here for studying conformational transitions of proteins due to denaturing agents: capillary zone electrophoresis (CZE) in acidic, isoelectric buffers. The sample is run in 50 mM isoelectric glutamic acid (pH = pI = 3.2) added with 1 mM oligoamine (tetraethylene pentamine) for quenching protein interaction to the capillary wall (final pH = 3.3). Muscle acylphosphatase (AcP),
High Resolution Two-Dimensional Electrophoresis of Human Plasma Proteins
Leigh Anderson; Norman G. Anderson
The two-dimensional electrophoretic technique of O'Farrell has been adapted to the analysis of human plasma proteins, and 30 polypeptides have been identified in the pattern produced. Genetic variants involving charge (isoelectric point) or size (molecular weight in the presence of sodium dodecyl sulfate) changes should be routinely detectable in at least 20 proteins at once, facilitating studies of human mutation
From: Methods in Molecular Biology, vol. 276: Capillary Electrophoresis of Proteins and Peptides Edited by: M. A. Strege and A. L. Lagu Humana Press Inc., Totowa, NJ
Dubin, Paul D.
FACCE 217 217 From: Methods in Molecular Biology, vol. 276: Capillary Electrophoresis of Proteins Continuous Capillary Electrophoresis for ProteinŁPolyelectrolyte Binding Studies Emek Seyrek, Toshiaki electrophoresis (FACCE), has been described as an effective way to study proteinŁpolyelectrolyte binding. FACCE
Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries
A hybrid microchip/capillary electrophoresis (CE) system was developed to allow unbiased and lossless sample loading and high-throughput repeated injections. This new hybrid CE system consists of a poly(dimethylsiloxane) (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel, and a fused-silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channel and the fused-silica capillary separation column. Analytes are rapidly separated in the fused-silica capillary, and following separation, high-sensitivity MS detection is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high-throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates, and CE separation voltages. PMID:24865952
Interpretive Reporting of Protein Electrophoresis Data by Microcomputer
Talamo, Thomas S.; Losos, Frank J.; Kessler, G. Frederick
A microcomputer based system for interpretive reporting of protein electrophoretic data has been developed. Data for serum, urine and cerebrospinal fluid protein electrophoreses as well as immunoelectrophoresis can be entered. Patient demographic information is entered through the keyboard followed by manual entry of total and fractionated protein levels obtained after densitometer scanning of the electrophoretic strip. The patterns are then coded, interpreted, and final reports generated. In most cases interpretation time is less than one second. Misinterpretation by computer is uncommon and can be corrected by edit functions within the system. These discrepancies between computer and pathologist interpretation are automatically stored in a data file for later review and possible program modification. Any or all previous tests on a patient may be reviewed with graphic display of the electrophoretic pattern. The system has been in use for several months and is presently well accepted by both laboratory and clinical staff. It also allows rapid storage, retrieval and analysis of protein electrophoretic datab.
Human plasma protein adsorption onto dextranized surfaces: a two-dimensional electrophoresis and mass spectrometry study
Tsai, Irene Y.; Tomczyk, Nancy; Eckmann, Joshua I.; Composto, Russell J.; Eckmann, David M.
Protein adsorption is fundamental to thrombosis and to the design of biocompatible materials. We report a two-dimensional electrophoresis and mass spectrometry study to characterize multiple human plasma proteins adsorbed onto four different types of model surfaces: silicon oxide, dextranized silicon, polyurethane and dextranized polyurethane. Dextran was grafted onto the surfaces of silicon and polyurethane to mimic the blood-contacting endothelial cell glycocalyx surface. Surface topography and hydrophobicity/hydrophilicity were determined and analyzed using atomic force microscopy and water contact angle measurements, respectively. Using two-dimensional electrophoresis, we show that, relative to the unmodified surfaces, dextranization significantly inhibits the adsorption of several human plasma proteins including IGHG1 protein, fibrinogen, haptoglobin, Apo A-IV, Apo A-I, immunoglobulin, serum retinal-binding protein and truncated serum albumin. We further demonstrate the selectivity of plasma protein adsorbed onto the different functionalized surfaces and the potential to control and manipulate proteins adsorption on the surfaces of medical devices, implants and microfluidic devices. This result shows that adsorption experiments using a single protein or a binary mixture of proteins are consistent with competitive protein adsorption studies. In summary, these studies indicate that coating blood-contacting biomedical applications with dextran is an effective route to reduce thrombo-inflammatory responses and to surface-direct biological activities. PMID:21277175
Monitoring nutritional quality of milk powders: capillary electrophoresis of the whey protein fraction compared with other methods
J De Block; M Merchiers; L Mortier; A Braekman; W Ooghe; R Van Renterghem
Deterioration due to Maillard reaction, of milk powder upon storage was monitored by capillary electrophoresis, IEF, amino acid analysis and determination of furosine, HMF, browning index and available lysine. In comparison with these other methods, capillary electrophoresis of ?-lactoglobulin, revealing a native and a modified fraction of this protein, proved to be a fast, easy and sensitive method for monitoring
Fully automated two-dimensional electrophoresis system for high-throughput protein analysis.
Hiratsuka, Atsunori; Kinoshita, Hideki; Maruo, Yuji; Takahashi, Katsuyoshi; Akutsu, Satonari; Hayashida, Chie; Sakairi, Koji; Usui, Keisuke; Shiseki, Kisho; Inamochi, Hajime; Nakada, Yoshiko; Yodoya, Kouhei; Namatame, Ichiji; Unuma, Yutaka; Nakamura, Makoto; Ueyama, Kosuke; Ishii, Yoshinori; Yano, Kazuyoshi; Yokoyama, Kenji
We developed a fully automated electrophoresis system for rapid and highly reproducible protein analysis. All the two-dimensional (2D) electrophoresis procedures including isoelectric focusing (IEF), on-part protein staining, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and in situ protein detection were automatically completed. The system comprised Peltiert devices, high-voltage generating devices, electrodes, and three disposable polymethylmethacrylate (PMMA) parts for IEF, reaction chambers, and SDS-PAGE. Because of miniaturization of the IEF part, rapid IEF was achieved in 30 min. A gel with a tapered edge gel on the SDS-PAGE part realized a connection between the parts without use of a gluing material. A biaxial conveyer was employed for the part relocation, sample introduction, and washing processes to realize a low-maintenance and cost-effective automation system. Performances of the system and a commercial minigel system were compared in terms of detected number, resolution, and reproducibility of the protein spots. The system achieved high-resolution comparable to the minigel system despite shorter focusing time and smaller part dimensions. The resulting reproducibility was better or comparable to the performance of the minigel system. Complete 2D separation was achieved within 1.5 h. The system is practical, portable, and has automation capabilities. PMID:17602572
Amino Acid Composition, Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L.) Proteins and Protein Fractionations
Mao, Xiaoying; Hua, Yufei; Chen, Guogang
As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE) showed that the isoelectric point was mainly in the range of 4.8¢6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa. PMID:24473146
Determination of protein-ligand affinity constants from direct migration time in capillary electrophoresis.
Nilsson, Mikael; Harang, Valerie; Bergstr÷m, Maria; Ohlson, Sten; Isaksson, Roland; Johansson, Gunnar
A simple method to calculate dissociation constants for protein-ligand interactions by partial-filling capillary electrophoresis is demonstrated. The method uses raw migration time data for the ligand and needs only additional information about capillary inner radius and the absolute amount of protein loaded. A theoretical study supported by experimental data also demonstrates that the retention of analyte in affinity capillary electrophoresis (ACE) using the partial-filling technique depends linearly on the absolute amount of selector added but is independent of both selector zone length and selector mobility. Factors such as field strength and electroosmotic flow are also cancelled out if they are kept constant. The theory is confirmed and the usefulness of the method is demonstrated by enantioseparations using alpha-acid glycoprotein (AGP) and cellulase (Cel 7A) as chiral selectors. PMID:15213981
Poly(methylmethacrylate) microchip electrophoresis of proteins using linear-poly(acrylamide) solutions as separation matrix.
Okada, Hiroki; Kaji, Noritada; Tokeshi, Manabu; Baba, Yoshinobu
Poly(methylmethacrylate) (PMMA) microchip electrophoresis of sodium dodecyl sulfate-protein complexes (SDS-PC) using linear-poly(acrylamide) (L-PA) as a separation matrix was investigated. Prior to electrophoresis, channel walls of PMMA were modified with methylcellulose (MC) to prevent adsorption between channel walls and SDS-PC. Size-based protein separation (SBPS) was successfully performed using the MC-coated microchips with Ferguson plot-fittings. The entangled L-PA solution provided high resolution of peaks of SDS-PC when the concentration of L-PA was increased. Some investigations into the separation mechanism, such as the plot of the logarithm of mobility of each SDS-PC versus the logarithm of the molecular weight of the complex exhibiting linear behavior, indicated that the separation mechanism was dependent on mass discrimination, in accordance with Ogston model. PMID:18332537
The effect of sample treatment on separation profiles of tear fluid proteins: Qualitative and semi-quantitative protein determination by an automated analysis system
Otto Schmut; Jutta Horwath-Winter; Andrea Zenker; Gabriele Trummer
Purpose. Qualitative and quantitative determination of tear fluid components is of increasing interest in ophthalmology. Until now, for diagnosis and course control of some diseases of the anterior parts of the eye, different methods for tear fluid protein analysis are available. Results can be obtained by polyacrylamide gel electrophoresis (PAGE), immunochemistry, and high-performance liquid chromatography (HPLC). A new method for
Sodium dodecyl sulfate-agarose gel electrophoresis of urinary proteins: application to multiple myeloma
Thierry Le Bricon; Danielle Erlich; Djaouida Bengoufa; Michelle Dussaucy; Jean-Pierre Garnier; Bernard Bousquet
We evaluated a new sodium dodecyl sulfate-agarose gel electrophoresis (SDS-AGE) for urinary protein analysis in patients with multiple myeloma (MM; n 5 47; ages, 62 6 2 years, mean 6 SE). Abnormal proteinuria (mean 5 1872 6 360 mg\\/24 h) was present in 95% of the samples; 75% of the patients had some sign of renal dysfunction (glomerular and\\/or tubular)
Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis
Lee, Jae Eun; Lee, Jae Young; Kim, Hong Rye; Shin, Hyun Young; Lin, Tao; Jin, Dong Il
Two dimensional-fluorescence difference gel electrophoresis (2D DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum. PMID:25925056
Recent advances in the analysis of therapeutic proteins by capillary and microchip electrophoresis
Creamer, Jessica S.; Oborny, Nathan J.; Lunte, Susan M.
The development of therapeutic proteins and peptides is an expensive and time-intensive process. Biologics, which have become a multi-billion dollar industry, are chemically complex products that require constant observation during each stage of development and production. Post-translational modifications along with chemical and physical degradation from oxidation, deamidation, and aggregation, lead to high levels of heterogeneity that affect drug quality and efficacy. The various separation modes of capillary electrophoresis (CE) are commonly utilized to perform quality control and assess protein heterogeneity. This review attempts to highlight the most recent developments and applications of CE separation techniques for the characterization of protein and peptide therapeutics by focusing on papers accepted for publication in the in the two-year period between January 2012 and December 2013. The separation principles and technological advances of CE, capillary gel electrophoresis, capillary isoelectric focusing, capillary electrochromatography and CE-mass spectrometry are discussed, along with exciting new applications of these techniques to relevant pharmaceutical issues. Also included is a small selection of papers on microchip electrophoresis to show the direction this field is moving with regards to the development of inexpensive and portable analysis systems for on-site, high-throughput analysis. PMID:25126117
Sample Collection, Preparation, and Quantitation in the Micellar Electrokinetic Capillary Electrophoresis of Gunshot Residues
David M. Northrop; William A. Mac Crehan
Application of micellar electrokinetic capillary electrophoresis (MECE) to gunshot residue (GSR) analysis was accomplished by developing appropriate sample collection and handling techniques. Masking adhesive-tape particle collection was used to minimize analyte losses and coextraction of sample matrix interferences associated with solvent swabbing collection methods. In addition, ethylene glycol (EG) was added to the extraction solvent to prevent analyte loss during
Direct analysis of cellular proteins by capillary electrophoresis FTICR MS
Hofstadler, S.A.; Severs, J.; Gale, D.C. [Pacific Northwest Lab., Richland, WA (United States)] [and others
Direct chemical analysis of living cells has received considerable attention in recent years; the single cell approach provides a major step towards answering important questions in the field of cellular biochemistry. In this work, the authors present preliminary results which demonstrate the feasibility of using the CE-ESI-FTICR combination as a high performance detection scheme for the analysis of cellular proteins acquired directly from small populations of intact living cells. The human erythrocyte (red blood cell) was chosen as a model system owing to its availability, relatively homogeneous composition, and thorough documentation of contents by previous researchers. The contents of the erythrocyte are unusually homogeneous; nearly the entire volume of the cell is filled with hemoglobin, approximately 450 amol per cell, a challenging but attainable level for mass spectrometric detection with current instrumentation. In this work, the authors demonstrate the on-line acquisition of high resolution mass spectra (average resolution {ge} 45,000 FWHM) of the {alpha} and {Beta} hemoglobin chains acquired from the injection of as few as 10 human erythrocytes (this corresponds to {approx} 4.5 fmol of hemoglobin). Additionally, when used in conjunction with quadrupolar axialization and sustained off-resonance irradiation, it is possible to directly obtain partial sequence information of selected cellular components obviating the need for additional isolation/purification steps. Given the extremely small volume of the human erythrocyte (typically {approx} 87 fL/cell), the authors are optimistic that the techniques implemented here will be adaptable to the study of many larger mammalian cell systems.
Separation of fibrate-type antihyperlipidemic drugs by capillary electrophoresis and their quantitation in pharmaceuticals
?ukasz Komsta; Genowefa Misztal; Ewa Majchrzak; Agnieszka Hauzer
Six antihyperlipidemic agentsŚbezafibrate, ciprofibrate, clofibrate, clofibric acid, fenofibrate and gemfibrozil were separated by means of capillary electrophoresis, using unmodified fused silica tubing of 75?? m internal diameter and 87?cm length (65?cm to the UV detector at 227?nm). Migration time and selectivity were examined in differing pH of separation buffer, varying separation voltage and differing temperature. Optimal separation was achieved using
The qualitative and quantitative determination of quinolones of first and second generation by capillary electrophoresis
C Fierens; S Hillaert; W Van den Bossche
Capillary electrophoresis (CE) was applied to the study of 10 quinolones of first and second generation Ś nalidixic acid, oxolinic acid, pipemidic acid, cinoxacin, norfloxacin, ciprofloxacin, ofloxacin, pefloxacin, fleroxacin, and flumequine. Separation was performed on a fused silica capillary (75 ?m¢60 cm) using a phosphate buffer (pH 7.0, 125 mM). Detection was at 214 nm. Only norfloxacin and ciprofloxacin cannot
Dynamic coating using methylcellulose and polysorbate 20 for nondenaturing electrophoresis of proteins on plastic microchips.
Mohamadi, Mohamad Reza; Mahmoudian, Laili; Kaji, Noritada; Tokeshi, Manabu; Baba, Yoshinobu
A dynamic coating using methylcellulose (MC) and a nonionic detergent (polysorbate 20) was developed, which controlled protein adsorption onto the surface of microchannels on a microchip made of poly(methyl methacrylate) (PMMA). Optimum concentration of polysorbate 20 in combination with the range of MC concentrations controlled the protein adsorption onto the microchannel surface, and increased the solubility of the protein samples while facilitating the injection of high concentrations of MC solutions into the microchannels. Higher concentrations of nonionic detergent increased the EOF mobility as opposed to the electrophoretic mobility and caused the electrophoresis to fail. Nondenaturing microchip electrophoresis of protein samples with molecular masses ranging from 20 to 100 kDa were completed in 100 s. Also, successful separation of a BSA sample and its complex with anti-BSA mAb ( 220 kDa) was achieved on a PMMA microchip. The separation exhibited high reproducibility in both migration time (RSD = 1%) and peak area (RSD = 10-15%). PMID:17274100
Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots
Zhang, Jian-Shi (Shanghai, CN); Giometti, Carol S. (Glenview, IL); Tollaksen, Sandra L. (Montgomery, IL)
After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.
Ultrasensitive staining-free protein detection after PAA gel electrophoresis using deep UV fluorescence.
Riaplov, Eugene; Li, Qiang; Seeger, Stefan
We present the observation of separated protein bands after polyacrylamide (PAA) gel electrophoresis based on the staining-free detection of their ultra violet (UV)-induced fluorescence employing deep UV confocal fluorescence microscopy. Mixtures of the three biological compounds beta-Galactosidase (from Escherichia coli), apo-Transferrin (bovine) and bovine serum albumin (BSA) have been separated and a staining free detection limit below 80 pg (7.0 x 10(8) molecules) per band has been achieved. This corresponds to approximately 270 molecules in the detection volume for confocal microscopy. PMID:17897099
Silica colloidal crystals as emerging materials for high-throughput protein electrophoresis.
Njoya, Nadine K; Birdsall, Robert E; Wirth, Mary J
Silica colloidal crystals are a new type of media for protein electrophoresis, and they are assessed for their promise in rapidly measuring aggregation of monoclonal antibodies. The nature of silica colloidal crystals is described in the context of the need for a high-throughput separation tool for optimizing the formulations of protein drugs for minimal aggregation. The fundamental relations between molecular weight and mobility in electrophoresis are used to make a theoretical comparison of selectivity between gels and colloidal crystals. The results show that the selectivity is similar for these media, but slightly higher, 10%, for gels, and the velocity is inherently lower than that for gels due to the smaller free volume fraction. These factors are more than compensated for by lower broadening in colloidal crystals. These new media give plate heights of only 0.15 ?m for the antibody monomer and 0.42 ?m for the antibody dimer. The monoclonal antibody is separated from its dimer in 72 s over a distance of only 6.5 mm. This is five times faster than size-exclusion chromatography, with more than tenfold miniaturization, and amenable to parallel separations, all of which are promising for the design of high-throughput devices for optimizing protein drug formulations. PMID:23800834
Electrophoresis and spectrometric analyses of adaptation-related proteins in thermally stressed Chromobacterium violaceum.
Cordeiro, I B; Castro, D P; Nogueira, P P O; Angelo, P C S; Nogueira, P A; Gonńalves, J F C; Pereira, A M R F; Garcia, J S; Souza, G H M F; Arruda, M A Z; Eberlin, M N; Astolfi-Filho, S; Andrade, E V; L¾pez-Lozano, J L
Chromobacterium violaceum is a Gram-negative proteobacteria found in water and soil; it is widely distributed in tropical and subtropical regions, such as the Amazon rainforest. We examined protein expression changes that occur in C. violaceum at different growth temperatures using electrophoresis and mass spectrometry. The total number of spots detected was 1985; the number ranged from 99 to 380 in each assay. The proteins that were identified spectrometrically were categorized as chaperones, proteins expressed exclusively under heat stress, enzymes involved in the respiratory and fermentation cycles, ribosomal proteins, and proteins related to transport and secretion. Controlling inverted repeat of chaperone expression and inverted repeat DNA binding sequences, as well as regions recognized by sigma factor 32, elements involved in the genetic regulation of the bacterial stress response, were identified in the promoter regions of several of the genes coding proteins, involved in the C. violaceum stress response. We found that 30 ░C is the optimal growth temperature for C. violaceum, whereas 25, 35, and 40 ░C are stressful temperatures that trigger the expression of chaperones, superoxide dismutase, a probable small heat shock protein, a probable phasing, ferrichrome-iron receptor protein, elongation factor P, and an ornithine carbamoyltransferase catabolite. This information improves our comprehension of the mechanisms involved in stress adaptation by C. violaceum. PMID:24301767
Optimizing Capillary Electrophoresis for Top-Down Proteomics of 30¢80 kDa Proteins
Li, Yihan; Compton, Philip D.; Tran, John C.; Ntai, Ioanna; Kelleher, Neil L.
The direct analysis of intact proteins via mass spectrometry offers compelling advantages in comparison to alternative methods due to the direct and unambiguous identification and characterization of protein sequences it provides. The inability to efficiently analyze proteins in the æmiddle mass rangeÆ, defined here as proteins from 30¢80 kDa, in a robust fashion has limited the adoption of these ōtop-downö methods. Largely a result of poor liquid chromatographic performance, the limitations in this mass range may be addressed by alternative separations that replace chromatography. Herein, the short migration times of capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) have been extended to size-sorted whole proteins in complex mixtures from Pseudomonas aeruginosa PA01. An electrokinetically pumped nanospray interface, a coated capillary and a stacking method for on-column sample concentration were developed to achieve high loading capacity and separation resolution. We achieved full width at half maximum of 8¢16 seconds for model proteins up to 29 kDa and identified 30 proteins in the mass range of 30¢80 kDa from Pseudomonas aeruginosa PA01 whole cell lysate. These results suggest that CZE-ESI-MS/MS is capable of identifying proteins in the middle mass range in top-down proteomics. PMID:24596178
Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research.
Wiese, Sebastian; Reidegeld, Kai A; Meyer, Helmut E; Warscheid, Bettina
A novel, MS-based approach for the relative quantification of proteins, relying on the derivatization of primary amino groups in intact proteins using isobaric tag for relative and absolute quantitation (iTRAQ) is presented. Due to the isobaric mass design of the iTRAQ reagents, differentially labeled proteins do not differ in mass; accordingly, their corresponding proteolytic peptides appear as single peaks in MS scans. Because quantitative information is provided by isotope-encoded reporter ions that can only be observed in MS/MS spectra, we analyzed the fragmentation behavior of ESI and MALDI ions of peptides generated from iTRAQ-labeled proteins using a TOF/TOF and/or a QTOF instrument. We observed efficient liberation of reporter ions for singly protonated peptides at low-energy collision conditions. In contrast, increased collision energies were required to liberate the iTRAQ label from lysine side chains of doubly charged peptides and, thus, to observe reporter ions suitable for relative quantification of proteins with high accuracy. We then developed a quantitative strategy that comprises labeling of intact proteins by iTRAQ followed by gel electrophoresis and peptide MS/MS analyses. As proof of principle, mixtures of five different proteins in various concentration ratios were quantified, demonstrating the general applicability of the approach presented here to quantitative MS-based proteomics. PMID:17177251
Use of capillary sodium dodecyl sulfate gel electrophoresis to detect the prion protein extracted from scrapie-infected sheep
Mary Jo Schmerr; Allen Jenny; Randall C. Cutlip
Scrapie in sheep and in goats is the prototype of a group of transmissible spongiform encephalopathies (TSE). A feature of these diseases is the accumulation in the brain of rod shaped fibrils that form from an aggregated protein that is a protease-resistant form of a modified normal host cell protein. In this study, we compared SDS gel capillary electrophoresis to
Identification of the major membrane and core proteins of vaccinia virus by two-dimensional electrophoresis.
Jensen, O N; Houthaeve, T; Shevchenko, A; Cudmore, S; Ashford, T; Mann, M; Griffiths, G; Krijnse Locker, J
Vaccinia virus assembly has been well studied at the ultrastructural level, but little is known about the molecular events that occur during that process. Towards this goal, we have identified the major membrane and core proteins of the intracellular mature virus (IMV). Pure IMV preparations were subjected to Nonidet P-40 (NP-40) and dithiothreitol (DTT) treatment to separate the core proteins from the membrane proteins. These proteins were subsequently separated by two-dimensional (2D) gel electrophoresis, and the major polypeptide spots, as detected by silver staining and 35S labeling, were identified by either matrix-assisted laser desorption/ionization mass spectrometry, N-terminal amino acid sequencing, or immunoprecipitation with defined antibodies. Sixteen major spots that partitioned into the NP-40-DTT-soluble fraction were identified; 11 of these were previously described virally encoded proteins and 5 were cellular proteins, mostly of mitochondrial origin. The core fraction revealed four major spots of previously described core proteins, two of which were also detected in the membrane fraction. Subsequently, the NP-40-DTT-soluble and -insoluble fractions from purified virus preparations, separated by 2D gels, were compared with postnuclear supernatants of infected cells that had been metabolically labeled at late times (6 to 8 h) postinfection. This relatively short labeling period as well as the apparent shutoff of host protein synthesis allowed the selective detection in such postnuclear supernatants of virus-encoded proteins. These postnuclear supernatants were subsequently treated with Triton X-114 or with sodium carbonate to distinguish the membrane proteins from the soluble proteins. We have identified the major late membrane and nonmembrane proteins of the IMV as they occur in the virus as well as in infected cells. This 2D gel map should provide an important reference for future molecular studies of vaccinia virus morphogenesis. PMID:8892867
Urine Proteins Identified by Two-Dimensional Differential Gel Electrophoresis Facilitate the Differential Diagnoses of Scrapie
Lamoureux, Lise; Simon, Sharon L. R.; Plews, Margot; Ruddat, Viola; Brunet, Simone; Graham, Catherine; Czub, Stefanie; Knox, J. David
The difficulty in developing a diagnostic assay for Creutzfeldt - Jakob disease (CJD) and other transmissible spongiform encephalopathies (TSEs) stems in part from the fact that the infectious agent is an aberrantly folded form of an endogenous cellular protein. This precludes the use of the powerful gene based technologies currently applied to the direct detection of other infectious agents. To circumvent this problem our research objective has been to identify a set of proteins exhibiting characteristic differential abundance in response to TSE infection. The objective of the present study was to assess the disease specificity of differentially abundant urine proteins able to identify scrapie infected mice. Two-dimensional differential gel electrophoresis was used to analyze longitudinal collections of urine samples from both prion-infected mice and a transgenic mouse model of Alzheimer's disease. The introduction of fluorescent dyes, that allow multiple samples to be co-resolved and visualized on one two dimensional gel, have increased the accuracy of this methodology for the discovery of robust protein biomarkers for disease. The accuracy of a small panel of differentially abundant proteins to correctly classify an independent na've sample set was determined. The results demonstrated that at the time of clinical presentation the differential abundance of urine proteins were capable of identifying the prion infected mice with 87% sensitivity and 93% specificity. The identity of the diagnostic differentially abundant proteins was investigated by mass spectrometry. PMID:23704971
Resolution of Fusarium sporotrichioides proteins by two-dimensional polyacrylamide gel electrophoresis and identification by sequence homology comparison in protein data base
Lu-Ping Chow; Nobuhito Fukaya; Norifumi Miyatake; Katsuhisa Horimoto; Yoshitsugu Sugiura; Kiyoshi Tabuchi; Yoshio Ueno; Akira Tsugita
Proteins fromFusarium sporotrichioides M-1-1, a T2-toxin-producing strain, were separated by two-dimensional polyacrylamide gel electrophoresis. One thousand two hundred and forty-four protein spots were resolved and 103 protein spots were subjected to N-terminal sequencing. Fifty-eight protein spots were sequenced and 48 proteins were observed to have blocked N termini. Forty out of 58 sequenced proteins were identified by homology search against
Serum protein electrophoresis by using high-resolution agarose gel in clinically healthy and Aspergillus species-infected falcons.
Kummrow, Maya; Silvanose, Christudas; Di Somma, Antonio; Bailey, Thomas A; Vorbr³ggen, Susanne
Serum protein electrophoresis has gained importance in avian medicine during the past decade. Interpretation of electrophoretic patterns should be based on species-specific reference intervals and the electrophoresis gel system. In this study, serum protein electrophoresis by using high-resolution agarose gels was performed on blood samples collected from 105 falcons, including peregrine falcons (Falco peregrinus), gyrfalcons (Falco rusticolus), saker falcons (Falco cherrug), red-naped shaheens (Falco pelegrinoides babylonicus), and hybrid falcons, that were submitted to the Dubai Falcon Hospital (Dubai, United Arab Emirates) between 2003 and 2006. Reference values were established in clinically healthy birds and compared with values from falcons infected with Aspergillus species (n = 32). Falcons with confirmed aspergillosis showed significantly lower prealbumin values, which is a novel finding. Prealbumin has been documented in many avian species, but further investigation is required to illuminate the diagnostic significance of this negative acute-phase protein. PMID:23409432
Quantitation of radiation-, chemical-, or enzyme-induced single strand breaks in nonradioactive DNA by alkaline gel electrophoresis: application to pyrimidine dimers
S. E. Freeman; A. D. Blackett; D. C. Monteleone; R. B. Setlow; B. M. Sutherland; J. C. Sutherland
The authors have developed an alkaline agarose gel method for quantitating single strand breaks in nanogram quantities of nonradioactive DNA. After electrophoresis together with molecular length standards, the DNA is neutralized, stained with ethidium bromide, photographed, and the density profiles recorded with a computer controller scanner. The medium lengths, number average molecular lengths, and length average molecular lengths of the
Quantitative analysis of pungent and anti-inflammatory phenolic compounds in olive oil by capillary electrophoresis.
Vulcano, Isabella; Halabalaki, Maria; Skaltsounis, Leandros; Ganzera, Markus
The first CE procedure for the quantitative determination of pharmacologically relevant secoiridoids in olive oil, oleocanthal and oleacein, is described. Together with their precursors tyrosol and hydroxytyrosol they could be baseline separated in less than 15min using a borax buffer with pH 9.5, at 25kV and 30░C. Method validation confirmed that the procedure is selective, accurate (recovery rates from 94.0 to 104.6%), reproducible (?max?6.8%) and precise (inter-day precision?6.4%), and that the compounds do not degrade quickly if non-aqueous acetonitrile is used as solvent. Quantitative results indicated a low occurrence of oleocanthal (0.004-0.021%) and oleacein (0.002-0.048%) in olive oil samples, which is in agreement to published HPLC data. The CE method impresses with its simple instrumental and methodological design, combined with reproducible and valid quantitative results. PMID:25236241
Difference gel electrophoresis (DiGE) identifies differentially expressed proteins in endoscopically-collected pancreatic fluid
Paulo, Joao A.; Lee, Linda S.; Banks, Peter A.; Steen, Hanno; Conwell, Darwin L.
Alterations in the pancreatic fluid proteome of individuals with chronic pancreatitis may offer insights into the development and progression of the disease. The endoscopic pancreas function test (ePFT) can safely collect large volumes of pancreatic fluid that are potentially amenable to proteomic analyses using difference gel electrophoresis (DiGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Pancreatic fluid was collected endoscopically using the ePFT method following secretin stimulation from three individuals with severe chronic pancreatitis and three chronic abdominal pain controls. The fluid was processed to minimize protein degradation and the protein profiles of each cohort, as determined by DiGE and LC-MS/MS, were compared. This DiGE-LC-MS/MS analysis reveals proteins that are differentially expressed in chronic pancreatitis compared to chronic abdominal pain controls. Proteins with higher abundance in pancreatic fluid from chronic pancreatitis individuals include: actin, desmoplankin, alpha-1-antitrypsin, SNC73, and serotransferrin. Those of relatively lower abundance include carboxypeptidase B, lipase, alpha-1-antichymotrypsin, alpha-2-macroglobulin, Arp2/3 subunit 4, glyceraldehyde-3-phosphate dehydrogenase, and protein disulfide isomerase. Endoscopic collection (ePFT) in tandem with DiGE-LC-MS/MS is a suitable approach for pancreatic fluid proteome analysis, however, further optimization of our protocol, as outlined herein, may improve proteome coverage in future analyses. PMID:21792986
Quantitative Multiple Reaction Monitoring of Peptide Abundance Introduced via a Capillary Zone Electrophoresis-Electrospray Interface
Li, Yihan; Wojcik, Roza; Dovichi, Norman J.
We demonstrate the use of capillary zone electrophoresis with an electrokinetic sheath-flow electrospray interface coupled to a triple quadrupole mass spectrometer for the accurate and precise quantification of leu-enkaphalin in a complex mixture using multiple-reaction monitoring (MRM). Assay time is <6 minutes, with no re-equilibration required between runs. A standard curve of Leu-enkephalin was performed in the presence of a background tryptic digest of bovine albumin. We demonstrate reasonably reproducible peak heights (21% relative standard deviation), retention times (better than 1% relative standard deviation), and robust electrospray quality. Our limit-of detection (3?) was 60 pM, which corresponds to the injection of 115 zeptomole of peptide. This is a 10¢20-fold improvement in mass sensitivity than we have obtained by nano HPLC/MRM and substantially better than reported for LC/MS/MS. Further quantification was performed in the presence of stable-isotope labeled versions of the peptides; under these conditions, linearity was observed across nearly four orders of magnitude. The concentration detection limit was 240 pM for the stable-isotope labeled quantification. PMID:22690842
Analysis of total proteins in pollen of Humulus scandens Lour in Wuhan Region of China by two-dimensional electrophoresis
Dongdong Li; Shaoheng He
Total proteins in the pollen of Humulus scandens Lour, one of the most popular aeroallergens in China, were analyzed by two-dimensional electrophoresis in the current study.\\u000a The proteins were extracted by Trichloracetic acid (TCA) method, and then separated by isoelectric focusing as the first dimension\\u000a and SDS-PAGE as the second dimension. The spots of proteins were visualized by staining with
Performing Isoelectric Focusing and Simultaneous Fractionation of Proteins on A Rotary Valve Followed by Sodium Dodecyl ¢ Polyacrylamide Gel Electrophoresis
Wang, Wei; Lu, Joann J.; Gu, Congying; Zhou, Lei; Liu, Shaorong
In this technical note, we design and fabricate a novel rotary valve and demonstrate its feasibility for performing isoelectric focusing and simultaneous fractionation of proteins, followed by sodium dodecyl ¢ polyacrylamide gel electrophoresis. The valve has two positions. In one position, the valve routes a series of capillary loops together into a single capillary tube where capillary isoelectric focusing (CIEF) is performed. By switching the valve to another position, the CIEF-resolved proteins in all capillary loops are isolated simultaneously, and samples in the loops are removed and collected in vials. After the collected samples are briefly processed, they are separated via sodium dodecyl ¢ polyacrylamide gel electrophoresis (SDS-PAGE, the 2nd-D separation) on either a capillary gel electrophoresis instrument or a slab-gel system. The detailed valve configuration is illustrated, and the experimental conditions and operation protocols are discussed. PMID:23819755
Electrophoresis characterisation of protein as a method to establish the entomological origin of stingless bee honeys.
Ram¾n-Sierra, Jes·s Manuel; Ruiz-Ruiz, Jorge Carlos; de la Luz Ortiz-Vßzquez, Elizabeth
Increasing production of stingless-bee honey and the prospect of broader marker for natural and organic products indicate the need to establish parameters to determinate the entomological origin and authenticity of honey. In this research, honeys of Apis mellifera, Melipona beecheii and Trigona spp. were collected in Yucatan, Mexico. Stingless-bee honeys contained more water and less total sugars and reducing sugars. SDS-PAGE patterns show distinctive bands for each kind of honey. The SDS-PAGE pattern of A. mellifera proteins honey showed three bands with molecular weights between 10.2 and 74.8kDa, there were five proteins bands in M. beecheii honey with molecular weights between 6.1 and 97.0kDa and nine for Trigona spp. proteins between 9.3 and 86.7kDa. Conventional physicochemical parameters along with electrophoresis profiles of stingless-bee honeys proteins could be an alternative for determination of entomological origin. PMID:25863608
Sensitive detection of C-reactive protein in serum by immunoprecipitation-microchip capillary gel electrophoresis.
Herwig, Ela; Marchetti-Deschmann, Martina; Wenz, Christian; R³fer, Andreas; Redl, Heinz; Bahrami, Soheyl; Allmaier, G³nter
Sepsis represents a significant cause of mortality in intensive care units. Early diagnosis of sepsis is essential to increase the survival rate of patients. Among others, C-reactive protein (CRP) is commonly used as a sepsis marker. In this work we introduce immune precipitation combined with microchip capillary gel electrophoresis (IP-MCGE) for the detection and quantification of CRP in serum samples. First high-abundance proteins (HSA, IgG) are removed from serum samples using affinity spin cartridges, and then the remaining proteins are labeled with a fluorescence dye and incubated with an anti-CRP antibody, and the antigen/antibody complex is precipitated with protein G-coated magnetic beads. After precipitation the complex is eluted from the beads and loaded onto the MCGE system. CRP could be reliably detected and quantified, with a detection limit of 25ng/?l in serum samples and 126pg/?l in matrix-free samples. The overall sensitivity (LOQ=75ng/?l, R(2)=0.9668) of the method is lower than that of some specially developed methods (e.g., immune radiometric assay) but is comparable to those of clinically accepted ELISA methods. The straightforward sample preparation (not prone to mistakes), reduced sample and reagent volumes (including the antibodies), and high throughput (10 samples/3h) are advantages and therefore IP-MCGE bears potential for point-of-care diagnosis. PMID:25778394
Microchip capillary electrophoresis-electrospray ionization-mass spectrometry of intact proteins using uncoated Ormocomp microchips.
Sikanen, Tiina; Aura, Susanna; Franssila, Sami; Kotiaho, Tapio; Kostiainen, Risto
We present rapid (<5 min) and efficient intact protein analysis by mass spectrometry (MS) using fully microfabricated and monolithically integrated capillary electrophoresis-electrospray ionization (CE-ESI) microchips. The microchips are fabricated fully of commercial inorganic-organic hybrid material, Ormocomp, by UV-embossing and adhesive Ormocomp-Ormocomp bonding (CE microchannels). A sheath-flow ESI interface is monolithically integrated with the UV-embossed separation channels by cutting a rectangular emitter tip in the end with a dicing saw. As a result, electrospray was produced from the corner of chip with good reproducibility between parallel tips (stability within 3.8-9.2% RSD). Thanks to its inherent biocompatibility and stable (negative) surface charge, Ormocomp microchips enable efficient intact protein analysis with up to ?10(4) theoretical separation plates per meter without any chemical or physical surface modification before analysis. The same microchip setup is also feasible for rapid peptide sequencing and mass fingerprinting and shows excellent migration time repeatability from run to run for both peptides (5.6-5.9% RSD, n=4) and intact proteins (1.3-7.5% RSD, n=3). Thus, the Ormocomp microchips provide a versatile new tool for MS-based proteomics. Particularly, the feasibility of the Ormocomp chips for rapid analysis of intact proteins with such a simple setup is a valuable increment to the current technology. PMID:22152798
Determination of cows' milk in goats' milk and cheese by capillary electrophoresis of the whey protein fractions
Giampaolo Cartoni; Franco Coccioli; Renata Jasionowska; Maurizio Masci
The use of capillary zone electrophoresis to determine the adulteration of cows' milk in goats' milk products is described. The detection and quantification of cows' milk was based on the presence of the specific whey proteins: the relative calibration curve is reported. The peaks of interest were well resolved by using sodium borate at pH 9.2 as background electrolyte in
Capillary Electrophoresis and Dynamic Light Scattering Studies of Structure and Binding Characteristics of Protein-Polyelectrolyte Complexes
Dubin, Paul D.
Capillary Electrophoresis and Dynamic Light Scattering Studies of Structure and Binding scattering (DLS),14-16 static light scattering,14,17 fluores- cence spectroscopy,19 electrophoretic light polystyrenesulfonate (NaPSS) and two proteins, bovine serum albumin and -lactoglobulin, was studied by dynamic light
Capillary Electrophoresis of the Whey Protein Fraction of Milk Powders. A Possible Method for Monitoring Storage Conditions
Jan De Block; Martine Merchiers; Roland Van Renterghem
A method is presented for the evaluation of the keeping quality of milk powders as a result of heating and storage conditions. Capillary electrophoresis of ?-lactoglobulin reveals a native and a modified fraction of this protein. The modifications are a result of Maillard reaction, changing the apparent pI of the polypeptides and are due to heating and storage conditions. This
Definition of the quantitative contents of gossypol in selection samples of cotton by capillary electrophoresis method
Technology Transfer Automated Retrieval System (TEKTRAN)
Oil-seed meal from cotton seed contains high-quality protein and can be used in the animal industry. However, its application is limited by the presence of a poisonous substance called gossypol. There is a need to analyze the amount of gossypol in cottonseed as part of the current breeding program...
Quantitative determination of (+)- and (-)-Gossypol in flower petals of selected cotton cultivars using capillary zone electrophoresis
Technology Transfer Automated Retrieval System (TEKTRAN)
Cottonseeds provide a high quality protein that is currently under utilized because of the presence of a toxic compound called gossypol. Gossypol is biosynthesized by the free radical coupling of two molecules of hemigossypol. This coupling reaction produces two optically active enantiomers. One ...
Characterization of low viscosity polymer solutions for microchip electrophoresis of non-denatured proteins on plastic chips.
Yasui, Takao; Reza Mohamadi, Mohamad; Kaji, Noritada; Okamoto, Yukihiro; Tokeshi, Manabu; Baba, Yoshinobu
In this paper, we study characteristics of polymers (methylcellulose, hypromellose ((hydroxypropyl)methyl cellulose), poly(vinylpyrrolidone), and poly(vinyl alcohol)) with different chemical structures for microchip electrophoresis of non-denatured protein samples in a plastic microchip made of poly(methyl methacrylate) (PMMA). Coating efficiency of these polymers for controlling protein adsorption onto the channel surface of the plastic microchip, wettability of the PMMA surface, and electroosmotic flow in the PMMA microchannels in the presence of these polymers were compared. Also relative electrophoretic mobility of protein samples in solutions of these polymers was studied. We showed that when using low polymer concentrations (lower than the polymer entanglement point) where the sieving effect is substantially negligible, the interaction of the samples with the polymer affected the electrophoretic mobility of the samples. This effect can be used for achieving better resolution in microchip electrophoresis of protein samples. PMID:22685502
Two-Dimensional Electrophoresis for Analysis of Mycobacterium tuberculosis Culture Filtrate and Purification and Characterization of Six Novel Proteins
KARIN WELDINGH; IDA ROSENKRANDS; SUSANNE JACOBSEN; PETER BIRK RASMUSSEN; MARTIN J. ELHAY; PETER ANDERSEN; Statens Immunology
Culture filtrate from Mycobacterium tuberculosis contains molecules which promote high levels of protective immunity in animal models of subunit vaccination against tuberculosis. We have used two-dimensional electrophoresis for analysis and purification of six novel M. tuberculosis culture filtrate proteins (CFPs): CFP17, CFP20, CFP21, CFP22, CFP25, and CFP28. The proteins were tested for recognition by M. tuberculosis- reactive memory cells from
A comprehensive platform to investigate protein-metal ion interactions by affinity capillary electrophoresis.
Alhazmi, Hassan A; Nachbar, Markus; Albishri, Hassan M; Abd El-Hady, Deia; Redweik, Sabine; El Deeb, Sami; Wõtzig, Hermann
In this work, the behavior of several metal ions with different globular proteins was investigated by affinity capillary electrophoresis. Screening was conducted by applying a proper rinsing protocol developed by our group. The use of 0.1M EDTA in the rinsing solution successfully desorbs metal ions from the capillary wall. The mobility ratio was used to evaluate the precision of the method. Excellent precision for repeated runs was achieved for different protein metal ion interactions (RSD% of 0.05-1.0%). Run times were less than 6 min for all of the investigated interactions. The method has been successfully applied for the interaction study of Li(+), Na(+), Mg(2+), Ca(2+), Ba(2+), Al(3+), Ga(3+), La(3+), Pd(2+), Ir(3+), Ru(3+), Rh(3+), Pt(2+), Pt(4+), Os(3+), Au(3+), Au(+), Ag(+), Cu(1+), Cu(2+), Fe(2+), Fe(3+), Co(2+), Ni(2+), Cr(3+), V(3+), MoO4(2-) and SeO3(2-) with bovine serum albumin, ovalbumin, ?-lactoglobulin and myoglobin. Different interaction values were obtained for most of the tested metal ions even for that in the same metal group. Results were discussed and compared in view of metal and semimetal group's interaction behavior with the tested proteins. The calculated normalized difference of mobility ratios for each protein-metal ion interaction and its sign (positive and negative) has been successfully used to detect the interaction and estimate further coordination of the bound metal ion, respectively. The comprehensive platform summarizes all the obtained interaction results, and is valuable for any future protein-metal ion investigation. PMID:25638307
A multi-channel gel electrophoresis and continuous fraction collection apparatus for high throughput protein separation and characterization
Choi, Megan; Nordmeyer, Robert A.; Cornell, Earl; Dong, Ming; Biggin, Mark D.; Jin, Jian
To facilitate a direct interface between protein separation by PAGE and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. The device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A Counter Free-Flow elution technique then allows continuous and simultaneous fraction collection from multiple channels at low cost. We demonstrate that rapid, high-resolution separation of a complex protein mixture can be achieved on this system using SDS-PAGE. In a 2.5 h electrophoresis run, for example, each sample was separated and eluted into 48-96 fractions over a mass range of 10-150 kDa; sample recovery rates were 50percent or higher; each channel was loaded with up to 0.3 mg of protein in 0.4 mL; and a purified band was eluted in two to three fractions (200 L/fraction). Similar results were obtained when running native gel electrophoresis, but protein aggregation limited the loading capacity to about 50 g per channel and reduced resolution.
Two-dimensional gel electrophoresis method for investigation of human plasma proteins: detection of subtle changes during filtration leukapheresis.
Lonberg-Holm, K; Bagley, E A; Nusbacher, J; Heal, J M
Special problems are associated with analysis of human plasma proteins by standard "high-resolution" two-dimensional gel electrophoresis methods in which isoelectric focusing is followed by electrophoresis in sodium dodecyl sulfate/polyacrylamide gels (SDS-PAGE). Individual plasma proteins are often separated into overlapping groups of multiple spots, and identification of individual spots is further confounded by genetic variation. Analytical recovery of components of high molecular mass is also low or variable. These problems may be reduced or overcome by use of a "low-resolution" method consisting of electrophoresis of native proteins at pH 8.6 in an agarose gel followed by SDS-PAGE without added reducing agent. About 60 proteins can be resolved, most as single spots. About 25 of these proteins have been "mapped," and tentatively identified. We have examined 119 plasma samples taken from six donors who were undergoing filtration leukapheresis and 10 donors who were undergoing centrifugation leukapheresis or plateletpheresis. In all cases, passage of blood through a nylon filter induced a significant increase in a doublet of spots tentatively identified as complement component C3c. This was detected in the effluent from the filter throughout the first 30 min of filtration, and to a lesser extent in the venous blood. These spots were not induced by the centrifugation procedures. One filtration donor also showed increased acute-phase proteins 24 h after the procedure. PMID:7074886
Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Quantitative Analysis of Glycans Labeled with Multiplex Carbonyl-Reactive Tandem Mass Tags.
Zhong, Xuefei; Chen, Zhengwei; Snovida, Sergei; Liu, Yan; Rogers, John C; Li, Lingjun
Recently developed carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) reagents enable multiplexed characterization and quantitative comparison of structurally complex glycans between different biological samples. Compared to some previously reported isotopic labeling strategies for glycans, the use of the aminoxyTMT method features a simple labeling procedure, excellent labeling efficiency, and reduced spectral complexity at the MS(1) level. Presence of the tertiary amine functionality in the reporter region of the aminoxyTMT labels leads to increased ionization efficiency of the labeled glycans thus improving electrospray ionization (ESI)-mass spectrometry (MS) detection sensitivity. The use of the labeling reagent also makes electrophoretic separation of the labeled neutral and acidic glycans feasible. In this work, we characterized the ESI and collision induced dissociation (CID) behavior of the aminoxyTMT-labeled neutral and sialylated glycans. For the high-mannose N-glycans and small sialylated oligosaccharides, CID fragmentation of [M + Na + H](2+) provides the most informative MS(2) spectra for both quantitative and qualitative analysis. For complex N-glycans, MS(3) of the protonated Y1(H) ion can be used for relative quantification without interference from the HexNAc fragments. Online capillary electrophoresis (CE)-ESI-MS/MS analyses of multiplexed aminoxyTMT-labeled human milk oligosaccharides (HMOs) and different types of N-glycans released from glycoprotein standards were demonstrated. Improved resolution and quantification accuracy of the labeled HMO isomers was achieved by coupling CE with traveling wave ion mobility (TWIM)-CID-MS/MS. N-Glycans released from human serum protein digests were labeled with six-plex aminoxyTMT and subjected to CE-ESI-MS/pseudo-MS(3) analysis, which demonstrated the potential utility of this glycan relative quantification platform for more complex biological samples. PMID:25981625
A versatile electrophoresis system for the analysis of high and low molecular weight proteins Christophe Tastet1, Pierre Lescuyer1, Hlne Diemer2, Sylvie Luche1, Alain van Dorsselaer2
Paris-Sud XI, Universitķ de
A versatile electrophoresis system for the analysis of high and low molecular weight proteins sodium dodecyl sulfate- polyacrylamide gel electrophoresis of proteins in the relative molecular weight electrophoresis, allows complete stacking and destacking of proteins in the above Mw range. The buffer system uses
Deep UV laser-induced fluorescence detection of unlabeled drugs and proteins in microchip electrophoresis.
Schulze, Philipp; Ludwig, Martin; Kohler, Frank; Belder, Detlev
Deep UV fluorescence detection at 266-nm excitation wavelength has been realized for sensitive detection in microchip electrophoresis. For this purpose, an epifluorescence setup was developed enabling the coupling of a deep UV laser into a commercial fluorescence microscope. Deep UV laser excitation utilizing a frequency quadrupled pulsed laser operating at 266 nm shows an impressive performance for native fluorescence detection of various compounds in fused-silica microfluidic devices. Aromatic low molecular weight compounds such as serotonin, propranolol, a diol, and tryptophan could be detected at low-micromolar concentrations. Deep UV fluorescence detection was also successfully employed for the detection of unlabeled basic proteins. For this purpose, fused-silica chips dynamically coated with hydroxypropylmethyl cellulose were employed to suppress analyte adsorption. Utilizing fused-silica chips permanently coated with poly(vinyl alcohol), it was also possible to separate and detect egg white chicken proteins. These data show that deep UV fluorescence detection significantly widens the application range of fluorescence detection in chip-based analysis techniques. PMID:15732914
Monitoring equilibria and kinetics of protein folding/unfolding reactions by capillary zone electrophoresis.
Verzola, B; Chiti, F; Manao, G; Righetti, P G
A method is described here for studying conformational transitions of proteins due to denaturing agents: capillary zone electrophoresis (CZE) in acidic, isoelectric buffers. The sample is run in 50 mM isoelectric glutamic acid (pH = pI = 3.2) added with 1 mM oligoamine (tetraethylene pentamine) for quenching protein interaction to the capillary wall (final pH = 3.3). Muscle acylphosphatase (AcP), in this buffer, exhibited a free solution mobility of 2.63 x 10(-4) cm(2) V(-1) s(-1). By studying the unfolding kinetics, as a function of time of incubation in 7 M urea, it was possible to measure the rate constant of the unfolding reaction, estimated to be 0.00030+/-0.00006 s(-1). The same measurements, when repeated via spectroscopic monitoring of intrinsic fluorescence, gave a value of 0.00034+/-0.00002 s(-1), thus in excellent agreement with CZE data. By equilibrium unfolding CZE studies, it was possible to construct the typical sigmoidal transition of unfolding vs urea molarity: the midpoint of this transition, at which the folded and unfolded states should be equally populated, was estimated to be at 4.56 M urea. Similar experiments by fluorometric analysis gave a value of 4.60 M urea as midpoint of the unfolding curve. PMID:10873279
High-throughput viscosity measurement using capillary electrophoresis instrumentation and its application to protein formulation.
Allmendinger, Andrea; Dieu, Le-Ha; Fischer, Stefan; Mueller, Robert; Mahler, Hanns-Christian; Huwyler, J÷rg
Viscosity characterization of protein formulations is of utmost importance for the development of subcutaneously administered formulations. However, viscosity determinations are time-consuming and require large sample volumes in the range of hundreds of microliters to a few milliliters, depending on the method used. In this article, an automated, high-throughput method is described to determine dynamic viscosity of Newtonian fluids using standard capillary electrophoresis (CE) equipment. CE is an analytical method routinely used for the separation and characterization of proteins. In our set-up, the capillary is filled with the test sample, and a constant pressure is applied. A small aliquot of riboflavin is subsequently loaded into the capillary and used as a dye to monitor movement of protein samples. Migration time of the riboflavin peak moving through the filled capillary is converted to the viscosity by applying the Hagen-Poiseuille's law. The instrument is operated without using an electrical field. Repeatability, robustness, linearity, and reproducibility were demonstrated for different capillary lots and instruments, as well as for different capillary lengths and diameters. Accuracy was verified by comparing the viscosity data obtained by CE instrumentation with those obtained by plate/cone rheometry. The suitability of the method for protein formulations was demonstrated, and limitations were discussed. Typical viscosities in the range of 5-40mPas were reliably measured with this method. Advantages of the CE instrumentation-based method included short measurement times (1-15min), small sample volumes (few microliters) for a capillary with a diameter of 50?m and a length of 20.5cm as well as potential to be suitable for high-throughput measurements. PMID:25077704
Hybrid Phospholipid Bilayer Coatings for Separations of Cationic Proteins in Capillary Zone Electrophoresis
Gallagher, Elyssia S.; Adem, Seid M.; Bright, Leonard K.; Calderon, Isen A. C.; Mansfield, Elisabeth; Aspinwall, Craig A.
Protein separations in capillary zone electrophoresis (CZE) suffer from non-specific adsorption of analytes to the capillary surface. Semi-permanent phospholipid bilayers (PLBs) have been used to minimize adsorption, but must be regenerated regularly to ensure reproducibility. We investigated the formation, characterization, and use of hybrid phospholipid bilayers (HPBs) as more stable biosurfactant capillary coatings for CZE protein separations. HPBs are formed by covalently modifying a support with a hydrophobic monolayer onto which a self-assembled lipid monolayer is deposited. Monolayers prepared in capillaries using 3-cyanopropyldimethylchlorosilane (CPDCS) or n-octyldimethylchlorosilane (ODCS) yielded hydrophobic surfaces with lowered surface free energies of 6.0 ▒ 0.3 or 0.2 ▒ 0.1 mJ m?2, respectively, compared to 17 ▒ 1 mJ m?2 for bare silica capillaries. HPBs were formed by subsequently fusing vesicles comprised of 1,2-dilauroyl-sn-glycero-3-phosphocholine or 1,2-dioleoyl-sn-glycero-3-phosphocholine to CPDCS- or ODCS-modified capillaries. The resultant HPB coatings shielded the capillary surface and yielded reduced electroosmotic mobility (1.3 ¢ 1.9 ū 10?4 cm2 V?1s?1) compared to CPDCS- and ODCS-modified or bare capillaries (3.6 ▒ 0.2 ū 10?4 cm2 V?1s?1, 4.8 ▒ 0.4 ū 10?4 cm2 V?1s?1, and 6.0 ▒ 0.2 ū 10?4 cm2 V?1s?1, respectively), with increased stability compared to PLB coatings. HPB-coated capillaries yielded reproducible protein migration times (RSD ? 3.6 %, n ? 6) with separation efficiencies as high as 200,000 plates m?1. PMID:24459085
Proteins of human urine. II. Identification by two-dimensional electrophoresis of a new candidate marker for prostatic cancer
Edwards, J.J. (Argonne National Lab., IL); Anderson, N.G.; Tollaksen, S.L.; von Eschenbach, A.C.; Guevara, J. Jr.
A protein series common to the urine and prostatic tissue of 16 of 17 patients with prostatic adenocarcinoma has been identified by high-resolution two-dimensional gel electrophoresis. These proteins, designated PCA-1, have a relative molecular mass in sodium dodecyl sulfate of about 40,000. Analyses of urines from eight age-matched controls, seven patients with other types of urogenital malignancies, two patients with benign prostatic hyperplasia, and five patients with malignancies not associated with the urogenital system failed to show PCA-1 in the patterns. These preliminary findings suggest that this protein should be systematically investigated as a candidate marker for prostatic adenocarcinoma in man.
Changes in protein expression in maturing equine testis: a quantitative DIGE analysisĀ
Roper-Foo, Pilar
and protein expression levels in the light regions are factors contributing to successful sperm production. Differential Gel Electrophoresis (DIGE) and DeCyder Image analysis of testicular extracts from prepubertal stallions has identified forty proteins...
Quantitative determination of dopamine in single rat pheochromocytoma cells by microchip electrophoresis with only one high-voltage power supply.
Sha, Cuicui; Fan, Yuejuan; Cheng, Jieke; Cheng, Han
We developed a method for the direct identification of dopamine in single cultured rat pheochromocytoma cells by capillary electrophoresis using an end-channel carbon fiber nanoelectrode amperometric detector. The operation mode was designed to achieve single-cell injection and lysis in microfluidic chip electrophoresis with only one high-voltage power supply. The separation and detection conditions were optimized. Four catecholamines were baseline-separated and determined with this system, and the cell density and liquid height of the reservoirs were accommodated for single cell loading, docking and analysis. The microchip capillary electrophoresis system was successfully applied to determine dopamine in single cultured rat pheochromocytoma cells. PMID:25893961
Streamlined sign-out of capillary protein electrophoresis using middleware and an open-source macro application
Mathur, Gagan; Haugen, Thomas H.; Davis, Scott L.; Krasowski, Matthew D.
Background: Interfacing of clinical laboratory instruments with the laboratory information system (LIS) via ōmiddlewareö software is increasingly common. Our clinical laboratory implemented capillary electrophoresis using a Sebia« Capillarys-2Ö (Norcross, GA, USA) instrument for serum and urine protein electrophoresis. Using Data Innovations Instrument Manager, an interface was established with the LIS (Cerner) that allowed for bi-directional transmission of numeric data. However, the text of the interpretive pathology report was not properly transferred. To reduce manual effort and possibility for error in text data transfer, we developed scripts in AutoHotkey, a free, open-source macro-creation and automation software utility. Materials and Methods: Scripts were written to create macros that automated mouse and key strokes. The scripts retrieve the specimen accession number, capture user input text, and insert the text interpretation in the correct patient record in the desired format. Results: The scripts accurately and precisely transfer narrative interpretation into the LIS. Combined with bar-code reading by the electrophoresis instrument, the scripts transfer data efficiently to the correct patient record. In addition, the AutoHotKey script automated repetitive key strokes required for manual entry into the LIS, making protein electrophoresis sign-out easier to learn and faster to use by the pathology residents. Scripts allow for either preliminary verification by residents or final sign-out by the attending pathologist. Conclusions: Using the open-source AutoHotKey software, we successfully improved the transfer of text data between capillary electrophoresis software and the LIS. The use of open-source software tools should not be overlooked as tools to improve interfacing of laboratory instruments. PMID:25337433
Aleutian disease serology, protein electrophoresis, and pathology of the European mink (Mustela lutreola) from Navarra, Spain.
Sßnchez-Migall¾n Guzmßn, David; Carvajal, Ana; GarcĒa-MarĒn, Juan F; Ferreras, MarĒa C; Pķrez, ValentĒn; Mitchell, Mark; Urra, FermĒn; Ce±a, Juan C
The European mink, Mustela lutreola, has suffered a dramatic decline in Europe during the 20th century and is one of the most endangered carnivores in the world. The subpopulation of European mink from Navarra, Spain, estimated to number approximately 420, represents approximately two thirds of the total number of mink in Spain. Aleutian Disease Virus (ADV) is a parvovirus with a high degree of variability that can infect a broad range of mustelid hosts. The pathogenesis of this virus in small carnivores is variable and can be influenced by both host factors (e.g., species, American mink genotype, and immune status) and viral strain. A cross-sectional study was conducted during the pre-reproductive period of February-March 2004 and 2005 and the postreproductive period of September-December 2004. Mink were intensively trapped along seven rivers that were representative of the European mink habitat in Navarra. Antibody counter immunoelectrophoresis against ADV was performed on 84 European mink blood samples. All the samples were negative. Protein electrophoresis was performed on 93 plasma samples. Nine of those samples (9.6%) had gamma globulin levels exceeding 20% of the total plasma protein. Complete necropsies were performed on 23 cadavers of European mink collected in the area between 2000 and 2005. Seventeen of the mink (74%) had traumatic and hemorrhagic lesions compatible with vehicular impact injuries. Although there were no histopathologic lesions associated with ADV, this study documents the first description of a naturally occurring canine distemper virus infection in a European mink. In addition, pulmonary adiaspiromycosis in three European mink from Spain was reported. PMID:18816991
Fully denaturing two-dimensional electrophoresis of membrane proteins: a critical update. Thierry Rabilloud 1,2, Mireille Chevallet 1,2, Sylvie Luche 1,2, Ccile Lelong 1,2
Paris-Sud XI, Universitķ de
Fully denaturing two-dimensional electrophoresis of membrane proteins: a critical update. Thierry-dimensional electrophoresis separating only denatured proteins. Traditional 2D methods, i.e.methods using isoelectric focusing in the first dimension are compared to methods using only zone electrophoresis in both dimensions, i
Quantification of carbonylated proteins in rat skeletal muscle mitochondria using capillary sieving electrophoresis with laser-induced fluorescence detection.
Feng, Juan; Arriaga, Edgar A
Carbonyl-modified proteins are markers of oxidative damage. Here, we report a new method for detecting and quantifying carbonylated proteins by capillary sieving electrophoresis (CSE) with LIF detection (CSE-LIF). Alexa 488 hydrazide is used for the specific labeling of carbonyls while 3-(2-furoyl) quinoline-2-carboxaldehyde (FQ) is used for protein labeling. BSA subjected to metal-catalyzed oxidation is used to optimize the labeling reactions, confirm the separation power of CSE, and characterize the response of the LIF detector. The method is capable of detecting femtomole (fmol) amounts of carbonyls in proteins with molecular masses ranging from 26 to 30 kDa. Using this method, we determined that mitochondrial proteins isolated from skeletal muscle contains 2.1 +/- 0.1 (average +/- SD; n = 3) nmol carbonyl/mg protein. The methodology described here should be compatible with the analysis of single cells and needle biopsies taken from oxidative stress animal models. PMID:18064596
Lithium Dodecyl Sulfate\\/Polyacrylamide Gel Electrophoresis of Thylakoid Membranes at 4 degrees C: Characterizations of Two Additional Chlorophyll A-Protein Complexes
Philippe Delepelaire; Nam-Hai Chua
Lithium dodecyl sulfate\\/polyacrylamide gel electrophoresis of Chlamydomonas reinhardtii thylakoid membranes at room temperature gave two chlorophyll-protein complexes, CP I and CP II, as had been reported previously. However, when the electrophoresis was performed at 4 degrees C, there was an increase in the amount of chlorophyll associated with CP I and CP II, and in addition, three other chlorophyll-protein complexes
Speciation of iodine-containing proteins in Nori seaweed by gel electrophoresis laser ablation ICP-MS.
RomarĒs-Hortas, V; Bianga, J; Moreda-Pi±eiro, A; Bermejo-Barrera, P; Szpunar, J
An analytical approach providing an insight into speciation of iodine in water insoluble fraction of edible seaweed (Nori) was developed. The seaweed, harvested in the Galician coast (Northwestern Spain), contained 67.7▒1.3 ?g g(-1) iodine of which 25% was water soluble and could be identifies as iodide. Extraction conditions of water insoluble residue using urea, NaOH, SDS and Triton X-100 were investigated. The protein pellets obtained in optimized conditions (after precipitation of urea extracts with acetone), were digested with trypsin and protease XIV. Size exclusion chromatography-ICP-MS of both enzymatic digests demonstrated the occurrence of iodoaminoacids putatively present in proteins. Intact proteins could be separated by gel electrophoresis after an additional extraction of the protein extract with phenol. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) with laser ablation ICP-MS detection of (127)I indicated the presence of iodine in protein bands corresponding to molecular masses of 110 kDa, 40 kDa, 27 kDa, 20 kDa and 10 kDa. 2D IEF-SDS PAGE with laser ablation ICP-MS (127)I imaging allowed the detection of 5 iodine containing protein spots in the alkaline pI range. PMID:24913873
Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state
Migliore, Luciana; Rotini, Alice; Randazzo, Davide; Albanese, Nadia N; Giallongo, Agata
Background The endemic seagrass Posidonia oceanica (L.) Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on Posidonia meadows has been tested. Quantification of a putative stress indicator, i.e. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples. Results The overall expression pattern from Posidonia rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by pI and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples. Conclusion Posidonia showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor Posidonia meadows health state. PMID:17663776
Improving sodium dodecyl sulfate polyacrylamide gel electrophoresis detection of low-abundance protein samples by rapid freeze centrifugation.
Virgen-OrtĒz, J J; Ibarra-Junquera, V; Escalante-Minakata, P; Osuna-Castro, J A; Ornelas-Paz, J de J; Mancilla-Margalli, N A; Casta±eda-Aguilar, R L
This work presents a rapid and simple freeze centrifugation method to concentrate dilute protein solutions for detection by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) Coomassie blue staining. Moreover, a simple way to assemble a cryoconcentration device is presented, and its use is discussed. Commercial purified protein standard and an enzyme with high fructosyltransferase (FTase) activity, coming from target fractions obtained by chromatographic separation, were used as an example. FTase, coming directly from the chromatographic fractions, was difficult to view through SDS-PAGE analysis; however, it was easily visualized, and its activity was enhanced, after the application of the freeze centrifugation protocol presented here. PMID:24050966
Capillary electrophoresis with lamp-based wavelength-resolved fluorescence detection for the probing of protein conformational changes.
de Kort, Bregje J; ten Kate, Geert A; de Jong, Gerhardus J; Somsen, Govert W
Native protein fluorescence spectra encompass information on protein conformation. In this study, capillary electrophoresis (CE) combined with lamp-based wavelength-resolved fluorescence detection (wrFlu) is presented as a novel tool for the analysis of protein mixtures and the monitoring of protein unfolding. The CE-wrFlu system provides three-dimensional data (time, emission wavelength, intensity) from which electropherograms and accurate emission spectra of separated proteins can be extracted. For model proteins, linear detector responses (peak height vs concentration) were obtained (R(2) > 0.96) with detection limits (LODs) in the 6-32 nM range. The minimum protein concentration required for precise determination of the maximum emission wavelength by CE-wrFlu was about 15 times the LOD. Unfolding of various model proteins was induced by protein incubation and analysis in background electrolyte (BGE) containing 7.0 M urea. CE-wrFlu of the unfolded species revealed peaks with clear red-shifted spectra, which adequately corresponded to reference spectra obtained on a standard spectrophotometer. Moreover, unfolded proteins showed a significant decrease in effective electrophoretic mobility (after correction for BGE viscosity) due to the increase of their molecular hydrodynamic radii. It is concluded that the CE-wrFlu system provides two independent indicators for changes in protein folding and will allow the simultaneous assessment of protein purity and conformation. PMID:21699162
Quantitative thermodynamic model for globular protein folding
NASA Astrophysics Data System (ADS)
Yakubovich, Alexander V.; Solov'yov, Andrey V.
We present a statistical mechanics formalism for theoretical description of the process of protein folding ? unfolding transition in water environment. The formalism is based on the construction of the partition function of a protein obeying two-stage-like folding kinetics. Using the statistical mechanics model of solvation of hydrophobic hydrocarbons we obtain the partition function of infinitely diluted solution of proteins in water environment. The calculated dependencies of the protein heat capacities upon temperature are compared with the corresponding results of experimental measurements for staphylococcal nuclease and metmyoglobin.
Definition of Mycobacterium tuberculosis Culture Filtrate Proteins by Two-Dimensional Polyacrylamide Gel Electrophoresis, N-Terminal Amino Acid Sequencing, and Electrospray Mass Spectrometry
A number of the culture filtrate proteins secreted by Mycobacterium tuberculosis are known to contribute to the immunology of tuberculosis and to possess enzymatic activities associated with pathogenicity. However, a complete analysis of the protein composition of this fraction has been lacking. By using two-dimensional polyacrylamide gel electrophoresis, detailed maps of the culture filtrate proteins of M. tuberculosis H37Rv were
Protein a quantitation by competitive ELISA using penicillinase
N. Muniasamy; G. M. Bhopale; S. S. Ambedkar; S. R. Naik
A simple, sensitive and specific competitive ELISA method using penicillinase as a marker for quantitation of protein A has been developed. The sensitivity of the assay is 20 ng\\/ml. This method is useful for estimating the protein A concentration in fermented and extracted samples.
Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.
Vaganan, M Mayil; Sarumathi, S; Nandakumar, A; Ravi, I; Mustaffa, M M
Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield. PMID:26040117
Cationic electrophoresis and eastern blotting.
Buxbaum, Engelbert
Denaturing, discontinuous electrophoresis in the presence of SDS has become a standard method for the protein scientist. However, there are situations where this method produces suboptimal results. In these cases electrophoresis in the presence of positively charged detergents like cetyltrimethylammonium bromide (CTAB) may work considerably better. Methods for electrophoresis, staining, and blotting of such gels are presented. PMID:26044000
Measurement of Protein Sulfhydryls in Response to Cellular Oxidative Stress Using Gel Electrophoresis and Multiplexed Fluorescent Imaging Analysis
Spiess, Page C.; Morin, Dexter; Jewell, William T.; Buckpitt, Alan R.
The significance of free radicals in biology has been established by numerous investigations spanning a period of over 40 years. Whereas there are many intracellular targets for these radical species, the importance of cysteine thiol posttranslational modification has received considerable attention. The current studies present a highly sensitive method for measurement of the posttranslational modification of protein thiols. This method is based on labeling of proteins with monofunctional maleimide dyes followed by 2D gel electrophoresis to separate proteins and multiplexed fluorescent imaging analysis. The method correctly interrogates the thiol/disulfide ratio present in commercially available proteins. Exposure of pulmonary airway epithelial cells to high concentrations of menadione or t-butyl hydroperoxide resulted in the modification of cysteines in more than 141 proteins of which 60 were subsequently identified by MALDI-TOF/TOF MS. Although some proteins were modified similarly by these two oxidants, several showed detectably different maleimide ratios in response to these two agents. Proteins that were modified by one or both oxidants include those involved in transcription, protein synthesis and folding, and cell death/growth. In conclusion, these studies provide a novel procedure for measuring the redox status of cysteine thiols on individual proteins with a clearly demonstrated applicability to interactions of chemicals with pulmonary epithelial cells. PMID:18416539
Optimized Protocol for Protein Extraction from the Breast Tissue that is Compatible with Two-Dimensional Gel Electrophoresis
Zakharchenko, Olena; Greenwood, Christina; Alldridge, Louise; Souchelnytskyi, Serhiy
Proteomics is a highly informative approach to analyze cancer-associated transformation in tissues. The main challenge to use a tissue for proteomics studies is the small sample size and difficulties to extract and preserve proteins. The choice of a buffer compatible with proteomics applications is also a challenge. Here we describe a protocol optimized for the most efficient extraction of proteins from the human breast tissue in a buffer compatible with two-dimensional gel electrophoresis (2D-GE). This protocol is based on mechanically assisted disintegration of tissues directly in the 2D-GE buffer. Our method is simple, robust and easy to apply in clinical practice. We demonstrate high quality of separation of proteins prepared according to the reported here protocol. PMID:21494400
Proteomic analysis of plasma proteins in diabetic rats by 2D electrophoresis and MALDI-TOF-MS.
Karthik, D; Ilavenil, S; Kaleeswaran, B; Sunil, S; Ravikumar, S
Despite tremendous advances in our understanding of the molecular basis of diabetes mellitus, substantial gaps still remain in our understanding of disease pathogenesis and in the development of effective strategies for early diagnosis and treatment. The proteomic approach has offered many opportunities and challenges in identifying new marker proteins and therapeutic targets, i.e., using 2D-polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. The differential protein expressions were analyzed in alloxan-induced diabetic rats treated with Cynodon dactylon leaf extract. The plant extract was administered for 15 days that resulted in a significant increase in plasma insulin and C-peptide levels. We have also identified four differentially expressed proteins from rat plasma. These four diabetes-associated proteins were broadly classified into three groups as per their function: (1) lipid metabolism-associated protein (Apo A-IV), (2) antioxidant activity-related proteins [preprohaptoglobin and heat shock proteins B8 (HspB8)], and (3) muscle function-related protein (TPM3). Apo A-IV, HspB8, and preprohaptoglobin may play a key role in the recovery of diabetes mellitus and also prevent the diabetes-associated complications such as prevention of oxidative stress due to free radical and free hemoglobin. These results show the value of proteomic approach in identifying the potential markers that may eventually serve as diagnostic markers or therapeutic targets. PMID:22258647
Characterization of proteins in latex of the opium poppy (Papaver somniferum) using two-dimensional gel electrophoresis and microsequencing.
Decker, G; Wanner, G; Zenk, M H; Lottspeich, F
The opium poppy (Papaver somniferum) belongs to the group of latex-containing plants. Latex is the milky-like fluid within laticifer cells. In this study, poppy latex was analyzed with respect to ultrastructure, alkaloid, and protein content. The main goal of this project was the examination of the proteins by two-dimensional gel electrophoresis. In a proteomics approach, we investigated two main fractions of the latex, namely the cytosolic serum and the sedimented fraction containing the alkaloid-accumulating vesicles. Of the serum, representing the protein-rich part of the latex, 75 spots were analyzed by internal peptide microsequencing, followed by a database searching. For 69 proteins a function could be assigned due to homology to known proteins, whereas six spots could not be identified. Furthermore, codeinone reductase, a representative of the specific enzyme system in morphine biosynthesis, could be detected within the cytosolic serum fraction. In the vesicle-containing pellet, 23 protein spots were analyzed. An attempt was also made to separate the vesicle pellet by density centrifugation, followed by investigation of the alkaloid content, ultrastructure, and protein pattern. This study describes the first database of soluble proteins present in the latex of P. somniferum PMID:11079569
NSDL National Science Digital Library
University of Utah
In this activity, learners follow step-by-step instructions to build a gel electrophoresis chamber using inexpensive materials from local hardware and electronic stores. Then, learners follow instructions to simulate DNA electrophoresis using food colors from the kitchen pantry.
Proteomics analysis in mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritive, and allergenic proteins
Technology Transfer Automated Retrieval System (TEKTRAN)
Protein profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano electrospray ionization liquid chromatography tandem mass ...
Quantitation, networking, and function of protein phosphorylation in plant cell
Zhu, Lin; Li, Ning
Protein phosphorylation is one of the most important post-translational modifications (PTMs) as it participates in regulating various cellular processes and biological functions. It is therefore crucial to identify phosphorylated proteins to construct a phosphor-relay network, and eventually to understand the underlying molecular regulatory mechanism in response to both internal and external stimuli. The changes in phosphorylation status at these novel phosphosites can be accurately measured using a 15N-stable isotopic labeling in Arabidopsis (SILIA) quantitative proteomic approach in a high-throughput manner. One of the unique characteristics of the SILIA quantitative phosphoproteomic approach is the preservation of native PTM status on protein during the entire peptide preparation procedure. Evolved from SILIA is another quantitative PTM proteomic approach, AQUIP (absolute quantitation of isoforms of post-translationally modified proteins), which was developed by combining the advantages of targeted proteomics with SILIA. Bioinformatics-based phosphorylation site prediction coupled with an MS-based in vitro kinase assay is an additional way to extend the capability of phosphosite identification from the total cellular protein. The combined use of SILIA and AQUIP provides a novel strategy for molecular systems biological study and for investigation of in vivo biological functions of these phosphoprotein isoforms and combinatorial codes of PTMs. PMID:23316209
Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences
Wei Wang; Jibin Sun; Manfred Nimtz; Wolf-Dieter Deckwer; An-Ping Zeng
Separation of proteins by two-dimensional gel electrophoresis (2-DE) coupled with identification of proteins through peptide mass fingerprinting (PMF) by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an
In-spray supercharging of intact proteins by capillary electrophoresis-electrospray ionization-mass spectrometry using sheath liquid interface.
Bonvin, Grķgoire; Rudaz, Serge; Schappler, Julie
Capillary electrophoresis (CE) coupled with electrospray ionization (ESI) mass spectrometry (MS) is a suitable technique for the analysis of intact proteins. The main configuration to realize this coupling is the sheath liquid interface, which is characterized by the addition of a make-up liquid providing the electric contact as well as the appropriate flow and solvent composition for optimal ionization and evaporation. One main advantage of this interface is that the composition of the sheath liquid can be tuned to modify the ionization without affecting CE selectivity and efficiency. In the case of protein ionization, this feature is particularly interesting to modulate their charge-state distribution (CSD), while keeping the separation performance unchanged. In this context, the current work evaluated the effect on proteins' CSD of adding supercharging molecules to the sheath liquid. Several supercharging reagents were tested with different background electrolyte (BGE) and their impact was estimated for three model proteins (i.e., human insulin, human growth hormone, hemoglobin A0) exhibiting various properties in terms of ionization, conformation, and flexibility. Their influence on the global sensitivity for each protein was also assessed. Among the supercharging reagents tested, m-NBA and sulfolane led to supercharging effect whose magnitude depended on the proteins as well of the BGE pH. The sensitivity and separation performance remained globally unchanged for each protein and supercharging additive, while sulfolane led in some cases to a sensitivity improvement. PMID:24528666
Microfluidic two-dimensional separation of proteins combining temperature gradient focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Shameli, Seyed Mostafa; Ren, Carolyn L
A two-dimensional separation system is presented combining scanning temperature gradient focusing (TGF) and sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) in a PDMS/glass microfluidic chip. Denatured proteins are first focused and separated in a 15 mm long channel via TGF with a temperature range of 16-47 ░C and a pressure scanning rate of -0.5 Pa/s and then further separated via SDS-PAGE in a 25 mm long channel. A side channel is designed at the intersection between the two dimensions to continuously inject SDS into the gel, allowing SDS molecules to be compiled within the focused bands. Separation experiments are performed using several fluorescently labeled proteins with single point detection. Experimental results show a dramatic improvement in peak capacity over one-dimensional separation techniques. PMID:25787346
Characterization by affinity electrophoresis of an alpha-1,6-glucan-binding protein from Streptococcus sobrinus.
Landale, E C; McCabe, M M
Glucan-binding protein 1 (GBP1), the most abundant glucan-binding protein isolated from culture supernatants of Streptococcus sobrinus 6715-49, has been purified by affinity chromatography on Sephadex G-50 followed by gel permeation chromatography with Bio-Gel P-10. The specificity and affinity of GBP1 for glucans were assessed by affinity electrophoresis. GBP1 did not detectably bind to glucans lacking linear arrays of alpha-1,6 linkages. The association constant for the linear alpha-1,6-glucan Dextran T2000 was 3 x 10(7) M-1. Providing small isomaltosaccharide ligands to compete with this dextran indicated that the binding site maximally accommodated isomaltosaccharides with a degree of polymerization of 8. When glucans produced by purified S. sobrinus glucosyltransferases were tested, GBP1 displayed the highest affinity for the glucan from the soluble-product, primer-independent glucosyltransferase. Images PMID:2445685
Quantitating Metabolites in Protein Precipitated Serum Using NMR Spectroscopy
Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a ōsmart isotope tag,ö 15N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. 1H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10¢74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood. PMID:24796490
Binary Oscillatory Crossflow Electrophoresis
NASA Technical Reports Server (NTRS)
Molloy, Richard F.; Gallagher, Christopher T.; Leighton, David T., Jr.
We present preliminary results of our implementation of a novel electrophoresis separation technique: Binary Oscillatory Cross flow Electrophoresis (BOCE). The technique utilizes the interaction of two driving forces, an oscillatory electric field and an oscillatory shear flow, to create an active binary filter for the separation of charged species. Analytical and numerical studies have indicated that this technique is capable of separating proteins with electrophoretic mobilities differing by less than 10%. With an experimental device containing a separation chamber 20 cm long, 5 cm wide, and 1 mm thick, an order of magnitude increase in throughput over commercially available electrophoresis devices is theoretically possible.
Proteins of the Inner Membrane of Escherichia coli: Identification of Succinate Dehydrogenase by Polyacrylamide Gel Electrophoresis with sdh Amber Mutants
Spencer, Margaret E.; Guest, J. R.
The inner or cytoplasmic membrane fraction of the cell envelope of Escherichia coli was isolated by isopycnic centrifugation on sucrose gradients. The membrane proteins were analyzed by electrophoresis in sodium dodecyl sulfate-polyacrylamide gels (8.5%), and up to 56 bands were resolved. Different preparations gave very similar patterns of proteins. Succinate dehydrogenase mutants (sdh) were isolated which could not grow on succinate minimal medium, although growth on fumarate was unimpaired. The protein patterns of inner membrane preparations from sdh amber mutants were compared with the wild type, and one major band was greatly reduced in the mutants. This component, which represented approximately 5% of the inner membrane protein, was restored by introducing an amber suppressor gene (supU), which also restored the Sdh+ phenotype. The band corresponded to a protein with a molecular weight of 67,000 daltons, which is close to that for the large subunits of the succinate dehydrogenases of Rhodospirillum rubrum and beef heart mitochondria. Images PMID:4591960
Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins
Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling
Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469
Protein\\/RNA coextraction and small two-dimensional polyacrylamide gel electrophoresis for proteomic\\/gene expression analysis of renal cancer biopsies
Giovanna Barbero; Franco Carta; Giuliana Giribaldi; Giorgia Mandili; Salvatore Crobu; Carlo Ceruti; Dario Fontana; Paolo Destefanis; Francesco Turrini
A small amount of bioptic tissue (?5¢10mg of fresh tissue) usually does not contain enough material to extract protein and RNA separately, to obtain preparative two-dimensional polyacrylamide gel electrophoresis (2-DE), and to identify a large number of separated proteins by MS. We tested a method, on small renal cancer specimens, for the coextraction of protein and RNA coupled with 2-DE
Increase in local protein concentration by field-inversion gel electrophoresis
Henghang Tsai; Teck Yew Low; Steve Freeby; Aran Paulus; Kalpana Ramnarayanan; Chung-pui Paul Cheng; Hon-chiu Eastwood Leung
BACKGROUND: Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing
Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis
Zi, Jin; Zhang, Jiyuan; Wang, Quanhui; Zhou, Baojin; Zhong, Junyan; Zhang, Chaoliang; Qiu, Xuemei; Wen, Bo; Zhang, Shenyan; Fu, Xiqin; Lin, Liang; Liu, Siqi
Embryogenesis is the initial step in a plantÆs life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation. PMID:24058531
Extracting gene function from protein¢protein interactions using Quantitative BAC InteraCtomics (QUBIC)
Nina C. Hubner; Matthias Mann
Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein¢protein interaction studies are of great interest. In recent years many protein¢protein interactions have been determined by affinity purification followed by mass spectrometry (AP¢MS). Among many different AP¢MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive
Quantitation of carcinogen bound protein adducts by fluorescence measurements
NASA Astrophysics Data System (ADS)
Gan, Liang-Shang; Otteson, Michael S.; Doxtader, Mark M.; Skipper, Paul L.; Dasari, Ramachandra R.; Tannenbaum, Steven R.
A highly significant correlation of aflatoxin B 1 serum albumin adduct level with daily aflatoxin B 1 intake was observed in a molecular epidemiological study of aflatoxin carcinogenesis which used conventional fluorescence spectroscopy methods for adduct quantitation. Synchronous fluorescence spectroscopy and laser induced fluorescence techniques have been employed to quantitate antibenzo[ a]pyrene diol epoxide derived globin peptide adducts. Fast and efficient methods to isolate the peptide adducts as well as eliminate protein fluorescence background are described. A detection limit of several femtomoles has been achieved. Experimental and technical considerations of low temperature synchronous fluorescence spectroscopy and fluorescence line narrowing to improve the detection sensitivities are also presented.
Fusion-Related Host Proteins Are Actively Regulated by NA during Influenza Infection as Revealed by Quantitative Proteomics Analysis
Sui, Zhiwei; Wen, Bo; Gao, Zhimin; Chen, Quanjiao
Three recombinant influenza A viruses with different neuraminidases (NAs) in the background of A/PR/8/34 (PR8), named rPR8-H5N1NA, rPR8-H9N2NA, and rPR8-H1N1NA, derived from H5N1, H9N2, H1N1 (swine) viruses, respectively, were constructed. We performed a quantitative proteomics analysis to investigate differential protein expression in Madin-Darby canine kidney (MDCK) cells infected with recombinant and wild-type influenza viruses to determine whether NA replacement would alter host cell gene expression. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF MS) and two-dimensional gel electrophoresis (2-DE), we identified 12 up-regulated and 49 down-regulated protein spots, including cytoskeletal proteins, molecular biosynthesis proteins, ubiquitin-proteasome pathway proteins, and heat shock proteins. The most significant changes in infected cells were observed for molecular biosynthesis proteins. We found more differentially expressed protein spots in cells infected with rPR8-H5N1NA or rPR8-H9N2NA viruses than cells infected with wild-type virus. Many of those proteins are postulated to be involved in cell-cell fusion, but the full mechanism remains to be explored. Meanwhile, our data demonstrate that the wild-type virus has evolutionary advantages over recombinant viruses. PMID:25153908
Fusion-related host proteins are actively regulated by NA during influenza infection as revealed by quantitative proteomics analysis.
Sui, Zhiwei; Wen, Bo; Gao, Zhimin; Chen, Quanjiao
Three recombinant influenza A viruses with different neuraminidases (NAs) in the background of A/PR/8/34 (PR8), named rPR8-H5N1NA, rPR8-H9N2NA, and rPR8-H1N1NA, derived from H5N1, H9N2, H1N1 (swine) viruses, respectively, were constructed. We performed a quantitative proteomics analysis to investigate differential protein expression in Madin-Darby canine kidney (MDCK) cells infected with recombinant and wild-type influenza viruses to determine whether NA replacement would alter host cell gene expression. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF MS) and two-dimensional gel electrophoresis (2-DE), we identified 12 up-regulated and 49 down-regulated protein spots, including cytoskeletal proteins, molecular biosynthesis proteins, ubiquitin-proteasome pathway proteins, and heat shock proteins. The most significant changes in infected cells were observed for molecular biosynthesis proteins. We found more differentially expressed protein spots in cells infected with rPR8-H5N1NA or rPR8-H9N2NA viruses than cells infected with wild-type virus. Many of those proteins are postulated to be involved in cell-cell fusion, but the full mechanism remains to be explored. Meanwhile, our data demonstrate that the wild-type virus has evolutionary advantages over recombinant viruses. PMID:25153908
Multiplex and quantitative pathogen detection with high-resolution capillary electrophoresis-based single-strand conformation polymorphism.
Hwang, Hee Sung; Shin, Gi Won; Chung, Boram; Na, Jeongkyeong; Jung, Gyoo Yeol
Among the molecular diagnostic methods for bacteria-induced diseases, capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) combined with 16S rRNA gene-specific PCR has enormous potential because it can separate sequence variants using a simple procedure. However, conventional CE-SSCP systems have limited resolution and cannot separate most 16S rRNA gene-specific markers into separate peaks. A high-resolution CE-SSCP system that uses a poly(ethyleneoxide)-poly(propyleneoxide)-poly(ethyleneoxide) triblock copolymer matrix was recently developed and shown to effectively separate highly similar PCR products. In this report, a protocol for the detection of 12 pathogenic bacteria is provided. Pathogen markers were amplified by PCR using universal primers and separated by CE-SSCP; each marker peak was well separated at baseline and showed a characteristic mobility, allowing the easy identification of the pathogens. PMID:22976099
Detection and quantitation of heme-containing proteins by chemiluminescence.
Dorward, D W
A commercial assay for chemiluminescence (CL) has recently been developed for visualizing horseradish peroxidase-conjugated probes for antibodies and nucleic acids. To assess the utility of CL for detecting the peroxidase activity of other heme-containing proteins, the sensitivity of CL and a standard chromogenic stain for visualizing heme-proteins in SDS-polyacrylamide electrophoretic gels were compared. The ability of these systems to visualize heme-proteins on electroblots and dot blots was also examined. The chromogenic stain, which uses 3,3',5,5'-tetramethylbenzidine for a dye, and CL had equal sensitivity in electrophoretic gels. Both assays were affected by 2-mercaptoethanol in the solubilization buffer. In blotting assays, CL was 10- to 10,000-fold more sensitive for detecting samples including cytochrome C and blood. Quantities of protein requiring 18 h to detect by staining were visualized in minutes by CL. Scintillation spectroscopy of CL emitted by blood, urine containing supplemental blood, or urine from a patient with hematuria resulted in a linear relationship between peroxidase activity and concentration, allowing for quantitation of blood over a broad range of concentrations. These results indicate that CL can rapidly detect and quantitate heme-proteins and may facilitate both basic studies of heme-proteins and clinical and forensic analyses of blood. PMID:8470793
Study of extraction procedures for protein analysis in plankton samples by OFFGEL electrophoresis hyphenated with Lab-on-a-chip technology.
GarcĒa-Otero, Natalia; Barciela-Alonso, Ma Carmen; Moreda-Pi±eiro, Antonio; Bermejo-Barrera, Pilar
Extraction procedures for protein analysis from plankton samples were studied. OFFGEL electrophoresis combined with Lab-on-a-chip technology has been applied for protein analysis in plankton samples. BCR-414 (plankton) certified reference material from the European Commission was used to evaluate the protein extraction procedures. Three protein extraction procedures were studied: (1) by using Tris-HCl buffer containing a protease inhibitor cocktail, (2) urea/triton X-100 buffer extraction, and (3) using the phenol/sodium dodecyl sulphate method after different washing steps with 10% trichloroacetic acid/acetone solution and methanol. The pellet of proteins obtained was dried and then dissolved in the OFFGEL buffer. Proteins were separated according to their isoelectric points by OFFGEL electrophoresis. This separation was performed using 24 cm, pH 3-10 IPG Dry Strips. The proteins present in each liquid fraction (24 fractions) were separated according to their molecular weight using a microfluidic Lab-on-a-chip electrophoresis with the Protein 80 LabChip kit. This kit allows for the separation of proteins with a molecular weight ranging from 5 to 80 kDa. Taking into account the intensity and the number of the protein bands obtained, the protein extraction procedure using the phenol/sodium dodecyl sulphate after different wash steps with 10% trichloroacetic acid/acetone solution was selected. The developed method was applied for protein determination in a fresh marine plankton sample. The proteins found in this sample have a molecular weight ranging from 6.4 to 57.3 kDa, and the proteins with highest molecular weight were in the OFFGEL fractions with an isoelectric point ranging from 4.40 to 8.60. The concentration of proteins were calculated using external calibration with Bovine Serum Albumin, and the protein concentrations varied from 50.0 to 925.9 ng ĄL(-1). PMID:24054642
Enhanced protein electrophoresis technique for separating human skeletal muscle myosin heavy chain isoforms
NASA Technical Reports Server (NTRS)
Bamman, M. M.; Clarke, M. S.; Talmadge, R. J.; Feeback, D. L.
Talmadge and Roy (J. Appl. Physiol. 1993, 75, 2337-2340) previously established a sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE) protocol for separating all four rat skeletal muscle myosin heavy chain (MHC) isoforms (MHC I, IIa, IIx, IIb); however, when applied to human muscle, the type II MHC isoforms (Ila, IIx) are not clearly distinguished. In this brief paper we describe a modification of the SDS-PAGE protocol which yields distinct and consistent separation of all three adult human MHC isoforms (MHC I, IIa, IIx) in a minigel system. MHC specificity of each band was confirmed by Western blot using three monoclonal IgG antibodies (mAbs) immunoreactive against MHCI (mAb MHCs, Novacastra Laboratories), MHCI+IIa (mAb BF-35), and MHCIIa+IIx (mAb SC-71). Results provide a valuable SDS-PAGE minigel technique for separating MHC isoforms in human muscle without the difficult task of casting gradient gels.
Characterization of Renal Damage in Canine Leptospirosis by Sodium Dodecyl Sulphate¢Polyacrylamide Gel Electrophoresis (SDS¢PAGE) and Western Blotting of the Urinary Proteins
C. Zaragoza; R. Barrera; F. Centeno; J. A. Tapia; M. C. Ma±ķ
Canine leptospirosis is a zoonotic disease that can cause interstitial nephritis. As a consequence of the renal damage, proteinuria may occur. To determine the urine protein pattern in the disease we performed sodium dodecyl sulphate¢polyacrylamide gel electrophoresis (SDS¢PAGE) on the urine from 10 dogs with leptospirosis and 20 healthy dogs. Western blotting analysis of the urine samples with antibodies against
Characterization of Soluble Amaranth and Soybean Proteins Based on Fluorescence, Hydrophobicity, Electrophoresis, Amino Acid Analysis, Circular Dichroism, and Differential Scanning Calorimetry Measurements
Shela Gorinstein; Efren Delgado-Licon; Elke Pawelzik; Herry Heriyati Permady; Moshe Weisz; Simon Trakhtenberg
Intrinsic fluorescence (IF), surface hydrophobicity (So), electrophoresis, amino acid analysis, circular dichroism (CD), and differential scanning calorimetry (DSC) were used to study folded and unfolded soluble proteins from Amaranthus hypochondriacus (A. h.) and soybean (S). Globulin (Glo) and albumin subfractions (Alb-1 and Alb-2) were extracted from A. h. and S and denatured with urea. Electrophoretic and functional properties indicated a
Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry
Frances M Dupont; William H Vensel; Charlene K Tanaka; William J Hurkman; Susan B Altenbach
BackgroundĀĀWheat flour is one of the world's major food ingredients, in part because of the unique end-use qualities conferred by the\\u000a abundant glutamine- and proline-rich gluten proteins. Many wheat flour proteins also present dietary problems for consumers\\u000a with celiac disease or wheat allergies. Despite the importance of these proteins it has been particularly challenging to use\\u000a MS\\/MS to distinguish the
Quantitative evaluation of protein conformation in pharmaceuticals using cross-linking reactions coupled with LC-MS/MS analysis.
Yamaguchi, Hideto; Hirakura, Yutaka; Shirai, Hiroki; Mimura, Hisashi; Toyo'oka, Toshimasa
The need for a simple and high-throughput method for identifying the tertiary structure of protein pharmaceuticals has increased. In this study, a simple method for mapping the protein fold is proposed for use as a complementary quality test. This method is based on cross-linking a protein using a [bis(sulfosuccinimidyl)suberate (BS(3))], followed by peptide mapping by LC-MS. Consensus interferon (CIFN) was used as the model protein. The tryptic map obtained via liquid chromatography tandem mass spectroscopy (LC-MS/MS) and the mass mapping obtained via matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy were used to identify cross-linked peptides. While LC-MS/MS analyses found that BS(3) formed cross-links in the loop region of the protein, which was regarded as the biologically active site, sodium dodecyl-sulfate polyacrylamide gel electrophoresis demonstrated that cross-linking occurred within a protein molecule, but not between protein molecules. The occurrence of cross-links at the active site depends greatly on the conformation of the protein, which is determined by the denaturing conditions. Quantitative evaluation of the tertiary structure of CIFN was thus possible by monitoring the amounts of cross-linked peptides generated. Assuming that background information is available at the development stage, this method may be applicable to process development as a complementary test for quality control. PMID:21367553
Quantitative Tracking of Protein Trafficking to the Nucleus Using Cytosolic Protein Delivery by Nanoparticle-Stabilized Nanocapsules.
Ray, Moumita; Tang, Rui; Jiang, Ziwen; Rotello, Vincent M
We describe a method for quantitative monitoring of subcellular protein trafficking using nanoparticle-stabilized nanocapsules for protein delivery. This method provides rapid delivery of the protein into the cytosol, eliminating complications from protein homeostasis processes found with cellularly expressed proteins. After delivery, nuclear protein trafficking was followed by real time microscopic imaging. Quantitative analyses of the accumulation percentage and the import dynamics of the nuclear protein trafficking, demonstrate the utility of this method for studying intracellular trafficking systems. PMID:26011555
Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry
Technology Transfer Automated Retrieval System (TEKTRAN)
Wheat flour is one of the world's major food ingredients, but it is difficult to distinguish and identify the many proteins in a flour sample. The abundant glutamine and proline rich gluten proteins are responsible for many of the unique end-use qualities of wheat flour but it is challenging to dis...
Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry
Background Wheat flour is one of the world's major food ingredients, in part because of the unique end-use qualities conferred by the abundant glutamine- and proline-rich gluten proteins. Many wheat flour proteins also present dietary problems for consumers with celiac disease or wheat allergies. Despite the importance of these proteins it has been particularly challenging to use MS/MS to distinguish the many proteins in a flour sample and relate them to gene sequences. Results Grain from the extensively characterized spring wheat cultivar Triticum aestivum 'Butte 86' was milled to white flour from which proteins were extracted, then separated and quantified by 2-DE. Protein spots were identified by separate digestions with three proteases, followed by tandem mass spectrometry analysis of the peptides. The spectra were used to interrogate an improved protein sequence database and results were integrated using the Scaffold program. Inclusion of cultivar specific sequences in the database greatly improved the results, and 233 spots were identified, accounting for 93.1% of normalized spot volume. Identified proteins were assigned to 157 wheat sequences, many for proteins unique to wheat and nearly 40% from Butte 86. Alpha-gliadins accounted for 20.4% of flour protein, low molecular weight glutenin subunits 18.0%, high molecular weight glutenin subunits 17.1%, gamma-gliadins 12.2%, omega-gliadins 10.5%, amylase/protease inhibitors 4.1%, triticins 1.6%, serpins 1.6%, purinins 0.9%, farinins 0.8%, beta-amylase 0.5%, globulins 0.4%, other enzymes and factors 1.9%, and all other 3%. Conclusions This is the first successful effort to identify the majority of abundant flour proteins for a single wheat cultivar, relate them to individual gene sequences and estimate their relative levels. Many genes for wheat flour proteins are not expressed, so this study represents further progress in describing the expressed wheat genome. Use of cultivar-specific contigs helped to overcome the difficulties of matching peptides to gene sequences for members of highly similar, rapidly evolving storage protein families. Prospects for simplifying this process for routine analyses are discussed. The ability to measure expression levels for individual flour protein genes complements information gained from efforts to sequence the wheat genome and is essential for studies of effects of environment on gene expression. PMID:21314956
A closer look at the operating definition of protein recovery in capillary electrophoresis
Espinal, Jose H.; G¾mez, Jorge E.; Sandoval, Junior E.
Analyte recovery is an important figure to assess protein adsorption on fused-silica capillaries. In 1991 Regnier and coworkers estimated recovery by assuming the loss of analyte from adsorption and thus the decrease in peak area measured by two detectors to be proportional to the length of the capillary section between them. In this report we closely examine this concept and its adaptation to commercial CE instruments to determine protein recovery. We hypothesize that, once a steady-state migration is reached, protein adsorption is a first order process with respect to protein concentration and surface density of adsorbing sites. This hypothesis is shown to be valid over a reasonably wide range of capillary effective length and, as a result, protein recovery decreases exponentially with the migrated distance. However, unlike the traditional recovery figure obtained through a conventional spike process, protein recovery measured by this approach does not have the same merit since it is strongly dependent from capillary dimensions and applied electric field. Nevertheless, protein recovery and the slope of the logarithmic protein peak area vs. length plot are useful figures to compare protein adsorption on different capillary surfaces. Several literature reports dealing with the application of Regnier concept to calculate protein recovery are discussed. PMID:23400851
Acid and Base-Induced Proteins during Aerobic and Anaerobic Growth of Escherichia coli Revealed by Two-Dimensional Gel Electrophoresis
Proteins induced by acid or base, during long-term aerobic or anaerobic growth in complex medium, were identified in Escherichia coli. Two-dimensional gel electrophoresis revealed pH-dependent induction of 18 pro- teins, nine of which were identified by N-terminal sequencing. At pH 9, tryptophan deaminase (TnaA) was induced to a high level, becoming one of the most abundant proteins observed. TnaA may
Capillary HPLC¢ICP MS mapping of selenocompounds in spots obtained from the 2-D gel electrophoresis of the water-soluble protein fraction of selenized yeast
Laure Tastet; Dirk Schauml÷ffel; Brice Bouyssiere; Ryszard Lobinski
A method based on ICP collision-cell MS detection in capillary HPLC was developed to gain an insight into the purity and identity of selenium-containing proteins separated by 1-D and 2-D electrophoresis. The bands and spots obtained after the separation of water-soluble proteins in selenized yeast were digested with trypsin prior to chromatography. Selenium could be detected down to the subpicogram
Two-Dimensional Gel Electrophoresis of Acid-extractable Nuclear Proteins of Regenerating and Thioacetamide-treated Rat Liver, Morris 9618A Hepatoma, and Walker 256 Carcinosarcoma1
Lynn C. Yeoman; Charles W. Taylor; Harris Busch
SUMMARY The acid-soluble nuclear proteins of regenerating and thi- oacetamide-treated rat livers as well as the Morris 9618A hepatoma and the Walker 256 carcinosarcoma were ex tracted from citric acid-isolated nuclei with 0.4 N H2SO4. The nuclear extracts were analyzed by two-dimensional polyacrylamide gel electrophoresis. Although most of the protein spots were common to the livers and tumors stud ied,
Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis
Frank Schmidt; Monika Schmid; Peter R. Jungblut; Jens Mattow; Axel Facius; Klaus-Peter Pleissner
Peptide mass fingerprinting (PMF) is a powerful tool for identification of proteins separated by two-dimensional electrophoresis\\u000a (2-DE). With the increase in sensitivity of peptide mass determination it becomes obvious that even spots looking well separated\\u000a on a 2-DE gel may consist of several proteins. As a result the number of mass peaks in PMFs increased dramatically leaving\\u000a many unassigned after
Usefulness of visible dyes for the staining of protein or DNA in electrophoresis.
Jin, Li-Tai; Choi, Jung-Kap
Since 1993, we have studied visible organic dye stains for protein or DNA to improve methodologies and developed the counterion dye staining method. The method employs two oppositely charged dyes that form an ion-pair complex in the staining solution. The selective binding of free dye to protein or DNA in the staining solution improves detection sensitivity and speed. It is a rapid and sensitive procedure, involving fixing/staining or staining/quick destaining steps that are completed in 1-1.5 h. The lowest detection limits achieved are 4-8 ng of protein on polyacrylamide gels and approximately 10 ng of DNA on agarose gels. The focus of this review is to chronicle the development and current status of the counterion dye staining method for detection of protein or DNA. As an extended application of visible dyes, we also discuss the visible dye staining method for detecting protein on blotting membranes developed in our laboratory. PMID:15300759
Disease proteomics of high-molecular-mass proteins by two-dimensional gel electrophoresis with agarose gels in the first dimension (Agarose 2-DE).
Oh-Ishi, Masamichi; Maeda, Tadakazu
Agarose gel is the preferred electrophoretic medium currently used for separating high molecular mass (HMM) proteins (MW>100 kDa). Agarose gels are widely used for both SDS-agarose gel electrophoresis and agarose isoelectric focusing (IEF). A two-dimensional gel electrophoresis method employing agarose gels in the first dimension (agarose 2-DE) that is sufficiently good at separating up to 1.5mg of HMM proteins with molecular masses as large as 500 kDa has been used to separate proteins from various diseased tissues and cells. Although resolution of the agarose 2-DE pattern always depends on the tissue being analyzed, sample preparation procedures including (i) protein extraction with an SDS sample buffer; (ii) ultracentrifugation of a tissue homogenate; and (iii) 1% SDS in both stacking and separation gels of the second-dimension SDS-PAGE gel, are generally effective for HMM protein detection. In a comprehensive prostate cancer proteome study using agarose 2-DE, the HMM region of the gel was rich in proteins of particular gene/protein expression groups (39.1% of the HMM proteins but only 28.4% of the LMM ones were classified as transcription/translation-related proteins). Examples include transcription factors, DNA or RNA binding proteins, and ribosomal proteins. To understand oxidative stress-induced cellular damage at the protein level, a novel proteomic method, in which protein carbonyls were derivatized with biotin hydrazide followed by agarose 2-DE, was useful for detecting HMM protein carbonyls in tissues of both a diabetes model Ostuka Long-Evans Tokushima Fatty (OLETF) rat and a control Long-Evans Tokushima Otsuka (LETO) rat. In this paper, we review the use of agarose gels for separation of HMM proteins and disease proteomics of HMM proteins in general, with particular attention paid to our proteome analyzes based on the use of agarose 2-DE for protein separation followed by the use of mass spectrometry for protein identification. PMID:17141588
Low-flow sheathless capillary electrophoresis-mass spectrometry for sensitive glycoform profiling of intact pharmaceutical proteins.
Haselberg, Rob; de Jong, Gerhardus J; Somsen, Govert W
Capillary electrophoresis coupled to time-of-flight mass spectrometry (CE-TOF-MS) via a porous tip sheathless electrospray ionization (ESI) interface was studied for the characterization of pharmaceutical glycoproteins. To achieve optimal glycoform separation, background electrolytes of low pH were used in conjunction with a capillary with a neutral coating exhibiting near-zero electroosmotic flow. Crucial interfacing parameters, like ESI voltage and ESI tip-to-end plate distance, were optimized for very low flow rates (?5 nL/min) in order to attain maximum sensitivity and stable performance. Under optimal conditions, the sheathless CE-MS interface provided significantly increased ionization efficiencies for intact proteins and decreased ionization suppression leading to detection limits in the picomolar-range. Analysis of a sample of recombinant human interferon-? allowed the assignment of at least 18 glycoforms, plus a variety of deamidation, succinimide, and oxidation products, representing a considerable improvement over sheath-liquid CE-MS. The sheathless CE-MS system also proved highly suitable for the glycoprofiling of recombinant human erythropoietin, revealing 74 glycoforms in a 60-min run. In addition, oxidation and acetylation products were detected, overall resulting in assignment of more than 250 different isoforms. Semiquantitative glycoprofiles could be derived for both pharmaceutical proteins, with estimated glycoform concentrations analyzed ranging from 0.35 to 950 nM. These profiles may be very useful for quality control of biopharmaceuticals and their biosimilars. PMID:23323765
Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis.
Carpentier, Sebastien Christian; Witters, Erwin; Laukens, Kris; Deckers, Peter; Swennen, Rony; Panis, Bart
This study focuses on the specific problems of protein extraction from recalcitrant plant tissues and evaluates several methods to bypass them. Sample preparation is a critical step in a two-dimensional gel electrophoresis proteome approach and is absolutely essential for good results. We evaluated four methods: the classical trichloroacetic acid (TCA)/acetone precipitation, TCA/acetone precipitation and fractionation, an alternative based on fractionation and without precipitation, and phenol extraction methanol/ammonium acetate precipitation. We optimized the phenol extraction protocol for small amounts of tissue, which is essential when the study material is limited. The protocol was optimized for banana (Musa spp.) and was subsequently applied to two other plant species: apple (Malus domestica L.) and potato (Solanum tuberosum L.). Banana (Musa spp.) is a good representative of a "difficult" plant species since it contains many interfering metabolites. Only classical TCA/acetone precipitation and phenol extraction methods proved useful as standard methods. Both methods are associated with a minor but reproducible loss of proteins. Every extraction method and the subsequent analytical procedure have their physicochemical limitations; both methods should be investigated before selecting an appropriate protocol. The study, which is presented in this paper, is useful for guiding the experimental setup of many other nonmodel species, containing various interfering elements. PMID:15912556
Microfluidic Electrophoresis Assays for Rapid Characterization of Protein in Research and Development
NSDL National Science Digital Library
Sean Sanders (Science/AAAS; )
This presentation discussed the use of microfluidic-CE platforms for characterization assays such as purity assessment of monoclonal antibodies under reducing and nonreducing conditions, N-glycan profiling, and determination of protein charge heterogeneity.
Sequence analyses of rat liver cytosolic proteins separated by gel electrophoresis using MALDI mass spectrometry
Ens, Werner
of Pharmacy, University of Manitoba, Winnipeg, MB R3T 2N2,Canada Cytosolic proteins are normally separated was performed by in-gel tryptic digestion, MALDI mass spectrometry, and database search with peptide mass
Capillary gel electrophoresis for the quantification and purity determination of recombinant proteins in inclusion bodies.
Espinosa-de la Garza, Carlos E; Perdomo-Ab·ndez, Francisco C; Campos-GarcĒa, VĒctor R; Pķrez, Nķstor O; Flores-Ortiz, Luis F; Medina-Rivero, Emilio
In this work, a high-resolution CGE method for quantification and purity determination of recombinant proteins was developed, involving a single-component inclusion bodies (IBs) solubilization solution. Different recombinant proteins expressed as IBs were used to show method capabilities, using recombinant interferon-? 1b as the model protein for method validation. Method linearity was verified in the range from 0.05 to 0.40 mg/mL and a determination coefficient (r(2) ) of 0.99 was obtained. The LOQs and LODs were 0.018 and 0.006 mg/mL, respectively. RSD for protein content repeatability test was 2.29%. In addition, RSD for protein purity repeatability test was 4.24%. Method accuracy was higher than 90%. Specificity was confirmed, as the method was able to separate recombinant interferon-? 1b monomer from other aggregates and impurities. Sample content and purity was demonstrated to be stable for up to 48 h. Overall, this method is suitable for the analysis of recombinant proteins in IBs according to the attributes established on the International Conference for Harmonization guidelines. PMID:23857606
Quantitative determination of gossypol enantiomers using capillary zone electrophoresis of selected cotton cultivars possess high level of (+)-gossypol
Technology Transfer Automated Retrieval System (TEKTRAN)
As known, cotton oil-seed meal provides a high quality protein that is a valuable feed product for animal industries. However, its use is limited by the presence of a toxic compound called gossypol. This compound occurs in two enantiomeric forms that are designated as (+)- or (-)-gossypol; these ena...
Free-flow zone electrophoresis of peptides and proteins in PDMS microchip for narrow pI range sample prefractionation coupled with mass spectrometry.
Song, Yong-Ak; Chan, Michael; Celio, Chris; Tannenbaum, Steven R; Wishnok, John S; Han, Jongyoon
In this paper, we are evaluating the strategy of sorting peptides/proteins based on the charge to mass without resorting to ampholytes and/or isoelectric focusing, using a single- and two-step free-flow zone electrophoresis. We developed a simple fabrication method to create a salt bridge for free-flow zone electrophoresis in PDMS chips by surface printing a hydrophobic layer on a glass substrate. Since the surface-printed hydrophobic layer prevents plasma bonding between the PDMS chip and the substrate, an electrical junction gap can be created for free-flow zone electrophoresis. With this device, we demonstrated a separation of positive and negative peptides and proteins at a given pH in standard buffer systems and validated the sorting result with LC/MS. Furthermore, we coupled two sorting steps via off-chip titration and isolated peptides within specific pI ranges from sample mixtures, where the pI range was simply set by the pH values of the buffer solutions. This free-flow zone electrophoresis sorting device, with its simplicity of fabrication, and a sorting resolution of 0.5 pH unit, can potentially be a high-throughput sample fractionation tool for targeted proteomics using LC/MS. PMID:20163146
Native Electrophoresis-Coupled Activity Assays Reveal Catalytically-Active Protein Aggregates of Escherichia coli ?-Glucuronidase
Burchett, Gina G.; Folsom, Charles G.; Lane, Kimberly T.
?-glucuronidase is found as a functional homotetramer in a variety of organisms, including humans and other animals, as well as a number of bacteria. This enzyme is important in these organisms, catalyzing the hydrolytic removal of a glucuronide moiety from substrate molecules. This process serves to break down sugar conjugates in animals and provide sugars for metabolism in bacteria. While ?-glucuronidase is primarily found as a homotetramer, previous studies have indicated that the human form of the protein is also catalytically active as a dimer. Here we present evidence for not only an active dimer of the E. coli form of the protein, but also for several larger active complexes, including an octomer and a 16-mer. Additionally, we propose a model for the structures of these large complexes, based on computationally-derived molecular modeling studies. These structures may have application in the study of human disease, as several diseases have been associated with the aggregation of proteins. PMID:26121040
Separation of Teff Eragrostis tef (Zucc.) Trotter seed proteins by capillary electrophoresis
Technology Transfer Automated Retrieval System (TEKTRAN)
Teff (Eragrostis tef (Zucc.) Trotter) is an important food grain in Ethiopia where it is used in the preparation of the tradional flatbread injera. Teff is also used in celiac-safe food products due to its gluten-free status. Limited research has been reported on protein properties of this interesti...
Studies of proteinograms in dermatophytes by disc electrophoresis. 1. Protein bands in relation to growth phase
NASA Technical Reports Server (NTRS)
Danev, P.; Friedrich, E.; Balabanov, V.
Homogenates were prepared from various growth phases of Microsporum gypseum grown on different amino acids as the nitrogen source. When analyzed on 7.5% polyacrylamide disc gels, the water-soluble proteins in these homogenates gave essentially identical banding patterns.
Serum protein electrophoresis as a prognostic marker of chronic liver disease in dogs
E Sevelius; M Andersson
In a previous study in dogs with chronic liver disease it was found that a combination of clinical features and laboratory findings was useful in differentiating liver diseases but could not be used to evaluate a dog's prognosis. When an electrophoretic analysis of the serum proteins was included, marked decreases in the concentrations of albumin and the alpha-globulins alpha-1-antitrypsin and
Development of an SDS-gel electrophoresis method on SU-8 microchips for protein separation with LIF detection: Application to the analysis of whey proteins.
Del Mar Barrios-Romero, Maria; Crevillķn, AgustĒn G; Diez-Masa, Josķ Carlos
This work describes the development of an SDS-gel electrophoresis method for the analysis of major whey proteins (?-lactalbumin, ?-lactoglobulin, and BSA) carried out in SU-8 microchips. The method uses a low-viscosity solution of dextran as a sieving polymer. A commercial coating agent (EOTrol LN) was added to the separation buffer to control the EOF of the chips. The potential of this coating agent to prevent protein adsorption on the walls of the SU-8 channels was also evaluated. Additionally, the fluorescence background of the SU-8 material was studied to improve the sensitivity of the method. By selecting an excitation wavelength of 532 nm at which the background fluorescence remains low and by replacing the mercury arc lamp by a laser in the detection system, an LOD in the nanomolar range was achieved for proteins derivatized with the fluorogenic reagent Chromeo P540. Finally, the method was applied to the analysis of milk samples, demonstrating the potential of SU-8 microchips for the analysis of proteins in complex food samples. PMID:23720160
Protein determination by microchip capillary electrophoresis using an asymmetric squarylium dye: noncovalent labeling and nonequilibrium measurement of association constants.
Sloat, Amy L; Roper, Michael G; Lin, Xiuli; Ferrance, Jerome P; Landers, James P; Colyer, Christa L
In response to a growing interest in the use of smaller, faster microchip (mu-chip) methods for the separation of proteins, advancements are proposed that employ the asymmetric squarylium dye Red-1c as a noncovalent label in mu-chip CE separations. This work compares on-column and precolumn labeling methods for the proteins BSA, beta-lactoglobulin B (beta-LB), and alpha-lactalbumin (alpha-LA). Nonequilibrium CE of equilibrium mixtures (NECEEM) represents an efficient method to determine equilibrium parameters associated with the formation of intermolecular complexes, such as those formed between the dye and proteins in this work, and it allows for the use of weak affinity probes in protein quantitation. In particular, nonequilibrium methods employing both mu-chip and conventional CE systems were implemented to determine association constants governing the formation of noncovalent complexes of the red luminescent squarylium dye Red-1c with BSA and beta-LB. By our mu-chip NECEEM method, the association constants K(assoc) for beta-LB and BSA complexes with Red-1c were found to be 3.53 x 10(3) and 1.65 x 10(5) M(-1), respectively, whereas association constants found by our conventional CE-LIF NECEEM method for these same protein-dye systems were some ten times higher. Despite discrepancies between the two methods, both confirmed the preferential interaction of Red-1c with BSA. In addition, the effect of protein concentration on measured association constant was assessed by conventional CE methods. Although a small decrease in K(assoc) was observed with the increase in protein concentration, our studies indicate that absolute protein concentration may affect the equilibrium determination less than the relative concentration of protein-to-dye. PMID:18702052
A comparison of three serological assays, protein gel electrophoresis and the polymerase chain reaction for the detection of Chlomydia psittici infections in pet birdsĀ
Hofle, Michael David
revealed that therapeutic levels are not always achieved when administered intramuscularly. Adding the antibiotic to the drinking water or seed proved the most effective. Elevated liver enzymes and uric acid values were also reported in treated birds... Studies of Texas A82M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 1999 Major Subject: Veterinary Microbiology A COMPARISON OF THREE SEROLOGICAL ASSAYS, PROTEIN GEL ELECTROPHORESIS AND THE POLYMERASE...
Proteins pattern alteration in AZT-treated K562 cells detected by two-dimensional gel electrophoresis and peptide mass fingerprinting
Gabriele D'Andrea; Anna R Lizzi; Sara Venditti; Laura Di Francesco; Alessandra Giorgi; Giuseppina Mignogna; Arduino Oratore; Argante Bozzi
In this study we report the effect of AZT on the whole protein expression profile both in the control and the AZT-treated K562 cells, evidenced by two-dimensional gel electrophoresis and peptide mass fingerprinting analysis. Two-dimensional gels computer digital image analysis showed two spots that appeared up-regulated in AZT-treated cells and one spot present only in the drug exposed samples. Upon
Separation and identification of hen egg protein isoforms using SDS¢PAGE and 2D gel electrophoresis with MALDI-TOF mass spectrometry
Vassilios Raikos; Rasmus Hansen; Lydia Campbell; Stephen R. Euston
Knowledge of the chemical composition and physicochemical properties of native egg white and yolk is necessary to interpret the functional and biological properties attributed to specific egg components. To date, many of the proteins located in this complex biological fluid remain uncharacterised, if not unknown. High-resolution techniques for proteome analysis, including SDS¢PAGE and 2-dimensional (2D) gel electrophoresis, combined with mass
Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis.
Hebeler, Romano; Oeljeklaus, Silke; Reidegeld, Kai A; Eisenacher, Martin; Stephan, Christian; Sitek, Barbara; St³hler, Kai; Meyer, Helmut E; Sturre, Marcel J G; Dijkwel, Paul P; Warscheid, Bettina
Leaf senescence represents the final stage of leaf development and is associated with fundamental changes on the level of the proteome. For the quantitative analysis of changes in protein abundance related to early leaf senescence, we designed an elaborate double and reverse labeling strategy simultaneously employing fluorescent two-dimensional DIGE as well as metabolic (15)N labeling followed by MS. Reciprocal (14)N/(15)N labeling of entire Arabidopsis thaliana plants showed that full incorporation of (15)N into the proteins of the plant did not cause any adverse effects on development and protein expression. A direct comparison of DIGE and (15)N labeling combined with MS showed that results obtained by both quantification methods correlated well for proteins showing low to moderate regulation factors. Nano HPLC/ESI-MS/MS analysis of 21 protein spots that consistently exhibited abundance differences in nine biological replicates based on both DIGE and MS resulted in the identification of 13 distinct proteins and protein subunits that showed significant regulation in Arabidopsis mutant plants displaying advanced leaf senescence. Ribulose 1,5-bisphosphate carboxylase/oxygenase large and three of its four small subunits were found to be down-regulated, which reflects the degradation of the photosynthetic machinery during leaf senescence. Among the proteins showing higher abundance in mutant plants were several members of the glutathione S-transferase family class phi and quinone reductase. Up-regulation of these proteins fits well into the context of leaf senescence since they are generally involved in the protection of plant cells against reactive oxygen species which are increasingly generated by lipid degradation during leaf senescence. With the exception of one glutathione S-transferase isoform, none of these proteins has been linked to leaf senescence before. PMID:17878269
Separation of olive proteins combining a simple extraction method and a selective capillary electrophoresis (CE) approach: application to raw and table olive samples.
Montealegre, Cristina; Marina, Maria Luisa; GarcĒa-Ruiz, Carmen
A simple extraction method was developed to extract proteins from olive samples based on chloroform/methanol extraction followed by a protein precipitation with cold acetone. Then, a capillary electrophoresis (CE) method was carried out using an acid buffer (1 M formic acid at pH 2) to ensure a positive net charge for proteins and a neutral charge for potential interferents as polyphenols. The method developed was applied to raw and table olive samples. Interestingly, raw olive samples showed differences in protein profiles depending upon the botanical variety of olives and their geographical region. Protein profiles obtained for table olives also showed differences according to the sample treatment. Thus, a signal reduction in the electropherograms obtained for black olives was observed in comparison to those achieved for treated green olives. In this work, the use of protein profiles was demonstrated to be a powerful tool for studying variations among olive samples. PMID:21038920
Single-step quantitation of DNA in microchip electrophoresis with linear imaging UV detection and fluorescence detection through comigration with a digest.
Xu, Feng; Jabasini, Mohammad; Zhu, Bingmei; Ying, Ling; Cui, Xuezhi; Arai, Akihiro; Baba, Yoshinobu
We demonstrate a convenient single-step quantitation technique for double-stranded DNA (dsDNA) fragments in polymerase chain reaction (PCR) products based on microchip capillary electrophoresis (micro-CE)/UV or fluorescence detection. PCR products of polymorphisms on the human Y-chromosome related to spermatogenic failure did not need purification. They were premixed and comigrated with a DNA digest whose concentration was known. Hydroxyethyl cellulose (HEC) dissolved in 5x Tris-borate-EDTA (5x TBE, pH 8.3) was used as a separation matrix in a linear polyacrylamide-coated quartz microchip, while mixed poly(ethyl oxides) (PEOs) of different molar-masses dissolved in 1 x TBE (pH 8.3) containing 1 ng/microl ethidium bromide was used as a separation matrix in an uncoated poly(methyl methacrylate) (PMMA) microchip. Elution profiles were monitored under either real-time linear imaging UV detection in the snapshot mode where the total separation time is fixed, or light-emitting diode (LED) confocal fluorescence detection in the finishline mode where solutes migrate over the same separation length. It is found that, in both modes, a linear relation exists between the peak areas (A) and the multiplication of the digest concentrations (C) and the fragment sizes (L) in a DNA restrictive digest. Using the comigration electropherogram of a single-step experiment, the concentrations of PCR products were directly determined using the A versus LC linear relationship. The sole condition to obey is that the chosen digest has different fragment sizes with the PCR products of interest. This condition is easy to obey, because micro-CE owns high separation ability, and many digests are commercially available. The recovery of the technique was between 98 and 105%. The R.S.D. for chip-to-chip concentration measurements was less than 6.0% (n = 6). Hence, the technique was accurate and reliable for DNA assays. PMID:15532567
Development of a capillary electrophoresis-mass spectrometry method for the determination of rivastigmine in human plasma--optimization of the limits of detection and quantitation.
Nicolaou, Irene N; Kapnissi-Christodoulou, Constantina P
A capillary zone electrophoresis-electrospray ionization-mass spectrometry (CZE-ESI-MS) method was developed for the analysis of the acetylcholinesterase inhibitor rivastigmine. Several electrophoretic and ESI-MS parameters were investigated in order to improve sensitivity. These parameters were categorized in three areas: (i) background electrolyte (BGE) parameters, (ii) sheath liquid parameters, and (iii) spray chamber parameters. The optimized results were obtained by using 40-mM ammonium acetate at pH 9 as BGE, a sheath liquid of 1% acetic acid in water:MeOH (50:50 v/v) at a flow rate of 10Ā?L/min, and a drying gas flow rate that was set at 6 L/min and at a temperature of 200░C. These parameters provided limit of detection and limit of quantitation of 2.8Āng/mL and 8.4Āng/mL, respectively. The optimal CZE-ESI-MS conditions were applied to a plasma sample obtained from an Alzheimer's disease patient following rivastigmine patch administration, and the mean (▒standard deviation) plasma concentration was estimated to be 14.6 (▒1.7)Āng/mL. Several sample preparation procedures were examined, and solid-phase extraction using a C18 cartridge proved to be the most effective procedure, since higher sensitivity and recovery were obtained. In addition, precision was evaluated based on migration time and peak area in plasma, and the relative standard deviations were in the range of 0.10-0.16% and 0.62-9.0%, respectively. PMID:22451057
Gene expression patterns in the black blowfly (Phormia regina) as revealed by two-dimensional electrophoresis of proteins. I. Developmental stage-specific and sex-specific differences
Harrison, H.H. (The University of Chicago Pritzker School of Medicine, Il (United States)); Joslyn, D.J. (Rutgers University at Camden, NJ (United States))
The black blowfly, Phormia regina, has been implicated in human myiasis and as a contact vector of viral and bacterial diseases present in carrion to which female flies are attracted for egg deposition. Inbred strains of P. regina are an excellent model system for studying gene expression in the developmental stages of such holometabolous dipteran parasites. However, information regarding gene and protein expression patterns in regina is limited. The authors used ISO-DALT high-resolution, two-dimensional electrophoresis with solver staining to establish fundamental protein maps for examination of the stage-specific gene expression patterns in the 615 most abundant proteins of the eggs, first- and third-instar larvae, pupae, and male and female adults. They also used a differential extraction technique to identify the major cuticular proteins of the adults. The results show 48 clearly identifiable stage-specific and sex-specific proteins.
NSDL National Science Digital Library
In this activity, learners simulate the process of DNA fingerprinting by using electricity to separate colored dyes. Learners use simple materials to assemble a comb (electrophoresis chamber) to hold the samples, make a 0.2% sodium bicarbonate buffer and 1% gel solution, connect a high voltage power supply, and prepare 5 different samples. Then learners test their model and observe each sample.
Multiple injection technique for the determination and quantitation of insulin formulations by capillary electrophoresis and time-of-flight mass spectrometry.
Staub, Aline; Rudaz, Serge; Veuthey, Jean-Luc; Schappler, Julie
This paper describes an efficient CE-UV-ESI-TOF/MS method for the determination and quantitation of intact insulin (INS) in a pharmaceutical formulation. The CE conditions were optimized to avoid the adsorption of proteins onto the capillary wall. Particular attention was paid regarding the choice of the internal standard (IS). A strategy based on multiple injections was selected and the methodology was validated according to international guidelines. The optimized method was applied with success to the analysis of INS formulations obtained from regular and parallel markets. PMID:20863508
Pre-labeling of diverse protein samples with a fixed amount of Cy5 for sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis.
Bjerneld, Erik J; Johansson, Johan D; Laurin, Ylva; Hagner-McWhirter, ┼sa; R÷nn, Ola; Karlsson, Robert
A pre-labeling protocol based on Cy5 N-hydroxysuccinimide (NHS) ester labeling of proteins has been developed for one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. We show that a fixed amount of sulfonated Cy5 can be used in the labeling reaction to label proteins over a broad concentration range-more than three orders of magnitude. The optimal amount of Cy5 was found to be 50 to 250pmol in 20?l using a Tris-HCl labeling buffer at pH 8.7. Labeling protein samples with a fixed amount of dye in this range balances the requirements of sub-nanogram detection sensitivity and low dye-to-protein (D/P) ratios for SDS-PAGE. Simulations of the labeling reaction reproduced experimental observations of both labeling kinetics and D/P ratios. Two-dimensional electrophoresis was used to examine the labeling of proteins in a cell lysate using both sulfonated and non-sulfonated Cy5. For both types of Cy5, we observed efficient labeling across a broad range of molecular weights and isoelectric points. PMID:25957128
Beyond hairballs: the use of quantitative mass spectrometry data to understand protein-protein interactions
Gingras, Anne-Claude; Raught, Brian
The past 10 years have witnessed a dramatic proliferation in the availability of protein interaction data. However, for interaction mapping based on affinity purification coupled with mass spectrometry (AP-MS), there is a wealth of information present in the datasets that often goes unrecorded in public repositories, and as such remains largely unexplored. Further, how this type of data is represented and used by bioinformaticians has not been well established. Here, we point out some common mistakes in how AP-MS data are handled, and describe how protein complex organization and interaction dynamics can be inferred using quantitative AP-MS approaches. PMID:22710165
Electrophoresis experiments in microgravity
NASA Technical Reports Server (NTRS)
Snyder, Robert S.; Rhodes, Percy H.
The use of the microgravity environment to separate and purify biological cells and proteins has been a major activity since the beginning of the NASA Microgravity Science and Applications program. Purified populations of cells are needed for research, transplantation and analysis of specific cell constituents. Protein purification is a necessary step in research areas such as genetic engineering where the new protein has to be separated from the variety of other proteins synthesized from the microorganism. Sufficient data are available from the results of past electrophoresis experiments in space to show that these experiments were designed with incomplete knowledge of the fluid dynamics of the process including electrohydrodynamics. However, electrophoresis is still an important separation tool in the laboratory and thermal convection does limit its performance. Thus, there is a justification for electrophoresis but the emphasis of future space experiments must be directed toward basic research with model experiments to understand the microgravity environment and fluid analysis to test the basic principles of the process.
Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC).
Hubner, Nina C; Mann, Matthias
Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein-protein interaction studies are of great interest. In recent years many protein-protein interactions have been determined by affinity purification followed by mass spectrometry (AP-MS). Among many different AP-MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive as it uses tagged, full-length baits that are expressed under endogenous control. For QUBIC large cell line collections expressing tagged proteins from BAC transgenes or gene trap loci have been developed and are freely available. Here we describe detailed workflows on how to obtain specific protein binding partners with high confidence under physiological conditions. The methods are based on fast, streamlined and generic purification procedures followed by single run liquid chromatography-mass spectrometric analysis. Quantification is achieved either by the stable isotope labeling of amino acids in cell culture (SILAC) method or by a 'label-free' procedure. In either case data analysis is performed by using the freely available MaxQuant environment. The QUBIC approach enables biologists with access to high resolution mass spectrometry to perform small and large-scale protein interactome mappings. PMID:21184827
Electrophoresis of positioned nucleosomes
Castelnovo, M; Castelnovo, Martin
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as wrapped length of DNA on the electrophoretic mobility of the complex. The predictions of the model are in qualitative agreement with experimental results on mononucleosomes assembled on short DNA fragments (electrophoresis.
Quantitative analysis of pheromone-binding protein specificity
Katti, S.; Lokhande, N.; Gonzßlez, D.; Cassill, A.; Renthal, R.
Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins (OBPs), using ?-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila OBP that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in E. coli was assessed by measuring N-phenyl-1-naphthylamine (NPN) binding and F÷rster resonance energy transfer between LUSH tryptophan 123 (W123) and NPN. Binding of cVA was measured from quenching of W123 fluorescence as a function of cVA concentration. The equilibrium constant for transfer of cVA between ?-cyclodextrin and LUSH was determined from a linked equilibria model. This constant, multiplied by the ?-cyclodextrin-cVA dissociation constant, gives the LUSH-cVA dissociation constant: ~100 nM. It was also found that other ligands quench W123 fluorescence. The LUSH-ligand dissociation constants were determined to be ~200 nM for the silk moth pheromone bombykol and ~90 nM for methyl oleate. The results indicate that the ligand-binding cavity of LUSH can accommodate a variety ligands with strong binding interactions. Implications of this for the pheromone receptor model proposed by Laughlin et al. (Cell 133: 1255¢65, 2008) are discussed. PMID:23121132
Protein Alterations in Infiltrating Ductal Carcinomas of the Breast as Detected by Nonequilibrium pH Gradient Electrophoresis and Mass Spectrometry
Kabbage, Maria; Chahed, Karim; Hamrita, Bechr; Guillier, Christelle Lemaitre; Trimeche, Mounir; Remadi, Sami; Hoebeke, Johan; Chouchane, Lotfi
Improvement of breast-cancer detection through the identification of potential cancer biomarkers is considered as a promising strategy for effective assessment of the disease. The current study has used nonequilibrium pH gradient electrophoresis with subsequent analysis by mass spectrometry to identify protein alterations in invasive ductal carcinomas of the breast from Tunisian women. We have identified multiple protein alterations in tumor tissues that were picked, processed, and unambiguously assigned identities by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF). The proteins identified span a wide range of functions and are believed to have potential clinical applications as cancer biomarkers. They include glycolytic enzymes, molecular chaperones, cytoskeletal-related proteins, antioxydant enzymes, and immunologic related proteins. Among these proteins, enolase 1, phosphoglycerate kinase 1, deoxyhemoglobin, Mn-superoxyde dismutase, ?-B-crystallin, HSP27, Raf kinase inhibitor protein, heterogeneous nuclear ribonucleoprotein A2/B1, cofilin 1, and peptidylprolyl isomerase A were overexpressed in tumors compared with normal tissues. In contrast, the IGHG1 protein, the complement C3 component C3c, which are two newly identified protein markers, were downregulated in IDCA tissues. PMID:18401453
Sorbitol dehydrogenase overexpression and other aspects of dysregulated protein expression in human precancerous colorectal neoplasms: a quantitative proteomics study.
Uzozie, Anuli; Nanni, Paolo; Staiano, Teresa; Grossmann, Jonas; Barkow-Oesterreicher, Simon; Shay, Jerry W; Tiwari, Amit; Buffoli, Federico; Laczko, Endre; Marra, Giancarlo
Colorectal adenomas are cancer precursor lesions of the large bowel. A multitude of genomic and epigenomic changes have been documented in these preinvasive lesions, but their impact on the protein effectors of biological function has not been comprehensively explored. Using shotgun quantitative MS, we exhaustively investigated the proteome of 30 colorectal adenomas and paired samples of normal mucosa. Total protein extracts were prepared from these tissues (prospectively collected during colonoscopy) and from normal (HCEC) and cancerous (SW480, SW620, Caco2, HT29, CX1) colon epithelial cell lines. Peptides were labeled with isobaric tags (iTRAQ 8-plex), separated via OFFGEL electrophoresis, and analyzed by means of LC-MS/MS. Nonredundant protein families (4325 in tissues, 2017 in cell lines) were identified and quantified. Principal component analysis of the results clearly distinguished adenomas from normal mucosal samples and cancer cell lines from HCEC cells. Two hundred and twelve proteins displayed significant adenoma-related expression changes (q-value < 0.02, mean fold change versus normal mucosa ▒1.4), which correlated (r = 0.74) with similar changes previously identified by our group at the transcriptome level. Fifty-one (?25%) proteins displayed directionally similar expression changes in colorectal cancer cells (versus HCEC cells) and were therefore attributed to the epithelial component of adenomas. Although benign, adenomas already exhibited cancer-associated proteomic changes: 69 (91%) of the 76 protein up-regulations identified in these lesions have already been reported in cancers. One of the most striking changes involved sorbitol dehydrogenase, a key enzyme in the polyol pathway. Validation studies revealed dramatically increased sorbitol dehydrogenase concentrations and activity in adenomas and cancer cell lines, along with important changes in the expression of other enzymes in the same (AKR1B1) and related (KHK) pathways. Dysregulated polyol metabolism might represent a novel facet of metabolome remodeling associated with tumorigenesis. PMID:24567419
Sorbitol Dehydrogenase Overexpression and Other Aspects of Dysregulated Protein Expression in Human Precancerous Colorectal Neoplasms: A Quantitative Proteomics Study*
Uzozie, Anuli; Nanni, Paolo; Staiano, Teresa; Grossmann, Jonas; Barkow-Oesterreicher, Simon; Shay, Jerry W.; Tiwari, Amit; Buffoli, Federico; Laczko, Endre; Marra, Giancarlo
Colorectal adenomas are cancer precursor lesions of the large bowel. A multitude of genomic and epigenomic changes have been documented in these preinvasive lesions, but their impact on the protein effectors of biological function has not been comprehensively explored. Using shotgun quantitative MS, we exhaustively investigated the proteome of 30 colorectal adenomas and paired samples of normal mucosa. Total protein extracts were prepared from these tissues (prospectively collected during colonoscopy) and from normal (HCEC) and cancerous (SW480, SW620, Caco2, HT29, CX1) colon epithelial cell lines. Peptides were labeled with isobaric tags (iTRAQ 8-plex), separated via OFFGEL electrophoresis, and analyzed by means of LC-MS/MS. Nonredundant protein families (4325 in tissues, 2017 in cell lines) were identified and quantified. Principal component analysis of the results clearly distinguished adenomas from normal mucosal samples and cancer cell lines from HCEC cells. Two hundred and twelve proteins displayed significant adenoma-related expression changes (q-value < 0.02, mean fold change versus normal mucosa ▒1.4), which correlated (r = 0.74) with similar changes previously identified by our group at the transcriptome level. Fifty-one (?25%) proteins displayed directionally similar expression changes in colorectal cancer cells (versus HCEC cells) and were therefore attributed to the epithelial component of adenomas. Although benign, adenomas already exhibited cancer-associated proteomic changes: 69 (91%) of the 76 protein up-regulations identified in these lesions have already been reported in cancers. One of the most striking changes involved sorbitol dehydrogenase, a key enzyme in the polyol pathway. Validation studies revealed dramatically increased sorbitol dehydrogenase concentrations and activity in adenomas and cancer cell lines, along with important changes in the expression of other enzymes in the same (AKR1B1) and related (KHK) pathways. Dysregulated polyol metabolism might represent a novel facet of metabolome remodeling associated with tumorigenesis. PMID:24567419
A two-dimensional electrophoresis and mass spectrometry protein analysis of the antibiotic producer Nonomuraea sp. ATCC 39727 in different growth conditions.
Gnoni, Antonio; Lippolis, Rosa; Zanotti, Franco; Papa, Sergio; Palese, Luigi Leonardo
Nonomuraea sp. ATCC 39727 is an aerobic actinomycete, industrially important as a producer of the glycopeptide A40926, which is used as a precursor of the semi-synthetic antibiotic dalbavancin. Previous studies showed that the production of A40926 is depressed by calcium, but promoted by l-glutamine or l-asparagine. In this study, the protein expression changes of Nonomuraea sp. ATCC 39727 in these two different growth and antibiotic-production conditions have been investigated by two-dimensional electrophoresis and mass spectrometry (MS) analysis. Few protein spots show statistically significant expression changes, and, among this group of proteins, malate dehydrogenase (MDH) shows a significant decrease in the overproduction condition. The decrease of MDH is of particular interest because it is the first described significant change in the expression levels of enzymes of the central metabolism related with A40926 overproduction. PMID:17573934
Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry.
Bak-Jensen, Kristian Sass; Laugesen, Sabrina; Roepstorff, Peter; Svensson, Birte
A protocol was established for two-dimensional gel electrophoresis (2-DE) of barley seed and malt proteins in the pH range of 6-11. Proteins extracted from flour in a low-salt buffer were focused after cup-loading onto IPG strips. Successful separation in the second dimension was achieved using gradient gels in a horizontal SDS-PAGE system. Silver staining of gels visualized around 380 (seed) and 500 (malt) spots. Thirty-seven different proteins from seeds were identified in 60 spots, among these 46 were visualized also in the malt 2-D pattern. Proteins were identified by peptide mass fingerprinting and by tandem MS sequencing after in-gel digestion by trypsin. In addition, the N-terminal sequence of 10 different proteins from 11 spots was determined after electroblotting to a polyvinylidene difluoride (PVDF) membrane. Five identified proteins (in 9 spots) are involved in glycolysis, 12 in defence against pathogens (21 spots), 4 in storage, folding, and synthesis of proteins, and in nitrogen metabolism (5 spots), 6 in carbohydrate metabolism (11 spots), and 4 in stress and detoxification (9 spots). Six proteins (7 spots) were not grouped in these categories, and 3 were not ascribed a function. The presented 2-D patterns and identifications will be used to describe proteome differences between cultivars and changes during malting. PMID:14997495
Semi-quantitative measurement of specific proteins in human cumulus cells using reverse phase protein array
Background The ability to predict the developmental and implantation ability of embryos remains a major goal in human assisted-reproductive technology (ART) and most ART laboratories use morphological criteria to evaluate the oocyte competence despite the poor predictive value of this analysis. Transcriptomic and proteomic approaches on somatic cells surrounding the oocyte (granulosa cells, cumulus cells [CCs]) have been proposed for the identification of biomarkers of oocyte competence. We propose to use a Reverse Phase Protein Array (RPPA) approach to investigate new potential biomarkers of oocyte competence in human CCs at the protein level, an approach that is already used in cancer research to identify biomarkers in clinical diagnostics. Methods Antibodies targeting proteins of interest were validated for their utilisation in RPPA by measuring siRNA-mediated knockdown efficiency in HEK293 cells in parallel with Western blotting (WB) and RPPA from the same lysates. The proteins of interests were measured by RPPA across 13 individual human CCs from four patients undergoing intracytoplasmic sperm injection procedure. Results The knockdown efficiency of VCL, RGS2 and SRC were measured in HEK293 cells by WB and by RPPA and were acceptable for VCL and SRC proteins. The antibodies targeting these proteins were used for their detection in human CCs by RPPA. The detection of protein VCL, SRC and ERK2 (by using an antibody already validated for RPPA) was then carried out on individual CCs and signals were detected for each individual sample. After normalisation by VCL, we showed that the level of expression of ERK2 was almost the same across the 13 individual CCs while the level of expression of SRC was different between the 13 individual CCs of the four patients and between the CCs from one individual patient. Conclusions The exquisite sensitivity of RPPA allowed detection of specific proteins in individual CCs. Although the validation of antibodies for RPPA is labour intensive, RRPA is a sensitive and quantitative technique allowing the detection of specific proteins from very small quantities of biological samples. RPPA may be of great interest in clinical diagnostics to predict the oocyte competence prior to transfer of the embryo using robust protein biomarkers expressed by CCs. PMID:24148967
Quantitative characterization of protein-protein complexes involved in base excision DNA repair.
Moor, Nina A; Vasil'eva, Inna A; Anarbaev, Rashid O; Antson, Alfred A; Lavrik, Olga I
Base Excision Repair (BER) efficiently corrects the most common types of DNA damage in mammalian cells. Step-by-step coordination of BER is facilitated by multiple interactions between enzymes and accessory proteins involved. Here we characterize quantitatively a number of complexes formed by DNA polymerase ? (Pol?), apurinic/apyrimidinic endonuclease 1 (APE1), poly(ADP-ribose) polymerase 1 (PARP1), X-ray repair cross-complementing protein 1 (XRCC1) and tyrosyl-DNA phosphodiesterase 1 (TDP1), using fluorescence- and light scattering-based techniques. Direct physical interactions between the APE1-Pol?, APE1-TDP1, APE1-PARP1 and Pol?-TDP1 pairs have been detected and characterized for the first time. The combined results provide strong evidence that the most stable complex is formed between XRCC1 and Pol?. Model DNA intermediates of BER are shown to induce significant rearrangement of the Pol? complexes with XRCC1 and PARP1, while having no detectable influence on the protein-protein binding affinities. The strength of APE1 interaction with Pol?, XRCC1 and PARP1 is revealed to be modulated by BER intermediates to different extents, depending on the type of DNA damage. The affinity of APE1 for Pol? is higher in the complex with abasic site-containing DNA than after the APE1-catalyzed incision. Our findings advance understanding of the molecular mechanisms underlying coordination and regulation of the BER process. PMID:26013813
Gel Electrophoresis on a Budget to Dye For
NSDL National Science Digital Library
Julie H. Yu
Gel electrophoresis is one of the most important tools used in molecular biology and has facilitated the entire field of genetic engineering by enabling the separation of nucleic acids and proteins. However, commercial electrophoresis kits can cost up to
Capillary HPLC-ICP MS mapping of selenocompounds in spots obtained from the 2-D gel electrophoresis of the water-soluble protein fraction of selenized yeast.
Tastet, Laure; Schauml÷ffel, Dirk; Bouyssiere, Brice; Lobinski, Ryszard
A method based on ICP collision-cell MS detection in capillary HPLC was developed to gain an insight into the purity and identity of selenium-containing proteins separated by 1-D and 2-D electrophoresis. The bands and spots obtained after the separation of water-soluble proteins in selenized yeast were digested with trypsin prior to chromatography. Selenium could be detected down to the subpicogram level. The method, assisted by information obtained by MALDI TOF MS on the 5000 Da cut-off fraction, permitted the purity of bands and spots to be estimated and the efficiency of tryptic digestion and the quantity of selenium present in individual peptides to be evaluated. Owing to the high sensitivity and the lack of matrix suppression effects, the method provided chromatograms with signal-to-noise ratios of 10-1000 in conditions where the common ES Q-TOF MS detection failed. PMID:16791577
Variation and Genomic Localization of Genes Encoding DROSOPHILA MELANOGASTER Male Accessory Gland Proteins Separated by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis
Whalen, Michael; Wilson, Thomas G.
Accessory gland proteins from Drosophila melanogaster males have been separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis into nine major bands. When individual males from 175 strains were examined, considerable polymorphism for nearly one-half of the major protein bands was seen, including null alleles for three bands. Variation was observed not only among long-established laboratory strains but also among stocks recently derived from natural populations. There was little difference in the amount of variation between P and M strains, indicating that P element mutagenesis is not a factor producing the variation. Codominant expression of variants for each of five bands was found in heterozygotes, suggesting structural gene variation and not posttranslational modification variation. Stocks carrying electrophoretic variants of four of the major proteins were used to map the presumed structural genes for these proteins; the loci were found to be dispersed on the second chromosome. Since males homozygous for variant proteins were fertile, the polymorphism seems to have little immediate effect on successful sperm transfer. We propose that a high degree of polymorphism can be tolerated because these proteins play a nutritive rather than enzymatic role in Drosophila reproduction. PMID:3095182
Plasma Biomarker Discovery Using 3D Protein Profiling Coupled with Label-Free Quantitation
Beer, Lynn A.; Tang, Hsin-Yao; Barnhart, Kurt T.; Speicher, David W.
In-depth quantitative profiling of human plasma samples for biomarker discovery remains quite challenging. One promising alternative to chemical derivatization with stable isotope labels for quantitative comparisons is direct, label-free, quantitative comparison of raw LC¢MS data. But, in order to achieve high-sensitivity detection of low-abundance proteins, plasma proteins must be extensively pre-fractionated, and results from LC¢MS runs of all fractions must be integrated efficiently in order to avoid misidentification of variations in fractionation from sample to sample as ōapparentö biomarkers. This protocol describes a powerful 3D protein profiling method for comprehensive analysis of human serum or plasma proteomes, which combines abundant protein depletion and high-sensitivity GeLC¢MS/MS with label-free quantitation of candidate biomarkers. PMID:21468938
Detection of metals in proteins by means of polyacrylamide gel electrophoresis and laser ablation-inductively coupled plasma-mass spectrometry: application to selenium.
Chķry, Cyrille C; G³nther, Detlef; Cornelis, Rita; Vanhaecke, Frank; Moens, Luc
The capabilities of laser ablation-inductively coupled plasma-mass spectrometry for the detection of trace elements in a gel after gel electrophoresis were systematically studied. Figures of merit, such as limit of detection, linearity, and repeatability, were evaluated for various elements (Li, V, Cr, Mn, Ni, Cu, Zn, As, Se, Mo, Pd, Ag, Cd, Pt, Tl, Pb). Two ablation strategies were followed: single hole drilling, relevant for ablation of spots after two-dimensional (2-D) separations, and ablation with translation, i.e., on a line, relevant for one-dimensional (1-D) separations. This technique was applied to the detection of selenoproteins in red blood cells extracts after a 1-D separation (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and the detection of selenium-containing proteins in yeast after 2-D electrophoresis (2-DE). The detection procedure was further improved by using the dynamic reaction cell technology, which allowed the removal of the Ar_2(+) interference and hence the use of the most abundant Se isotope, (80)Se. Reaction gases were compared (methane, carbon monoxide, ammonia, oxygen and the combination of argon (collision gas) and hydrogen (reaction gas)). In each instance, the reaction cell parameters were optimized in order to obtain the lowest detection limit for Se (as (80)Se(+), (82)Se(+) or (77)Se(+); and as (80)Se(16)O(+), (82)Se(16)O(+) or (77)Se(16)O(+) with O(2) as the reaction gas). Carbon monoxide was found to offer the best performance. The detection limit with the use of DRC and He as transport gas was 0.07 microg Se g(-1) gel with single hole drilling and 0.15 microg Se g(-1) gel for ablation with translation. PMID:14595676
Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents
Philip L. Ross; Yulin N. Huang; Jason N. Marchese; Brian Williamson; Kenneth Parker; Stephen Hattan; Nikita Khainovski; Sasi Pillai; Subhakar Dey; Scott Daniels; Subhasish Purkayastha; Peter Juhasz; Stephen Martin; Michael Bartlet-Jones; Feng He; Allan Jacobson; Darryl J. Pappin
We describe here a multiplexed protein quantitation strat- egy that provides relative and absolute measurements of proteins in complex mixtures. At the core of this method- ology is a multiplexed set of isobaric reagents that yield amine-derivatized peptides. The derivatized peptides are indistinguishable in MS, but exhibit intense low-mass MS\\/MS signature ions that support quantitation. In this study, we have
Characterization of soluble amaranth and soybean proteins based on fluorescence, hydrophobicity, electrophoresis, amino Acid analysis, circular dichroism, and differential scanning calorimetry measurements.
Gorinstein, S; Delgado-Licon, E; Pawelzik, E; Permady, H H; Weisz, M; Trakhtenberg, S
Intrinsic fluorescence (IF), surface hydrophobicity (S(o)), electrophoresis, amino acid analysis, circular dichroism (CD), and differential scanning calorimetry (DSC) were used to study folded and unfolded soluble proteins from Amaranthus hypochondriacus (A. h.) and soybean (S). Globulin (Glo) and albumin subfractions (Alb-1 and Alb-2) were extracted from A. h. and S and denatured with urea. Electrophoretic and functional properties indicated a significant correlation between soluble protein fractions from soybean and amaranth. The protein fractions shared some common electrophoretic bands as well as a similar amino acid composition. The larger percent of denaturation in protein fractions, which is associated with enthalpy and the number of ruptured hydrogen bonds, corresponds to disappearance of alpha-helix. The obtained results provided evidence of differences in their secondary and tertiary structures. The most stable was Glo followed by the Alb-2 fraction. Predicted functional changes in model protein systems such as pseudocereals and legumes in response to processing conditions may be encountered in pharmaceutical and food industries. These plants can be a substitute for some cereals. PMID:11714365
Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size
Zhang, Haizhen; Burnum, Kristin E.; Luna, Maria L.; Petritis, Brianne O.; Kim, Jong Seo; Qian, Weijun; Moore, Ronald J.; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.; Pounds, Joel G.; Liu, Tao
In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled 'universal reference' into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein 'corona' that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.
Identification of selenium-containing proteins in selenium-rich yeast aqueous extract by 2D gel electrophoresis, nanoHPLC¢ICP MS and nanoHPLC¢ESI MS\\/MS
Laure Tastet; Dirk Schauml÷ffel; Brice Bouyssiere; Ryszard Lobinski
An approach based on the consecutive use of nanoHPLC¢ICP collision cell MS and nanoHPLC¢electrospray MS was proposed for the analysis of water-soluble selenium-containing proteins in selenium-rich yeast after their separation by 2D gel electrophoresis (GE). An ultrasonic probe was employed for fast protein extraction avoiding sample heating and thus reducing the risk of protein degradation. The efficiency of different extraction
Sequential phosphorylation analysis using dye-tethered peptides and microfluidic isoelectric focusing electrophoresis.
Choi, Hoseok; Choi, Nakchul; Lim, Butaek; Kim, Tae-Wuk; Song, Simon; Kim, Young-Pil
We report a simple method for analyzing sequential phosphorylation by protein kinases using fluorescent peptide substrates and microfluidic isoelectric focusing (?IEF) electrophoresis. When a dye-labeled peptide substrate was sequentially phosphorylated by two consecutive protein kinases (mitogen-activated protein kinase (MAPK) and glycogen synthase kinase 3 (GSK3)), its differently phosphorylated forms were easily separated and visualized by fluorescent focusing zones in the ?IEF channel based on a change in the isoelectric point (pI) by phosphorylation. As a result, ratiometric and quantitative analysis of the fluorescent focusing regions shifted by phosphorylation enabled the analysis of phosphorylation efficiency and the relevant inhibition of protein kinases (MAPK and GSK3) with high simplicity and selectivity. Furthermore, the GSK3 activity in the cell lysates was elucidated by ?IEF electrophoresis in combination with immunoprecipitation. Our results suggest that this method has great potential for analyzing the sequential phosphorylation of multiple protein kinases that are implicated in cellular signaling pathways. PMID:26050965
A Microfluidic Platform for High-Throughput Multiplexed Protein Quantitation
Volpetti, Francesca; Garcia-Cordero, Jose; Maerkl, Sebastian J.
We present a high-throughput microfluidic platform capable of quantitating up to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device contains 384 unit cells, which can be individually programmed with pairs of capture and detection antibody. Samples are quantitated in each unit cell by four independent MITOMI detection areas, allowing four samples to be analyzed in parallel for a total of 1,536 assays per device. We show that the device can be pre-assembled and stored for weeks at elevated temperature and we performed proof-of-concept experiments simultaneously quantitating IL-6, IL-1?, TNF-?, PSA, and GFP. Finally, we show that the platform can be used to identify functional antibody combinations by screening 64 antibody combinations requiring up to 384 unique assays per device. PMID:25680117
Definition of Mycobacterium tuberculosis culture filtrate proteins by two-dimensional polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and electrospray mass spectrometry.
Sonnenberg, M G; Belisle, J T
A number of the culture filtrate proteins secreted by Mycobacterium tuberculosis are known to contribute to the immunology of tuberculosis and to possess enzymatic activities associated with pathogenicity. However, a complete analysis of the protein composition of this fraction has been lacking. By using two-dimensional polyacrylamide gel electrophoresis, detailed maps of the culture filtrate proteins of M. tuberculosis H37Rv were generated. In total, 205 protein spots were observed. The coupling of this electrophoretic technique with Western blot analysis allowed the identification and mapping of 32 proteins. Further molecular characterization of abundant proteins within this fraction was achieved by N-terminal amino acid sequencing and liquid chromatography-mass spectrometry. Eighteen proteins were subjected to N-group analysis; of these, only 10 could be sequenced by Edman degradation. Among the most interesting were a novel 52-kDa protein demonstrating significant homology to an alpha-hydroxysteroid dehydrogenase of Eubacterium sp. strain VPI 12708, a 25-kDa protein corresponding to open reading frame 28 of the M. tuberculosis cosmid MTCY1A11, and a 31-kDa protein exhibiting an amino acid sequence identical to that of antigen 85A and 85B. This latter product migrated with an isoelectric point between those of antigen 85A and 85C but did not react with the antibody specific for this complex, suggesting that there is a fourth member of the antigen 85 complex. Novel N-terminal amino acid sequences were obtained for three additional culture filtrate proteins; however, these did not yield significant homology to known protein sequences. A protein cluster of 85 to 88 kDa, recognized by the monoclonal antibodies IT-57 and IT-42 and known to react with sera from a large proportion of tuberculosis patients, was refractory to N-group analysis. Nevertheless, mass spectrometry of peptides obtained from one member of this complex identified it as the M. tuberculosis KatG catalase/peroxidase. Thus, the detailed mapping of M. tuberculosis proteins, combined with state-of-the-art analytical techniques such as mass spectrometry, provides a basis for further analysis and rapid identification of biologically relevant molecules. PMID:9353028
Electrokinetic motion of heterogeneous particles Electrophoresis, induced-charge electrophoresis, transverse electrophoresis.
Bazant, Martin Z.
Electrokinetic motion of heterogeneous particles Synonyms Electrophoresis, induced-charge electrophoresis, transverse electrophoresis. Definition The electrokinetic motion of heterogeneous particles due to the combined effects of electrophoresis, induced-charge electrophoresis, and dielectrophoresis
Accelerated Articles Quantitative Analysis of Protein Phosphorylation in
Chait, Brian T.
reported hypothesis-driven multistage MS (HMS-MS) method (Chang, E. J.; Archambault, V.; McLachlin, D. T of the dominant loss of H3PO4 during MS/MS from singly charged phosphopeptide ions produced by matrix-assisted laser desorption/ionization (MALDI) in the ion trap mass spectrometer. In the present work, quantitation
Quantitative trait loci influencing protein and starch concentration in the Illinois Long Term Selection maize strains
I. L. Goldman; T. R. Rocheford; J. W. Dudley
A study was initiated to determine the number, chromosomal location, and magnitude of effect of QTL (quantitative trait loci or locus depending on context) controlling protein and starch concentration in the maize (Zea mays L.) kernel. Restriction fragment length polymorphism (RFLP) analysis was performed on 100 F3 families derived from a cross of two strains, Illinois High Protein (IHP), X
Quantitative structure activity relationship modelling of peptides and proteins as a tool in food science
Are Hugo Pripp; Tomas Isaksson; Leszek Stepaniak; Terje S°rhaug; Ylva Ard÷
Peptides and proteins contribute to physical properties, biological activities and sensory characteristics of foods. Studies on the isolation and characterisation of peptides and proteins allow compilation of data sets on their structures and properties\\/activities. Quantitative structure activity relationship (QSAR) modelling provides methodology to find mathematical expressions for such relationships which may then be useful for estimating activities of any related
Quantitative variation in cystic fibrosis-associated proteins in cystic fibrosis patients, carriers, and controls
A. Jamieson; Elizabeth Mackinlay; D. A. Aitken; A. Cooke; M. A. Ferguson-Smith
Serum samples from patients with cystic fibrosis (CF), obligate heterozygotes, and normal controls have been examined by isoelectric focusing (IEF). Our results suggest that cystic fibrosis protein (CFP) is a normal serum protein exhibiting quantitative variation primarily dependent on possession of the CF allele. It is concluded that detection of CFP by IEF is an inappropriate screening test for the
Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis.
Nissum, Mikkel; Foucher, Aude L
Due to ease of accessibility, plasma has become the sample of choice for proteomics studies directed towards biomarker discovery intended for use in diagnostics, prognostics and even in theranostics. The result of these extensive efforts is a long list of potential biomarkers, very few of which have led to clinical utility. Why have so many potential biomarkers failed validation? Herein, we address certain issues encountered, which complicate biomarker discovery efforts originating from plasma. The advantages of stabilizing the sample at collection by the addition of protease inhibitors are discussed. The principles of free-flow electrophoresis (FFE) separation are provided together with examples applying to various studies. Finally, particular attention is given to plasma or serum analysis using multidimensional separation strategies into which the FFE is incorporated. The advantages of using FFE separation in these workflows are discussed. PMID:18761468
Quantitation of human peptides and proteins via MS: review of analytically validated assays.
Chappell, Derek L; Lassman, Michael E; McAvoy, Thomas; Lin, Mingxiang; Spellman, Daniel S; Laterza, Omar F
Since the development of monoclonal antibodies in the 1970s, antibody-based assays have been used for the quantitation of proteins and peptides and, today, they are the most widely used technology in routine laboratory medicine and bioanalysis. However, in the last couple of decades, liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) techniques have been adopted in the quantitation of small molecules, and more recently have made significant contributions in the quantitation of proteins and peptides. In this article, we will review clinical MS-based assays for endogenous peptides, proteins, and therapeutic antibodies, for which validated methods exist. We will also cover the measurement of protein turnover and the unique solutions that MS can offer in this field. PMID:25157489
Use of lab-on-a-chip technology for protein sizing and quantitation.
Kuschel, Meike; Neumann, Tanja; Barthmaier, Peter; Kratzmeier, Martin
The performance of the Agilent 2100 bioanalyzer, the first commercial lab-on-a-chip system, and the Protein 200 Plus LabChip kit is compared with conventional protein analysis techniques such as SDS-PAGE, Lowry, or Bradford. Lab-on-a-chip technology for protein analysis allows for the integration of electrophoretic separation, staining, destaining, and fluorescence detection into a single process, and for it to be combined with data analysis. The chip-based protein assay allows purity analysis, sizing, and relative quantitation based on internal standards or absolute quantitation based on user-defined standards. The chip-based protein analysis is comparable in sensitivity, sizing accuracy, and reproducibility to SDS-PAGE stained with standard Coomassie. Resolution and linear dynamic range are improved. Absolute quantitation accuracy and reproducibility is improved in comparison to SDS-PAGE and is comparable to batch-based quantitation methods such as Lowry and Bradford. The lab-on-a-chip system has several additional advantages over conventional SDS-PAGE including fast analysis times, reduced manual labor, automated data analysis, and good reproducibility. With such a system, the protein of interest can be tracked during the whole purification procedure, for example, from cell lysates through column fractions to purified proteins. PMID:19498980
Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.
Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T
Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions. PMID:26182240
An evaluation of protein assays for quantitative determination of drugs.
Williams, Katherine M; Arthur, Sarah J; Burrell, Gillian; Kelly, Fionnuala; Phillips, Darren W; Marshall, Thomas
We have evaluated the response of six protein assays [the biuret, Lowry, bicinchoninic acid (BCA), Coomassie Brilliant Blue (CBB), Pyrogallol Red-Molybdate (PRM), and benzethonium chloride (BEC)] to 21 pharmaceutical drugs. The drugs evaluated were analgesics (acetaminophen, aspirin, codeine, methadone, morphine and pethidine), antibiotics (amoxicillin, ampicillin, gentamicin, neomycin, penicillin G and vancomycin), antipsychotics (chlorpromazine, fluphenazine, prochlorperazine, promazine and thioridazine) and water-soluble vitamins (ascorbic acid, niacinamide, pantothenic acid and pyridoxine). The biuret, Lowry and BCA assays responded strongly to most of the drugs tested. The PRM assay gave a sensitive response to the aminoglycoside antibiotics (gentamicin and neomycin) and the antipsychotic drugs. In contrast, the CBB assay showed little response to the aminoglycosides and gave a relatively poor response with the antipsychotics. The BEC assay did not respond significantly to the drugs tested. The response of the protein assays to the drugs was further evaluated by investigating the linearity of the response and the combined response of drug plus protein. The results are discussed with reference to drug interference in protein assays and the development of new methods for the quantification of drugs in protein-free solution. PMID:12834962
Determination of free and protein-bound glutathione in HepG2 cells using capillary electrophoresis with laser-induced fluorescence detection
Wang, Yan; Xie, Yi; Bernier, Michel; Wainer, Irving W.
A rapid method using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) was developed to determine free and protein-bound glutathione (GSH) in human HepG2 hepatocarcinoma cells. The samples were derivatized with 5-iodoacetamidofluorescein (5-IAF), and analyzed at 22 kV using sodium phosphate buffer (10 mM, pH 11.4) and an uncoated 58 cm ū 75 Ąm I.D. fused silica capillary. The analysis time was less than 10 min and N-acetylcysteine was used as internal standard. The derivatization conditions, such as reaction time, 5-IAF concentration, running buffer and cartridge temperature were optimized. Argon gas was used in the study to prevent the oxidization of GSH during sample preparation. The optimized method required only 30¢40 nl sample per analysis and was fast and sensitive. The method was applied to the analyses of HepG2 cells treated with the small metal chelating agent, pyrrolidine dithiocarbamate (PDTC). The results demonstrate that the amount of protein-bound GSH, which reflects the amount of protein S-glutathionylation, increased in a time-dependent manner upon cell treatment with PDTC, reaching a maximum of over 50% increase 2 h post-PDTC. PMID:18602637
Quantitative Analysis of Protein-Lipid Interactions Using Tryptophan Fluorescence
NSDL National Science Digital Library
Catherine A. Kraft (University of Pittsburgh School of Medicine; The Department of Pharmacology and Chemical Biology REV)
The fluorescent properties of the amino acid tryptophan make it a useful tool for fluorometric assays. Because tryptophan fluorescence is remarkably sensitive to the polarity of the environment, it can be used to determine the affinity of tryptophan-containing peptides for phospholipid vesicles of varying compositions. Here, we describe a method for using tryptophan fluorescence to determine the binding affinities of peptides derived from the proteins Raf-1 and KSR-1 to small unilamellar vesicles containing phosphatidic acid. The method can be extrapolated to measure the binding of other tryptophan-containing peptides or proteins to lipid vesicles.
Quantitative determination of curcuminoids in Curcuma rhizomes and rapid differentiation of Curcuma domestica Val. and Curcuma xanthorrhiza Roxb. by capillary electrophoresis.
Lechtenberg, Matthias; Quandt, Bettina; Nahrstedt, Adolf
The three major curcuminoids, curcumin, demethoxycurcumin and bis-demethoxycurcumin, from Curcuma domestica Val. (Curcuma longa L.) and Curcuma xanthorrhiza Roxb. (Zingiberaceae) were fully separated and quantified in less than 5 min using a capillary zone electrophoresis method with standard fused-silica capillaries and photodiode array detection. An electrolyte solution of 20 mM phosphate, 50 mM sodium hydroxide and 14 mM beta-cyclodextrin was found to be appropriate. Quantification was performed with 3,4-dimethoxy-trans-cinnamic acid as internal standard, and the limit of detection was 0.01 mg/mL. Extraction, stabilisation during sample storage and quantification procedures were optimised and carried out with drugs and commercial curry powder from different provenances. The results were compared with the photometric method of the monograph Curcumae xanthorrhizae rhizoma of the European Pharmacopoeia. PMID:15202598
A Quantitative Assessment of Heterogeneity for Surface-Immobilized Proteins
Leckband, Deborah E.
directly on a solid substrate or within a porous matrix and used to detect the presence of a target applications use protein receptors immobilized on solid supports. Although, in solution, these receptors-TNT antibodies. The antibodies were immobilized on silica fiber-optic probes via five different immobilization
An evaluation of protein assays for quantitative determination of drugs
Katherine M. Williams; Sarah J. Arthur; Gillian Burrell; Fionnuala Kelly; Darren W. Phillips; Thomas Marshall
We have evaluated the response of six protein assays [the biuret, Lowry, bicinchoninic acid (BCA), Coomassie Brilliant Blue (CBB), Pyrogallol Red¢Molybdate (PRM), and benzethonium chloride (BEC)] to 21 pharmaceutical drugs. The drugs evaluated were analgesics (acetaminophen, aspirin, codeine, methadone, morphine and pethidine), antibiotics (amoxicillin, ampicillin, gentamicin, neomycin, penicillin G and vancomycin), antipsychotics (chlorpromazine, fluphenazine, prochlorperazine, promazine and thioridazine) and water-soluble
Rapid Separation and Quantification of Major Caseins and Whey Proteins of Bovine Milk by Polyacrylamide Gel Electrophoresis
K. F. Ng-Kwai-Hang; E. M. Kroeker
A rapid polyacrylamide gel electro- phoretic method was developed for separating and quantifying major pro- teins in casein and whey protein fractions of bovine milk. For casein separation, best results were achieved by an 8% poly- acrylamide gel containing 4 M urea and a top layer of large pore sample gel; for whey protein the most_ satisfactory separation was with
Quantitative approaches to monitor protein¢nucleic acid interactions using fluorescent probes
Pagano, John M.; Clingman, Carina C.; Ryder, Sean P.
Sequence-specific recognition of nucleic acids by proteins is required for nearly every aspect of gene expression. Quantitative binding experiments are a useful tool to measure the ability of a protein to distinguish between multiple sequences. Here, we describe the use of fluorophore-labeled oligonucleotide probes to quantitatively monitor protein/nucleic acid interactions. We review two complementary experimental methods, fluorescence polarization and fluorescence electrophoretic mobility shift assays, that enable the quantitative measurement of binding affinity. We also present two strategies for post-synthetic end-labeling of DNA or RNA oligonucleotides with fluorescent dyes. The approaches discussed here are efficient and sensitive, providing a safe and accessible alternative to the more commonly used radio-isotopic methods. PMID:21098142
Secondary Reactions and Strategies to Improve Quantitative Protein Footprinting
Xu,G.; Kiselar, J.; He, Q.; Chance, M.
Hydroxyl radical-mediated footprinting permits detailed examination of structure and dynamic processes of proteins and large biological assemblies, as changes in the rate of reaction of radicals with target peptides are governed by changes in the solvent accessibility of the side-chain probe residues. The precise and accurate determination of peptide reaction rates is essential to successfully probing protein structure using footprinting. In this study, we specifically examine the magnitude and mechanisms of secondary oxidation occurring after radiolytic exposure and prior to mass spectrometric analysis. Secondary oxidation results from hydrogen peroxide and other oxidative species generated during radiolysis, significantly impacting the oxidation of Met and Cys but not aromatic or other reactive residues. Secondary oxidation of Met with formation of sulfoxide degrades data reproducibility and inflates the perceived solvent accessibility of Met-containing peptides. It can be suppressed by adding trace amounts of catalase or millimolar Met-NH{sub 2} (or Met-OH) buffer immediately after irradiation; this leads to greatly improved adherence to first-order kinetics and more precise observed oxidation rates. The strategy is shown to suppress secondary oxidation in model peptides and improve data quality in examining the reactivity of peptides within the Arp2/3 protein complex. Cysteine is also subject to secondary oxidation generating disulfide as the principal product. The disulfides can be reduced before mass spectrometric analysis by reducing agents such as TCEP, while methionine sulfoxide is refractory to reduction by this reagent under typical reducing conditions.
Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.
von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana
The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed. PMID:23677009
Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology
von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana
The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes (13C, 15N, 36S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed. PMID:23677009
Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors*
Deshmukh, Atul S.; Murgia, Marta; Nagaraj, Nagarjuna; Treebak, Jonas T.; Cox, J³rgen; Mann, Matthias
Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging because of highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art MS workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins. We obtain absolute abundances for proteins expressed in a muscle cell line and skeletal muscle, which should serve as a valuable resource. Quantitation of protein isoforms of glucose uptake signaling pathways and in glucose and lipid metabolic pathways provides a detailed metabolic map of the cell line compared with tissue. This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms. PMID:25616865
A rapid method of species identification of wild chironomids (Diptera: Chironomidae) via electrophoresis of hemoglobin proteins in sodium dodecyl sulfate polyacrylamide gel (SDS-PAGE).
Oh, J T; Epler, J H; Bentivegna, C S
Studying aquatic benthic macroinvertebrates (BMIs) in the field requires accurate taxonomic identification, which can be difficult and time consuming. Conventionally, head capsule morphology has been used to identify wild larvae of Chironomidae. However, due to the number of species and possible damage and/or deformity of their head capsules, another supporting approach for identification is needed. Here, we provide hemoglobin (Hb) protein in hemolymph of chironomids as a new biomarker that may help resolve some of the ambiguities and difficulties encountered during taxonomic identification. Chironomids collected from two locations in Maine and New Jersey, USA were identified to the genus level and in some cases to the species-level using head capsule and body morphologies. The head capsule for a particular individual was then associated with a corresponding Hb protein profile generated from sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Distinct Hb profiles were observed from one group (Thienemannimyia) and four genera (Chironomus, Cricotopus, Dicrotendipes, and Glyptotendipes) of chironomids. Several species were polymorphic, having more than one Hb profile and/or having bands of the same size as those of other species. However, major bands and the combination of bands could distinguish individuals at the genus and sometimes species-level. Overall, this study showed that Hb profiles can be used in combination with head capsule morphology to identify wild chironomids. PMID:24923437
Using quantitative proteomics of Arabidopsis roots and leaves to predict metabolic activity
Technology Transfer Automated Retrieval System (TEKTRAN)
Proteins isolated from developing roots and leaves of Arabidopsis thaliana were separated by high-resolution two-dimensional (2-D) electrophoresis. The resulting 2-D proteome maps are markedly different. Quantitative analysis of root and leaf protein spot pairs revealed that in most instances ther...
Absolute Quantitation of Isoforms of Post-translationally Modified Proteins in Transgenic Organism*
Li, Yaojun; Shu, Yiwei; Peng, Changchao; Zhu, Lin; Guo, Guangyu; Li, Ning
Post-translational modification isoforms of a protein are known to play versatile biological functions in diverse cellular processes. To measure the molar amount of each post-translational modification isoform (Pisf) of a target protein present in the total protein extract using mass spectrometry, a quantitative proteomic protocol, absolute quantitation of isoforms of post-translationally modified proteins (AQUIP), was developed. A recombinant ERF110 gene overexpression transgenic Arabidopsis plant was used as the model organism for demonstration of the proof of concept. Both Ser-62-independent 14N-coded synthetic peptide standards and 15N-coded ERF110 protein standard isolated from the heavy nitrogen-labeled transgenic plants were employed simultaneously to determine the concentration of all isoforms (Tisf) of ERF110 in the whole plant cell lysate, whereas a pair of Ser-62-dependent synthetic peptide standards were used to quantitate the Ser-62 phosphosite occupancy (Raqu). The Pisf was finally determined by integrating the two empirically measured variables using the following equation: Pisf = Tisf Ę Raqu. The absolute amount of Ser-62-phosphorylated isoform of ERF110 determined using AQUIP was substantiated with a stable isotope labeling in Arabidopsis-based relative and accurate quantitative proteomic approach. The biological role of the Ser-62-phosphorylated isoform was demonstrated in transgenic plants. PMID:22442259
Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis of ram seminal plasma proteins and their correlation with semen characteristics
Wenbin Yue; Lei Shi; Zhiming Bai; Youshe Ren; Youying Zhao
The present study was conducted to investigate fertility-associated proteins in ram seminal plasma and the correlation between specific protein and semen characteristics in sheep. Thirty-eight German merino sheep clinically proven healthy were chosen and divided into three groups according to fertility. Ejaculates were collected by an artificial vagina and semen characteristics (volume, pH value, motility, viability and concentration) were recorded.
NASA Technical Reports Server (NTRS)
Todd, P. W.
Tasks were undertaken in support of two objectives. They are: (1) to carry out electrophoresis experiments on cells in microgravity; and (2) assess the feasibility of using purified kidney cells from embryonic kidney cultures as a source of important cell products. Investigations were carried out in the following areas: (1) ground based electrophoresis technology; (2) cell culture technology; (3) electrophoresis of cells; (4) urokinase assay research; (5) zero-g electrophoresis; and (6) flow cytometry.
A Reusable Electrochemical Proximity Assay for Highly Selective, Real-Time Protein Quantitation in Biological Matrices
Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)Śas quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation. PMID:24827871
A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices.
Hu, Jiaming; Yu, Yajiao; Brooks, Jessica C; Godwin, Leah A; Somasundaram, Subramaniam; Torabinejad, Ferdous; Kim, Joonyul; Shannon, Curtis; Easley, Christopher J
Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)-as quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation. PMID:24827871
Identification of multiresistant Staphylococcus epidermidis in neonates of a secondary care hospital using pulsed field gel electrophoresis and quantitative antibiogram typing.
Sloos, J H; Horrevorts, A M; Van Boven, C P; Dijkshoorn, L
AIMS: To determine the diversity of types of Staphylococcus epidermidis in a neonatal care unit of a secondary care hospital in the Netherlands. METHODS: In a prospective study, specimens from nose, ear, axilla, umbilicus, and groin were taken from patients twice a week during a period of up to two weeks. All isolates were typed by both pulsed field gel electrophoresis (PFGE) and antibiogram analysis. RESULTS: Fifty three S epidermidis isolates from 15 of 24 patients were obtained in one to four surveys. Fourteen isolates from six patients had a common PFGE pattern and were of one multiresistant antibiogram type. The remaining 39 isolates were allocated to 24 sporadic PFGE types and were more susceptible to antibiotics. Colonisation with the multiresistant strain correlated with a long period of stay and with the use of specific antibiotics. The multiresistant isolates were related closely to isolates of S epidermidis found in a recent study in a teaching hospital in the vicinity of the secondary care hospital. CONCLUSION: Repeated sampling and the use of two typing methods allowed the identification of two closely related multiresistant S epidermidis strains in two hospitals in the same area. Images PMID:9577375
Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC¢MS\\/MS
John Sinclair; John F. Timms
Blood-borne biomarkers are urgently required for the early detection, accurate diagnosis and prognosis of disease. Additionally, improved methods of profiling serum and plasma proteins for biomarker discovery efforts are needed. Herein, we report a quantitative method based on amino-group labelling of serum proteins (rather than peptides) with isobaric tandem mass tags (TMT) and incorporating immune-based depletion, gel-based and strong anion
Casein - whey protein interactions in heated milk
Astrid Jolanda Vasbinder
Heating of milk is an essential step in the processing of various dairy products, like for example yoghurt. A major consequence of the heat treatment is the denaturation of whey proteins, which either associate with the casein micelle or form soluble whey protein aggregates. By combination of enzymatic fractionation and capillary electrophoresis we were able to quantitatively determine the distribution
A general method for the extraction of citrus leaf proteins and separation by 2D electrophoresis: a follow up.
Maserti, B E; Della Croce, C M; Luro, F; Morillon, R; Cini, M; Caltavuturo, L
With the aim of studying differentially expressed proteins as a function of abiotic and biotic stress in citrus plants, we optimized a protocol for the extraction of total leaf proteins and their 2-DE separation using commercially available immobilized pH gradient strips (IPGs) in the first dimension. Critical factors for good reproducibility of citrus leaf protein separation were identified: trichloroacetic acid (TCA)/acetone precipitation after extraction in lysis buffer, sample fractionation on narrow range overlapping IPGs and sample-cup loading at the anodic or cathodic end of the strip. The use of thiourea and a strong detergent (C7BzO) in the solubilization/rehydration buffer, coupled with the increase to 10% of SDS in the equilibration buffer before the second dimension seemed to affect positively the resolution of basic proteins. Using our protocol we resolved about 30 basic proteins on 6.3-8.3 pH range strips. Further, our protocol was successfully applied reproducibly on the analysis of control and salt exposed leaf samples of Citrus reshni Hort. Ex Tan. PMID:17035105
Matrix-assisted laser desorption\\/ionization time of flight mass spectrometry peptide mass fingerprints and post source decay: a tool for the identification and analysis of phloem proteins from Cucurbita maxima Duch. separated by two-dimensional polyacrylamide gel electrophoresis
Sophie Haebel; Julia Kehr
A combination of gel electrophoresis and mass spectrometry was used to analyze the soluble proteins from phloem sap of Cucurbita maxima Duch. Phloem proteins were separated using two-dimensional gel electrophoresis. Coomassie-stained spots were cut out and subjected to tryptic digestion. To identify proteins, peptide mass fingerprints were determined by matrix-assisted laser desorption\\/ionization time of flight (MALDI-TOF) mass spectrometry. In addition,
Time-domain fluorescence lifetime imaging microscopy: a quantitative method to follow transient protein-protein interactions in living cells.
Padilla-Parra, Sergi; Audugķ, Nicolas; Tramier, Marc; Coppey-Moisan, Ma'tķ
Quantitative analysis in F÷rster resonance energy transfer (FRET) imaging studies of protein-protein interactions within live cells is still a challenging issue. Many cellular biology applications aim at the determination of the space and time variations of the relative amount of interacting fluorescently tagged proteins occurring in cells. This relevant quantitative parameter can be, at least partially, obtained at a pixel-level resolution by using fluorescence lifetime imaging microscopy (FLIM). Indeed, fluorescence decay analysis of a two-component system (FRET and no FRET donor species), leads to the intrinsic FRET efficiency value (E) and the fraction of the donor-tagged protein that undergoes FRET (fD). To simultaneously obtain fD and E values from a two-exponential fit, data must be acquired with a high number of photons, so that the statistics are robust enough to reduce fitting ambiguities. This is a time-consuming procedure. However, when fast-FLIM acquisitions are used to monitor dynamic changes in protein-protein interactions at high spatial and temporal resolutions in living cells, photon statistics and time resolution are limited. In this case, fitting procedures are unreliable, even for single lifetime donors. We introduce the concept of a minimal fraction of donor molecules involved in FRET (mfD), obtained from the mathematical minimization of fD. Here, we discuss different FLIM techniques and the compromises that must be made between precision and time invested in acquiring FLIM measurements. We show that mfD constitutes an interesting quantitative parameter for fast FLIM because it gives quantitative information about transient interactions in live cells. PMID:26034312
Quantitative Laser Diffraction Method for the Assessment of Protein Subvisible Particles
Totoki, Shinichiro; Yamamoto, Gaku; Tsumoto, Kouhei; Uchiyama, Susumu; Fukui, Kiichi
Laser diffraction (LD) has been recognized as a method for estimating particle size distribution. Here, a recently developed quantitative LD (qLD) system, which is an LD method with extensive deconvolution analysis, was employed for the quantitative assessment of protein particles sizes, especially aimed at the quantification of 0.2¢10 ?m diameter subvisible particles (SVPs). The qLD accurately estimated concentration distributions for silica beads with diameters ranging from 0.2 to 10 ?m that have refractive indices similar to that of protein particles. The linearity of concentration for micrometer-diameter silica beads was confirmed in the presence of a fixed concentration of submicrometer diameter beads. Similarly, submicrometer-diameter silica beads could be quantified in the presence of micrometer-diameter beads. Subsequently, stir- and heat-stressed intravenous immunoglobulins were evaluated by using the qLD, in which the refractive index of protein particles that was determined experimentally was used in the deconvolution analysis. The results showed that the concentration distributions of protein particles in SVP size range differ for the two stresses. The number concentration of the protein particles estimated using the qLD agreed well with that obtained using flow microscopy. This work demonstrates that qLD can be used for quantitative estimation of protein aggregates in SVP size range. ® 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:618¢626, 2015 PMID:25449441
Quantitative laser diffraction method for the assessment of protein subvisible particles.
Totoki, Shinichiro; Yamamoto, Gaku; Tsumoto, Kouhei; Uchiyama, Susumu; Fukui, Kiichi
Laser diffraction (LD) has been recognized as a method for estimating particle size distribution. Here, a recently developed quantitative LD (qLD) system, which is an LD method with extensive deconvolution analysis, was employed for the quantitative assessment of protein particles sizes, especially aimed at the quantification of 0.2-10 ?m diameter subvisible particles (SVPs). The qLD accurately estimated concentration distributions for silica beads with diameters ranging from 0.2 to 10 ?m that have refractive indices similar to that of protein particles. The linearity of concentration for micrometer-diameter silica beads was confirmed in the presence of a fixed concentration of submicrometer diameter beads. Similarly, submicrometer-diameter silica beads could be quantified in the presence of micrometer-diameter beads. Subsequently, stir- and heat-stressed intravenous immunoglobulins were evaluated by using the qLD, in which the refractive index of protein particles that was determined experimentally was used in the deconvolution analysis. The results showed that the concentration distributions of protein particles in SVP size range differ for the two stresses. The number concentration of the protein particles estimated using the qLD agreed well with that obtained using flow microscopy. This work demonstrates that qLD can be used for quantitative estimation of protein aggregates in SVP size range. PMID:25449441
Protein labeling with red squarylium dyes for analysis by capillary electrophoresis with laser-induced fluorescence detection.
Yan, Weiying; Sloat, Amy L; Yagi, Shigeyuki; Nakazumi, Hiroyuki; Colyer, Christa L
Two new red luminescent asymmetric squarylium dyes (designated "Red-1c and Red-3") have been shown to exhibit absorbance shifts to longer wavelengths upon the addition of protein, along with a concomitant increase in fluorescence emission. Specifically, the absorbance maxima for Red-1c and Red-3 dyes are 607 and 622 nm, respectively, in the absence of HSA, and 642 and 640 nm in the presence of HSA, making the excitation of their protein complexes feasible with inexpensive and robust diode lasers. Fluorescence emission maxima, in the presence of HSA, are 656 and 644 nm for Red-1c and Red-3, respectively. Because of the inherently low fluorescence of the dyes in their free state, Red-1c and Red-3 were used as on-column labels (that is, with the dye incorporated into the separation buffer), thus eliminating the need for sample derivatization prior to injection and separation. A comparison of precolumn and on-column labeling of proteins with these squarylium dyes revealed higher efficiencies and greater sensitivities for on-column labeling, which, when conducted with a basic, high-salt content buffer, permitted baseline resolution of a mixture of five model proteins. LOD for model proteins, such as transferrin, alpha-lactalbumin, BSA, and beta-lactoglobulin A and B, labeled with these dyes and analyzed by CE with LIF detection (CE-LIF) were found to be dependent upon dye concentration and solution pH, and are as low as 5 nM for BSA. Satisfactory linear relationships between peak height (or peak area) and protein concentration were obtained by CE-LIF for this on-column labeling method with Red-3 and Red-1c. PMID:16568403
NanoOrange Protein Quantitation KitMP 06666 Revised: 22October2001
Lebendiker, Mario
or nucleic acids BCA method 1 0.5 Ąg/mL to 1.5 mg/mL Ę Samples must be read within 10 minutes by nucleic acids and other contaminants #12;NanoOrange« Protein Quantitation Kit2 Materials $ Nano for fluorescence determination in a fluorometer or minifluorometer. If the assay volume is reduced by 10-fold
Mass spectrometric quantitation of covalently bound cell wall proteins in Saccharomyces cerevisiae
Yin, Qing Yuan; de Groot, Piet W J; de Jong, Luitzen; Klis, Frans M; De Koster, Chris G
The cell wall of yeast consists of an internal skeletal layer and an external layer of glycoproteins covalently linked to the stress-bearing polysaccharides. The cell wall protein (CWP) population consists of over 20 different proteins, and may vary in composition. We present two complementary methods for quantifying CWPs, based on isobaric tagging and tandem MS: (1) absolute quantitation of individual CWPs, allowing estimation of surface densities; and (2) relative quantitation of CWPs, allowing monitoring of the dynamics of the CWP population. For absolute quantitation, we selected a representative group of five proteins (Cwp1p, Crh1p, Scw4p, Gas1p, and Ecm33p), which had 67 ū 103, 44 ū 103, 38 ū 103, 11 ū 103 and 6.5 ū 103 of wall-bound copies per cell, respectively. As Cwp1p is predominantly incorporated in the birth scar, this corresponds to a protein density of c. 22 ū 103 copies ?m?2. For relative quantitation, we compared wild-type cells to gas1? cells, in which the cell wall integrity pathway is constitutively activated. The levels of Crh1p, Crh2p, Ecm33p, Gas5p, Pst1p and Pir3p increased about three- to fivefold, whereas the level of Scw4p was significantly decreased. We propose that our methods are widely applicable to other fungi. PMID:17617218
High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography
Mass Spectrometry; Hui Zhang; Eugene C. Yi; Xiao-jun Li; Parag Mallick; Karen S. Kelly-Spratt; Christophe D. Masselon; David G. Camp II; Richard D. Smith; Christopher J. Kemp; Ruedi Aebersold
It is expected that the composition of the serum proteome can provide valuable information about the state of the human body in health and disease and that this informa- tion can be extracted via quantitative proteomic measure- ments. Suitable proteomic techniques need to be sensi- tive, reproducible, and robust to detect potential biomarkers below the level of highly expressed proteins,
Quantitative and Functional Characterization of the Hyper-Conserved Protein of Prochlorococcus and Marine Synechococcus
Zorz, Jackie K.; Joy, Andrew P.; Barnett, David A.; Johnson, Milo S.; Zhaxybayeva, Olga; Cockshutt, Amanda M.
A large fraction of any bacterial genome consists of hypothetical protein-coding open reading frames (ORFs). While most of these ORFs are present only in one or a few sequenced genomes, a few are conserved, often across large phylogenetic distances. Such conservation provides clues to likely uncharacterized cellular functions that need to be elucidated. Marine cyanobacteria from the Prochlorococcus/marine Synechococcus clade are dominant bacteria in oceanic waters and are significant contributors to global primary production. A Hyper Conserved Protein (PSHCP) of unknown function is 100% conserved at the amino acid level in genomes of Prochlorococcus/marine Synechococcus, but lacks homologs outside of this clade. In this study we investigated Prochlorococcus marinus strains MED4 and MIT 9313 and Synechococcus sp. strain WH 8102 for the transcription of the PSHCP gene using RT-Q-PCR, for the presence of the protein product through quantitative immunoblotting, and for the protein's binding partners in a pull down assay. Significant transcription of the gene was detected in all strains. The PSHCP protein content varied between 8▒1 fmol and 26▒9 fmol per ug total protein, depending on the strain. The 50 S ribosomal protein L2, the Photosystem I protein PsaD and the Ycf48-like protein were found associated with the PSHCP protein in all strains and not appreciably or at all in control experiments. We hypothesize that PSHCP is a protein associated with the ribosome, and is possibly involved in photosystem assembly. PMID:25360678
Detection, quantitation, purification, and identification of cardiac proteins S-thiolated during ischemia and reperfusion.
Eaton, Philip; Byers, Helen L; Leeds, Nicola; Ward, Malcolm A; Shattock, Michael J
We have developed methods that allow detection, quantitation, purification, and identification of cardiac proteins S-thiolated during ischemia and reperfusion. Cysteine was biotinylated and loaded into isolated rat hearts. During oxidative stress, biotin-cysteine forms a disulfide bond with reactive protein cysteines, and these can be detected by probing Western blots with streptavidin-horseradish peroxidase. S-Thiolated proteins were purified using streptavidin-agarose. Thus, we demonstrated that reperfusion and diamide treatment increased S-thiolation of a number of cardiac proteins by 3- and 10-fold, respectively. Dithiothreitol treatment of homogenates fully abolished the signals detected. Fractionation studies indicated that the modified proteins are located within the cytosol, membrane, and myofilament/cytoskeletal compartments of the cardiac cells. This shows that biotin-cysteine gains rapid and efficient intracellular access and acts as a probe for reactive protein cysteines in all cellular locations. Using Western blotting of affinity-purified proteins we identified actin, glyceraldehyde-3-phosphate dehydrogenase, HSP27, protein-tyrosine phosphatase 1B, protein kinase Calpha, and the small G-protein ras as substrates for S-thiolation during reperfusion of the ischemic rat heart. MALDI-TOF mass fingerprint analysis of tryptic peptides independently confirmed actin and glyceraldehyde-3-phosphate dehydrogenase S-thiolation during reperfusion. This approach has also shown that triosephosphate isomerase, aconitate hydratase, M-protein, nucleoside diphosphate kinase B, and myoglobin are S-thiolated during post-ischemic reperfusion. PMID:11777920
A high-throughput microchromatography platform for quantitative analytical scale protein sample preparation.
Fulton, Scott; Murphy, Steve; Reich, Jenn; Van Den Heuvel, Zachary; Sakowski, Robert; Smith, Ronald; Agee, Susan
Protein analysis (using either specific protein quantitation by methods such as HPLC and immunoassays or structural analysis by methods such as LC-MS) usually requires significant sample preparation, including quantitative purification of the target protein from complex sample matrices and potentially enzymatic treatment or labeling. We have developed platform for high-throughput microchromatography, capable of running 96 or more small volume samples in parallel, producing from 10 pg to 100 ?g of purified protein from each sample. The platform is based on disposable cartridge devices with 5 ?L packed bed of resin. The cartridges may be operated as spin columns or run on a modified 96-channel liquid handler with ultra-low dead volume syringes that directly connect to the cartridges, providing very precisely controlled positive-displacement flow control. A major application is quantitative purification of target proteins using affinity or physical chromatography. Using large diameter nonporous beads, standard microplate enzyme-linked immunosorbent assay reagents can be used to perform 30-min immunoassays. Enzymatic digestion methods have also been developed on the system for application in glycan profiling. PMID:22093303
Quantitative FRET analysis with the EGFP-mCherry fluorescent protein pair.
Albertazzi, Lorenzo; Arosio, Daniele; Marchetti, Laura; Ricci, Fernanda; Beltram, Fabio
Fluorescence resonance energy transfer (FRET) between fluorescent proteins (FPs) is a powerful tool to investigate protein-protein interaction and even protein modifications in living cells. Here, we analyze the E(0)GFP-mCherry pair and show that it can yield a reproducible quantitative determination of the energy transfer efficiency both in vivo and in vitro. The photophysics of the two proteins is reported and shows good spectral overlap (F÷rster radius R(0) = 51 A), low crosstalk between acceptor and donor channels, and independence of the emission spectra from pH and halide ion concentration. Acceptor photobleaching (APB) and one- and two-photon fluorescence lifetime imaging microscopy (FLIM) are used to quantitatively determine FRET efficiency values. A FRET standard is introduced based on a tandem construct comprising donor and acceptor together with a 20 amino acid long cleavable peptidic linker. Reference values are obtained via enzymatic cleavage of the linker and are used as benchmarks for APB and FLIM data. E(0)GFP-mCherry shows ideal properties for FLIM detection of FRET and yields high accuracy both in vitro and in vivo. Furthermore, the recently introduced phasor approach to FLIM is shown to yield straightforward and accurate two-photon FRET efficiency data even in suboptimal experimental conditions. The consistence of these results with the reference method (both in vitro and in vivo) reveals that this new pair can be used for very effective quantitative FRET imaging. PMID:18764891
Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS.
Sinclair, John; Timms, John F
Blood-borne biomarkers are urgently required for the early detection, accurate diagnosis and prognosis of disease. Additionally, improved methods of profiling serum and plasma proteins for biomarker discovery efforts are needed. Herein, we report a quantitative method based on amino-group labelling of serum proteins (rather than peptides) with isobaric tandem mass tags (TMT) and incorporating immune-based depletion, gel-based and strong anion exchange separation of proteins prior to differential endoproteinase treatment and liquid chromatography tandem mass spectrometry. We report a generally higher level of quantitative coverage of the serum proteome compared to other peptide-based isobaric tagging approaches and show the potential of the method by applying it to a set of unique samples that pre-date the diagnosis of pancreatic cancer. PMID:21397697
A rapid and quantitative coat protein complex II vesicle formation assay using luciferase reporters.
Fromme, J Chris; Kim, Jinoh
The majority of protein export from the endoplasmic reticulum (ER) is facilitated by coat protein complex II (COPII). The COPII proteins deform the ER membrane into vesicles at the ER exit sites. During the vesicle formation step, the COPII proteins load cargo molecules into the vesicles. Formation of COPII vesicles has been reconstituted in vitro in yeast and in mammalian systems. These in vitro COPII vesicle formation assays involve incubation of microsomal membranes and purified COPII proteins with nucleotides. COPII vesicles are separated from the microsomes by differential centrifugation. Interestingly, the efficiency of the COPII vesicle formation with purified recombinant mammalian COPII proteins is lower than that with cytosol, suggesting that an additional cytosolic factor(s) is involved in this process. Indeed, other studies have also implicated additional factors. To facilitate biochemical identification of such regulators, a rapid and quantitative COPII vesicle formation assay is necessary because the current assay is lengthy. To expedite this assay, we generated luciferase reporter constructs. The reporter proteins were packaged into COPII vesicles and yielded quantifiable luminescent signals, resulting in a rapid and quantitative COPII vesicle formation assay. PMID:22244805
A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.
Taipale, Mikko; Tucker, George; Peng, Jian; Krykbaeva, Irina; Lin, Zhen-Yuan; Larsen, Brett; Choi, Hyungwon; Berger, Bonnie; Gingras, Anne-Claude; Lindquist, Susan
Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of cofactors (cochaperones) that regulate their specificity and function. However, how these cochaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown. We combined mass spectrometry and quantitative high-throughput LUMIER assays to systematically characterize the chaperone-cochaperone-client interaction network in human cells. We uncover hundreds of chaperone clients, delineate their participation in specific cochaperone complexes, and establish a surprisingly distinct network of protein-protein interactions for cochaperones. As a salient example of the power of such analysis, we establish that NUDC family cochaperones specifically associate with structurally related but evolutionarily distinct ?-propeller folds. We provide a framework for deciphering the proteostasis network and its regulation in development and disease and expand the use of chaperones as sensors for drug-target engagement. PMID:25036637
[Quantitative determination of the protein content of milk by ultraviolet spectrophotometry. 3. Determination of proteins in preserved milk samples].
Reichardt, W; Sch³ler, E; Sieber, L; Sch³ler, E
It is reported upon the results of the quantitative estimation of protein content from preserved milk by means of ultraviolet spectrophotometry. In addition to the preservation by boric acid, bronopol, copper sulphate, potassium dichromate and ammonium peroxodisulphate storage at temperatures below 0 degrees C and freeze drying were tested. Besides bronopol and copper sulphate especially physical preservation methods proves fit for the protein estimation by measurements of absorbance at 210 nm, 235 and 280 nm or 210 and 220 nm. It is recommended to use solutions and filters of quartz with evaluated absorbance in daily calibrating of the spectrophotometer. PMID:3696199
Identification of selenium-containing proteins in selenium-rich yeast aqueous extract by 2D gel electrophoresis, nanoHPLC-ICP MS and nanoHPLC-ESI MS/MS.
Tastet, Laure; Schauml÷ffel, Dirk; Bouyssiere, Brice; Lobinski, Ryszard
An approach based on the consecutive use of nanoHPLC-ICP collision cell MS and nanoHPLC-electrospray MS was proposed for the analysis of water-soluble selenium-containing proteins in selenium-rich yeast after their separation by 2D gel electrophoresis (GE). An ultrasonic probe was employed for fast protein extraction avoiding sample heating and thus reducing the risk of protein degradation. The efficiency of different extraction steps were critically evaluated by total selenium analysis and size-exclusion chromatography (SEC)-ICP MS. Prior to electrophoresis proteins were purified by acetone precipitation. The protein-containing spots from 2D GE were excised and digested with trypsin. The digests obtained were analyzed by nanoHPLC-ICP MS in order to check for the presence of selenium-containing peptides; this allowed the detection of target proteins for further analyses (two out of five spots). The subsequent analyses of the selected digests by nanoHPLC-ES MS/MS allowed the attribution of amino acid sequences to peaks detected by ICP MS revealing the presence of two selenium-containing proteins: SIP 18 and HSP 12. PMID:18585195
Protein variations associated with in vitro aging of human fibroblasts and quantitative limits on the error catastrophe hypothesis.
Van Keuren, M L; Merril, C R; Goldman, D
Two-dimensional electrophoresis was used to examine protein alterations associated with in vitro cellular aging. Patterns of cellular proteins from early and late passage human fibroblasts of two strains (normal and trisomy 21) were analyzed in silver-stained gels and autoradiograms with computerized microdensitometry. Four proteins were significantly altered in density in both cell strains. In late passage cells, these proteins were from 6 to 66% the density in early passage cells. The error catastrophe hypothesis predicts that random amino acid substitutions accumulate with cellular aging. No new proteins or satellite spots due to such substitutions, however, were detected in late passage cells. An upper bound of 2.5% was set by high resolution densitometry for the fraction of abnormal protein that could be present but undetected by these methods. PMID:6226730
Quantitative multicolor subdiffraction imaging of bacterial protein ultrastructures in 3D
Gahlmann, Andreas; Ptacin, Jerod L.; Grover, Ginni; Quirin, Sean; von Diezmann, Alexander R. S.; Lee, Marissa K.; Backlund, Mikael P.; Shapiro, Lucy; Piestun, Rafael; Moerner, W. E.
We demonstrate quantitative multicolor 3D subdiffraction imaging of the structural arrangement of fluorescent protein fusions in living Caulobacter crescentus bacteria. Given single-molecule localization precisions of 20¢40 nm, a flexible locally-weighted image registration algorithm is critical to accurately combine the super-resolution data with <10 nm error. Simple surface-relief dielectric phase masks implement a double-helix response at two wavelengths to distinguish two different fluorescent labels and to quantitatively and precisely localize them relative to each other in 3D. PMID:23414562
Methods for Peptide and Protein Quantitation by Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry*
Zhang, Haixia; Liu, Qinfeng; Zimmerman, Lisa J.; Ham, Amy-Joan L.; Slebos, Robbert J. C.; Rahman, Jamshedur; Kikuchi, Takefume; Massion, Pierre P.; Carbone, David P.; Billheimer, Dean; Liebler, Daniel C.
Liquid chromatography-multiple reaction monitoring mass spectrometry of peptides using stable isotope dilution (SID) provides a powerful tool for targeted protein quantitation. However, the high cost of labeled peptide standards for SID poses an obstacle to multiple reaction monitoring studies. We compared SID to a labeled reference peptide (LRP) method, which uses a single labeled peptide as a reference standard for all measured peptides, and a label-free (LF) approach, in which quantitation is based on analysis of un-normalized peak areas for detected MRM transitions. We analyzed peptides from the Escherichia coli proteins alkaline phosphatase and ?-galactosidase spiked into lysates from human colon adenocarcinoma RKO cells. We also analyzed liquid chromatography-multiple reaction monitoring mass spectrometry data from a recently published interlaboratory study by the National Cancer Institute Clinical Proteomic Technology Assessment for Cancer network (Addona et al. (2009) Nat. Biotechnol. 27: 633¢641), in which unlabeled and isotopically labeled synthetic peptides or their corresponding proteins were spiked into human plasma. SID displayed the highest correlation coefficients and lowest coefficient of variation in regression analyses of both peptide and protein spike studies. In protein spike experiments, median coefficient of variation values were about 10% for SID and 20¢30% for LRP and LF methods. Power calculations indicated that differences in measurement error between the methods have much less impact on measured protein expression differences than biological variation. All three methods detected significant (p < 0.05) differential expression of three endogenous proteins in a test set of 10 pairs of human lung tumor and control tissues. Further, the LRP and LF methods both detected significant differences (p < 0.05) in levels of seven biomarker candidates between tumors and controls in the same set of lung tissue samples. The data indicate that the LRP and LF methods provide cost-effective alternatives to SID for many quantitative liquid chromatography-multiple reaction monitoring mass spectrometry applications. PMID:21357624
Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy
Gorsic, Lidija K.; Antao, Nirav N.; Wong, Shan S.; Chung, Sophie H.; Gill, Daniel F.; Im, Hae K.; Myers, Jamie L.; White, Kevin P.; Jones, Richard Baker; Dolan, M. Eileen
Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRNA rather than protein levels. Many variants remain without annotation. To address this problem, we measured the steady state abundance of 441 human signaling and transcription factor proteins from 68 Yoruba HapMap lymphoblastoid cell lines to identify novel relationships between inter-individual protein levels, genetic variants, and sensitivity to chemotherapeutic agents. Proteins were measured using micro-western and reverse phase protein arrays from three independent cell line thaws to permit mixed effect modeling of protein biological replicates. We observed enrichment of protein quantitative trait loci (pQTLs) for cellular sensitivity to two commonly used chemotherapeutics: cisplatin and paclitaxel. We functionally validated the target protein of a genome-wide significant trans-pQTL for its relevance in paclitaxel-induced apoptosis. GWAS overlap results of drug-induced apoptosis and cytotoxicity for paclitaxel and cisplatin revealed unique SNPs associated with the pharmacologic traits (at p<0.001). Interestingly, GWAS SNPs from various regions of the genome implicated the same target protein (p<0.0001) that correlated with drug induced cytotoxicity or apoptosis (p?0.05). Two genes were functionally validated for association with drug response using siRNA: SMC1A with cisplatin response and ZNF569 with paclitaxel response. This work allows pharmacogenomic discovery to progress from the transcriptome to the proteome and offers potential for identification of new therapeutic targets. This approach, linking targeted proteomic data to variation in pharmacologic response, can be generalized to other studies evaluating genotype-phenotype relationships and provide insight into chemotherapeutic mechanisms. PMID:24699359
Seasonal liver protein differences in a hibernator revealed by quantitative proteomics using whole animal isotopic labeling
Rose, J. Cameron; Epperson, L. Elaine; Carey, Hannah V.; Martin, Sandra L.
Hibernation is an energy-saving strategy used by diverse species of mammals to survive winter. It is characterized by cycles between multi-day periods of torpor with low body temperature (Tb), and short periods of rapid, spontaneous rewarming. The ability to retain cellular integrity and function throughout torpor and rewarming is a key attribute of hibernation. Livers from winter hibernators are resistant to cellular damage induced by cold storage followed by warm reperfusion. Identifying proteins that differ between the summer-sensitive and winter-protected phenotypic states is one useful approach that may elucidate the molecular mechanisms that underlie this protection. Here we employ a novel quantitative proteomics screening strategy whereby a newly-weaned 13-lined ground squirrel was metabolically labeled by ingesting heavy-isotope substituted (15N) Spirulina. The liver protein extract from this animal provided a common reference for quantitative evaluation of protein differences by its addition to extracts from pooled samples of summer active (SA) or winter entrance (Ent) phase hibernating ground squirrels. We identified 61 significantly different proteins between the two groups and compared them to proteins identified previously in the same samples using 2D gels. Of the 20 proteins common to the two datasets, the direction and magnitude of their differences were perfectly concordant for 18, providing confidence that both sets of altered proteins reflect bona fide differences between the two physiological states. Furthermore, the 41 novel proteins recovered in this study included many new enzymes in pathways identified previously: specifically, additional enzymes belonging to the urea cycle, amino acid and carbohydrate degradation, and lipid biosynthetic pathways were decreased, whereas enzymes involved in ketone body synthesis, fatty acid utilization, protein synthesis and gluconeogenesis were increased in the samples from entrance hibernators compared to summer active animals, providing additional specific evidence for the importance of these pathways in the hibernating phenotype. PMID:21481655
Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics*
Kirkwood, Kathryn J.; Ahmad, Yasmeen; Larance, Mark; Lamond, Angus I.
Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community. PMID:24043423
Quantitative screening of advanced glycation endproducts in cellular and extracellular proteins by tandem mass spectrometry.
Thornalley, Paul J; Battah, Sinan; Ahmed, Naila; Karachalias, Nikolaos; Agalou, Stamatina; Babaei-Jadidi, Roya; Dawnay, Anne
Glycation of proteins forms fructosamines and advanced glycation endproducts. Glycation adducts may be risk markers and risk factors of disease development. We measured the concentrations of the early glycation adduct fructosyl-lysine and 12 advanced glycation endproducts by liquid chromatography with tandem mass spectrometric detection. Underivatized analytes were detected free in physiological fluids and in enzymic hydrolysates of cellular and extracellular proteins. Hydroimidazolones were the most important glycation biomarkers quantitatively; monolysyl adducts (N(epsilon)-carboxymethyl-lysine and N(epsilon)-1-carboxyethyl-lysine) were found in moderate amounts, and bis(lysyl)imidazolium cross-links and pentosidine in lowest amounts. Quantitative screening showed high levels of advanced glycation endproducts in cellular protein and moderate levels in protein of blood plasma. Glycation adduct accumulation in tissues depended on the particular adduct and tissue type. Low levels of free advanced glycation endproducts were found in blood plasma and levels were 10-100-fold higher in urine. Advanced glycation endproduct residues were increased in blood plasma and at sites of vascular complications development in experimental diabetes; renal glomeruli, retina and peripheral nerve. In clinical uraemia, the concentrations of plasma protein advanced glycation endproduct residues increased 1-7-fold and free adduct concentrations increased up to 50-fold. Comprehensive screening of glycation adducts revealed the relative and quantitative importance of alpha-oxoaldehyde-derived advanced glycation endproducts in physiological modification of proteins-particularly hydroimidazolones, the efficient renal clearance of free adducts, and the marked increases of glycation adducts in diabetes and uraemia-particularly free advanced glycation endproducts in uraemia. Increased levels of these advanced glycation endproducts were associated with vascular complications in diabetes and uraemia. PMID:12885296
Enzyme-Linked Immunosorbent Assay for Quantitative Detection of Bacillus thuringiensis Crystal Protein
Smith, Robert A.; Ulrich, J. Terry
Accurate measurement of the toxic protein crystal produced during deep-tank fermentation of Bacillus thuringiensis is critical for optimum process yield. The currently accepted method is a bioassay that requires more time to generate data than to complete the fermentation itself. A noncompetitive enzyme-linked immunosorbent assay has been developed with purified B. thuringiensis crystals to generate rabbit antiserum. This technique gives a quantitative crystal protein value with a colorimetric endpoint for either liquids or powders within 4 h of sampling. Reproducibility of this enzyme-linked immunosorbent assay satisfies criteria for use in a commercial process. Images PMID:16346207
Quantitative variability of 342 plasma proteins in a human twin population
Liu, Yansheng; Buil, Alfonso; Collins, Ben C; Gillet, Ludovic CJ; Blum, Lorenz C; Cheng, Lin-Yang; Vitek, Olga; Mouritsen, Jeppe; Lachance, Genevieve; Spector, Tim D; Dermitzakis, Emmanouil T; Aebersold, Ruedi
The degree and the origins of quantitative variability of most human plasma proteins are largely unknown. Because the twin study design provides a natural opportunity to estimate the relative contribution of heritability and environment to different traits in human population, we applied here the highly accurate and reproducible SWATH mass spectrometry technique to quantify 1,904 peptides defining 342 unique plasma proteins in 232 plasma samples collected longitudinally from pairs of monozygotic and dizygotic twins at intervals of 2¢7Āyears, and proportioned the observed total quantitative variability to its root causes, genes, and environmental and longitudinal factors. The data indicate that different proteins show vastly different patterns of abundance variability among humans and that genetic control and longitudinal variation affect protein levels and biological processes to different degrees. The data further strongly suggest that the plasma concentrations of clinical biomarkers need to be calibrated against genetic and temporal factors. Moreover, we identified 13 cis-SNPs significantly influencing the level of specific plasma proteins. These results therefore have immediate implications for the effective design of blood-based biomarker studies. PMID:25652787
Quantitative determination of surface concentration of protein with surface plasmon resonance using radiolabeled proteins
A methodology to correlate the absolute surface concentration of protein to the surface plasmon resonance (SPR) response is described. The thickness and the optical constants for each layer on the sensor chip used were determined with different optical techniques. In a flow injection system, the steady- state SPR response was correlated to the absolute amount of radiolabeled protein adsorbed by
Monoclonal Antibody-Based Quantitation of Poly(ethylene glycol)-Derivatized Proteins, Liposomes, and Nanoparticles
Tian-Lu Cheng; Chiu-Min Cheng; Bing-Mae Chen; Der-An Tsao; Kuo-Hsiang Chuang; Sheng-Wen Hsiao; Yi-Hung Lin; Steve R. Roffler
Covalent attachment of poly(ethylene glycol) (PEG) molecules to drugs, proteins, and liposomes is a proven technology for improving their bioavailability, safety, and efficacy. Qualitative and quantitative analysis of PEG-derivatized molecules is important for both drug development and clinical applications. We previously reported the development of a monoclonal IgM antibody (AGP3) to PEG. We now describe a new IgG1 monoclonal antibody
Gene networks in hexaploid wheat: interacting quantitative trait loci for grain protein content
Pawan Kulwal; Neeraj Kumar; Ajay Kumar; Raj Kumar Gupta; Harindra Singh Balyan; Pushpendra Kumar Gupta
In hexaploid wheat, single-locus and two-locus quantitative trait loci (QTL) analyses for grain protein content (GPC) were conducted using two different mapping populations (PI and PII). Main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL ū environment interactions (QE, QQE) were detected using two-locus analyses in both the populations. Only a few QTLs were common in both the analyses, and
Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis.
Haebel, S; Jensen, C; Andersen, S O; Roepstorff, P
Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15-kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) time-course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two-dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants. PMID:7795523
Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution*S
Keshishian, Hasmik; Addona, Terri; Burgess, Michael; Kuhn, Eric; Carr, Steven A.
Biomarker discovery produces lists of candidate markers whose presence and level must be subsequently verified in serum or plasma. Verification represents a paradigm shift from unbiased discovery approaches to targeted, hypothesis-driven methods and relies upon specific, quantitative assays optimized for the selective detection of target proteins. Many protein biomarkers of clinical currency are present at or below the nanogram/milliliter range in plasma and have been inaccessible to date by MS-based methods. Using multiple reaction monitoring coupled with stable isotope dilution mass spectrometry, we describe here the development of quantitative, multiplexed assays for six proteins in plasma that achieve limits of quantitation in the 1¢10 ng/ml range with percent coefficients of variation from 3 to 15% without immunoaffinity enrichment of either proteins or peptides. Sample processing methods with sufficient throughput, recovery, and reproducibility to enable robust detection and quantitation of candidate biomarker proteins were developed and optimized by addition of exogenous proteins to immunoaffinity depleted plasma from a healthy donor. Quantitative multiple reaction monitoring assays were designed and optimized for signature peptides derived from the test proteins. Based upon calibration curves using known concentrations of spiked protein in plasma, we determined that each target protein had at least one signature peptide with a limit of quantitation in the 1¢10 ng/ml range and linearity typically over 2 orders of magnitude in the measurement range of interest. Limits of detection were frequently in the high picogram/milliliter range. These levels of assay performance represent up to a 1000-fold improvement compared with direct analysis of proteins in plasma by MS and were achieved by simple, robust sample processing involving abundant protein depletion and minimal fractionation by strong cation exchange chromatography at the peptide level prior to LC-multiple reaction monitoring/MS. The methods presented here provide a solid basis for developing quantitative MS-based assays of low level proteins in blood. PMID:17939991
Improved Protein Arrays for Quantitative Systems Analysis of the Dynamics of Signaling Pathway Interactions
Astronauts and workers in nuclear plants who repeatedly exposed to low doses of ionizing radiation (IR, <10 cGy) are likely to incur specific changes in signal transduction and gene expression in various tissues of their body. Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. An ultimate goal of systems biology is to develop dynamic mathematical models of interacting biological systems capable of simulating living systems in a computer. This Glue Grant is to complement Dr. BoothmanÆs existing DOE grant (No. DE-FG02-06ER64186) entitled ōThe IGF1/IGF-1R-MAPK-Secretory Clusterin (sCLU) Pathway: Mediator of a Low Dose IR-Inducible Bystander Effectö to develop sensitive and quantitative proteomic technology that suitable for low dose radiobiology researches. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. The signals are amplified by a confocal laser Quantum dot scanner resulting in ~1000-fold more sensitivity than traditional Western blots and show the good linearity that is impossible for the signals of HRP-amplification. Therefore this improved protein array technology is suitable to detect weak responses of low dose radiation. Software is developed to facilitate the quantitative readout of signaling network activities. Kinetics of EGFRvIII mutant signaling was analyzed to quantify cross-talks between EGFR and other signaling pathways.
Quantitative evaluation of interaction force between functional groups in protein and polymer brush surfaces.
Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko
To understand interactions between polymer surfaces and different functional groups in proteins, interaction forces were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Various polymer brush surfaces were systematically prepared by surface-initiated atom transfer radical polymerization as well-defined model surfaces to understand protein adsorption behavior. The polymer brush layers consisted of phosphorylcholine groups (zwitterionic/hydrophilic), trimethylammonium groups (cationic/hydrophilic), sulfonate groups (anionic/hydrophilic), hydroxyl groups (nonionic/hydrophilic), and n-butyl groups (nonionic/hydrophobic) in their side chains. The interaction forces between these polymer brush surfaces and different functional groups (carboxyl groups, amino groups, and methyl groups, which are typical functional groups existing in proteins) were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Furthermore, the amount of adsorbed protein on the polymer brush surfaces was quantified by surface plasmon resonance using albumin with a negative net charge and lysozyme with a positive net charge under physiological conditions. The amount of proteins adsorbed on the polymer brush surfaces corresponded to the interaction forces generated between the functional groups on the cantilever and the polymer brush surfaces. The weakest interaction force and least amount of protein adsorbed were observed in the case of the polymer brush surface with phosphorylcholine groups in the side chain. On the other hand, positive and negative surfaces generated strong forces against the oppositely charged functional groups. In addition, they showed significant adsorption with albumin and lysozyme, respectively. These results indicated that the interaction force at the functional group level might be a suitable parameter for understanding protein adsorption. PMID:24564418
Automatic multiple applicator electrophoresis
NASA Technical Reports Server (NTRS)
Grunbaum, B. W.
Easy-to-use, economical device permits electrophoresis on all known supporting media. System includes automatic multiple-sample applicator, sample holder, and electrophoresis apparatus. System has potential applicability to fields of taxonomy, immunology, and genetics. Apparatus is also used for electrofocusing.
NASA Technical Reports Server (NTRS)
Rhodes, P. H.; Snyder, R. S.
Several proposed modifications are expected to improve performance of a continous-flow electrophoresis cell. Changes would allow better control of buffer flow and would increase resolution by suppressing thermal gradients. Improved electrophoresis device would have high resolution and be easy to operate. Improvements would allow better flow control and heat dissipation.
Quantitative analysis of cohesin complex stoichiometry and SMC3 modification-dependent protein interactions
Ding, Chen; Li, Yehua; Kim, Beom-Jun; Malovannaya, Anna; Jung, Sung Yun; Wang, Yi; Qin, Jun
Cohesin is a protein complex that plays an essential role in pairing replicated sister chromatids during cell division 1-3. The vertebrate cohesin complex consists of four core components including structure maintenance of chromosomes proteins SMC1 and SMC3, RAD21 and SA2/SA1. Extensive research suggests that cohesin traps the sister chromatids by a V-shaped SMC1/SMC3 heterodimer bound to the RAD21 protein 4 that closes the ring. Accordingly, the single æringÆ model proposes that two sister chromatids are trapped in a single ring that is composed of one molecule each of the 4 subunits. However, evidence also exists for alternative models. The hand-cuff model suggests that each sister chromatid is trapped individually by two rings that are joined through the shared SA1/SA2 subunit. We report here the determination of cohesin subunit stoichiometry of endogenous cohesin complex by quantitative mass spectrometry. Using qConCAT-based isotope labeling, we show that the cohesin core complex contains equimolar of the 4 core components, suggesting that each cohesin ring is closed by one SA1/SA2 molecule. Furthermore, we applied this strategy to quantify post-translational modification-dependent cohesin interactions. We demonstrate that quantitative mass spectrometry is a powerful tool for measuring stoichiometry of endogenous protein core complex. PMID:21699228
Quantitative reduction of the TCR adapter protein SLP-76 unbalances immunity and immune regulation.
Siggs, Owen M; Miosge, Lisa A; Daley, Stephen R; Asquith, Kelly; Foster, Paul S; Liston, Adrian; Goodnow, Christopher C
Gene variants that disrupt TCR signaling can cause severe immune deficiency, yet less disruptive variants are sometimes associated with immune pathology. Null mutations of the gene encoding the scaffold protein Src homology 2 domain-containing leukocyte protein of 76 kDa (SLP-76), for example, cause an arrest of T cell positive selection, whereas a synthetic membrane-targeted allele allows limited positive selection but is associated with proinflammatory cytokine production and autoantibodies. Whether these and other enigmatic outcomes are due to a biochemical uncoupling of tolerogenic signaling, or simply a quantitative reduction of protein activity, remains to be determined. In this study we describe a splice variant of Lcp2 that reduced the amount of wild-type SLP-76 protein by ~90%, disrupting immunogenic and tolerogenic pathways to different degrees. Mutant mice produced excessive amounts of proinflammatory cytokines, autoantibodies, and IgE, revealing that simple quantitative reductions of SLP-76 were sufficient to trigger immune dysregulation. This allele reveals a dose-sensitive threshold for SLP-76 in the balance of immunity and immune dysregulation, a common disturbance of atypical clinical immune deficiencies. PMID:25662996
Western Blotting using Capillary Electrophoresis
Anderson, Gwendolyn J.; Cipolla, Cynthia; Kennedy, Robert T.
A microscale Western blotting system based on separating sodium-dodecyl sulfate protein complexes by capillary gel electrophoresis followed by deposition onto a blotting membrane for immunoassay is described. In the system, the separation capillary is grounded through a sheath capillary to a mobile X-Y translation stage which moves a blotting membrane past the capillary outlet for protein deposition. The blotting membrane is moistened with a methanol and buffer mixture to facilitate protein adsorption. Although discrete protein zones could be detected, bands were broadened by ~1.7-fold by transfer to membrane. A complete Western blot for lysozyme was completed in about one hour with 50 pg mass detection limit from low microgram per milliliter samples. These results demonstrate substantial reduction in time requirements and improvement in mass sensitivity compared to conventional Western blots. Western blotting using capillary electrophoresis shows promise to analyze low volume samples with reduced reagents and time, while retaining the information content of a typical Western blot. PMID:21265514
Quantitative changes in sets of proteins as markers of biological response
Giometti, C.S.; Taylor, J.; Gemmell, M.A.; Tollaksen, S.L. (Argonne National Lab., IL (USA)); Lalwani, N.D.; Reddy, J.K. (Northwestern Univ., Chicago, IL (USA))
Exposure to either physical or chemical insults triggers a cascade of bio-chemical events within the target cell. This response requires adjustment within the protein population of the cell, some proteins becoming more abundant (those involved in the cellular response), others less abundant (those not required or counterproductive to the response). Thus, quantitative changes in the global protein population of an exposed biological system may well serve as an indicator of exposure, provided the alterations observed are selective and dose-dependent. In this paper we present results from a study in which liver protein changes induced by exposure of mice to chemicals known to cause peroxisome proliferation and subsequent hepatocellular carcinoma where monitored. Clofibrate, and its chemical analog ciprofibrate, are hypolipidemic drugs. Di-(ethylhexyl)phthalate (DEHP) is a plasticizer used widely in disposable containers for blood products. WY-14643 is a chemical shown to cause hypolipidemic and peroxisome proliferation, similar to clofibrate, ciprofibrate and DEHP, but structurally different from these three chemicals. Thus, two of the four chemicals are structurally similar while the remaining two are very distinct, although all four chemicals cause the same gross biological response. Our results show that although common protein effects are observed in mice exposed to these chemicals, each chemical also causes specific alterations in selective subsets of proteins that could serve as markers of a particular exposure. 13 refs., 4 figs., 1 tab.
New insights into the brain protein metabolism of Gastrodia elata-treated rats by quantitative proteomics.
Manavalan, Arulmani; Feng, Lin; Sze, Siu Kwan; Hu, Jiang-Miao; Heese, Klaus
Gastrodia elata (tianma) is a traditional Chinese herbal medicine (TCM) often used for the treatment of cerebrovascular diseases. In this study, we investigated the effects of tianma on the brain protein metabolism by quantitative proteomics to gain evidence for a direct relationship between tianma treatment and brain functions. One-year-old rats were treated with tianma (~2.5 g/kg/day) for 3months and the brain tissue proteome was analyzed by using the iTRAQ (isobaric tag for relative and absolute quantification) technology. According to our results, the long-term treatment with tianma could modulate the brain protein metabolism at the proteome level by down-regulating the expressions of various proteins, such as Gnao1 and Dctn2, which are related to neuronal growth cone control and synaptic activities. In addition, tianma treatment also induced the up-regulation of molecular chaperons and proteins related to the misfolded protein response, like Anxa5, and also other proteins involved in Huntington's disease (HD) (e.g. Pacsin1 and Arf3). Concluding, tianma could eventually contribute to activities related to synaptic plasticity and neuro-restorative processes and thus might be a novel candidate agent for the treatment of neurodegenerative diseases by regulating the brain proteome. PMID:22402058
Quantitative proteomics reveals novel insights into isoniazid susceptibility in mycobacteria mediated by a universal stress protein.
Hu, Xinling; Li, Xiaojing; Huang, Lige; Chan, John; Chen, Yuling; Deng, Haiteng; Mi, Kaixia
Tuberculosis (TB) is caused by the ancient pathogen, Mycobacterium tuberculosis, and is one of the most serious infectious diseases in the world. Isoniazid (INH) is an important first-line drug for the treatment of active and latent TB. INH resistance is an increasing problem in the treatment of TB. Phenotypic resistance to INH, however, is poorly understood. In this study, we constructed a strain of Mycobacterium bovis BCG that overexpresses the latency-related universal stress protein (USP), BCG_2013, and designated this strain BCG-2013. BCG_2013 overexpression increased susceptibility to INH compared with that of the wild-type strain, BCG-pMV261. Quantitative proteomic analysis revealed that BCG_2013 overexpression resulted in the upregulation of 50 proteins and the downregulation of 26 proteins among the 1500 proteins identified. Upregulation of catalase-peroxidase KatG expression in BCG-2013 was observed and confirmed by qPCR, whereas expression of other INH resistance-related proteins did not change. In addition, differential expression of the mycobacterial persistence regulator MprA and its regulatory proteins was observed. BCG_2013 and katG mRNA levels increased in a Wayne dormancy model, whereas MprA mRNA levels decreased. Taken together, our results suggest that the increase in KatG levels induced by increased BCG_2013 levels underlies the phenotypic susceptibility of mycobacteria to INH. PMID:25664397
Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer
Goto, Rieko; Nakamura, Yasushi; Takami, Tomonori; Sanke, Tokio; Tozuka, Zenzaburo
The purpose of this study was to develop quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods for the analysis of proteins involved in metastasis of breast cancer for diagnosis and determining disease prognosis, as well as to further our understand of metastatic mechanisms. We have previously demonstrated that the protein type XIV collagen may be specifically expressed in metastatic tissues by two dimensional LC-MS/MS. In this study, we developed quantitative LC-MS/MS methods for type XIV collagen. Type XIV collagen was quantified by analyzing 2 peptides generated by digesting type XIV collagen using stable isotope-labeled peptides. The individual concentrations were equivalent between 2 different peptides of type XIV collagen by evaluation of imprecise transitions and using the best transition for the peptide concentration. The results indicated that type XIV collagen is highly expressed in metastatic tissues of patients with massive lymph node involvement compared to non-metastatic tissues. These findings were validated by quantitative real-time RT-PCR. Further studies on type XIV collagen are desired to verify its role as a prognostic factor and diagnosis marker for metastasis. PMID:26176947
Quantitative proteomics by amino acid labeling identifies novel NHR-49 regulated proteins in C. elegans
Fredens, Julius; Fµrgeman, Nils J.
Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology to quantitatively examine metabolic and signaling pathways in yeast, fruit flies, plants, cell cultures and mice. However, only metabolic labeling using 15N has been applied to examine such events in the nematode Caenorhabditis elegans. We have recently shown that C. elegans can be completely labeled with heavy-labeled lysine by feeding worms on prelabeled lysine auxotroph Escherichia coli for just one generation. We applied this methodology to examine the organismal response to functional loss or RNAi mediated knock down of the transcription factor NHR-49, and found numerous proteins involved in lipid metabolism to be downregulated, which is consistent with its previously proposed function as a transcriptional regulator of fatty acid metabolism. The combined use of quantitative proteomics and selective gene knockdown by RNAi provides a powerful tool with broad implications for C. elegans biology. PMID:24058826
iQuantitator: A tool for protein expression inference using iTRAQ
Schwacke, John H; Hill, Elizabeth G; Krug, Edward L; Comte-Walters, Susana; Schey, Kevin L
Background Isobaric Tags for Relative and Absolute Quantitation (iTRAQÖ) [Applied Biosystems] have seen increased application in differential protein expression analysis. To facilitate the growing need to analyze iTRAQ data, especially for cases involving multiple iTRAQ experiments, we have developed a modeling approach, statistical methods, and tools for estimating the relative changes in protein expression under various treatments and experimental conditions. Results This modeling approach provides a unified analysis of data from multiple iTRAQ experiments and links the observed quantity (reporter ion peak area) to the experiment design and the calculated quantity of interest (treatment-dependent protein and peptide fold change) through an additive model under log transformation. Others have demonstrated, through a case study, this modeling approach and noted the computational challenges of parameter inference in the unbalanced data set typical of multiple iTRAQ experiments. Here we present the development of an inference approach, based on hierarchical regression with batching of regression coefficients and Markov Chain Monte Carlo (MCMC) methods that overcomes some of these challenges. In addition to our discussion of the underlying method, we also present our implementation of the software, simulation results, experimental results, and sample output from the resulting analysis report. Conclusion iQuantitator's process-based modeling approach overcomes limitations in current methods and allows for application in a variety of experimental designs. Additionally, hypertext-linked documents produced by the tool aid in the interpretation and exploration of results. PMID:19835628
Quantitative Liver-Specific Protein Fingerprint in Blood: A Signature for Hepatotoxicity
Hu, Zhiyuan; Lausted, Christopher; Yoo, Hyuntae; Yan, Xiaowei; Brightman, Amy; Chen, Jiankui; Wang, Weizhi; Bu, Xiangli; Hood, Leroy
We discuss here a new approach to detecting hepatotoxicity by employing concentration changes of liver-specific blood proteins during disease progression. These proteins are capable of assessing the behaviors of their cognate liver biological networks for toxicity or disease perturbations. Blood biomarkers are highly desirable diagnostics as blood is easily accessible and baths virtually all organs. Fifteen liver-specific blood proteins were identified as markers of acetaminophen (APAP)-induced hepatotoxicity using three proteomic technologies: label-free antibody microarrays, quantitative immunoblotting, and targeted iTRAQ mass spectrometry. Liver-specific blood proteins produced a toxicity signature of eleven elevated and four attenuated blood protein levels. These blood protein perturbations begin to provide a systems view of key mechanistic features of APAP-induced liver injury relating to glutathione and S-adenosyl-L-methionine (SAMe) depletion, mitochondrial dysfunction, and liver responses to the stress. Two markers, elevated membrane-bound catechol-O-methyltransferase (MB-COMT) and attenuated retinol binding protein 4 (RBP4), report hepatic injury significantly earlier than the current gold standard liver biomarker, alanine transaminase (ALT). These biomarkers were perturbed prior to onset of irreversible liver injury. Ideal markers should be applicable for both rodent model studies and human clinical trials. Five of these mouse liver-specific blood markers had human orthologs that were also found to be responsive to human hepatotoxicity. This panel of liver-specific proteins has the potential to effectively identify the early toxicity onset, the nature and extent of liver injury and report on some of the APAP-perturbed liver networks. PMID:24465277
Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity.
Hu, Zhiyuan; Lausted, Christopher; Yoo, Hyuntae; Yan, Xiaowei; Brightman, Amy; Chen, Jiankui; Wang, Weizhi; Bu, Xiangli; Hood, Leroy
We discuss here a new approach to detecting hepatotoxicity by employing concentration changes of liver-specific blood proteins during disease progression. These proteins are capable of assessing the behaviors of their cognate liver biological networks for toxicity or disease perturbations. Blood biomarkers are highly desirable diagnostics as blood is easily accessible and baths virtually all organs. Fifteen liver-specific blood proteins were identified as markers of acetaminophen (APAP)-induced hepatotoxicity using three proteomic technologies: label-free antibody microarrays, quantitative immunoblotting, and targeted iTRAQ mass spectrometry. Liver-specific blood proteins produced a toxicity signature of eleven elevated and four attenuated blood protein levels. These blood protein perturbations begin to provide a systems view of key mechanistic features of APAP-induced liver injury relating to glutathione and S-adenosyl-L-methionine (SAMe) depletion, mitochondrial dysfunction, and liver responses to the stress. Two markers, elevated membrane-bound catechol-O-methyltransferase (MB-COMT) and attenuated retinol binding protein 4 (RBP4), report hepatic injury significantly earlier than the current gold standard liver biomarker, alanine transaminase (ALT). These biomarkers were perturbed prior to onset of irreversible liver injury. Ideal markers should be applicable for both rodent model studies and human clinical trials. Five of these mouse liver-specific blood markers had human orthologs that were also found to be responsive to human hepatotoxicity. This panel of liver-specific proteins has the potential to effectively identify the early toxicity onset, the nature and extent of liver injury and report on some of the APAP-perturbed liver networks. PMID:24465277
Quantitative analysis of nucleotide modulation of DNA binding by DnaC protein of Escherichia coli.
Biswas, Subhasis B; Flowers, Stephen; Biswas-Fiss, Esther E
In this study, we have presented the first report of Escherichia coli DnaC protein binding to ssDNA (single stranded DNA) in an apparent hexameric form. DnaC protein transfers DnaB helicase onto a nascent chromosomal DNA replication fork at oriC, the origin of E. coli DNA replication. In eukaryotes, Cdc6 protein may play a similar role in the DNA helicase loading in the replication fork during replication initiation at the origin. We have analysed the DNA-binding properties of DnaC protein and a quantitative analysis of the nucleotide regulation of DnaC-DNA and DnaC-DnaB interactions using fluorescence anisotropy and affinity sensor analysis. DnaC protein bound to ssDNA with low to moderate affinity and the affinity was strictly modulated by nucleotides. DnaC bound ssDNA in the complete absence of nucleotides. The DNA-binding affinity was significantly increased in the presence of ATP, but not ATP[S]. In the presence of ADP, the binding affinity decreased approximately fifty-fold. Both anisotropy and biosensor analyses demonstrated that with DnaC protein, ATP facilitated ssDNA binding, whereas ADP facilitated its dissociation from ssDNA, which is a characteristic of an ATP/ADP switch. Both ssDNA and nucleotides modulate DnaB6*DnaC6 complex formation, which has significant implications in DnaC protein function. Based on the thermodynamic data provided in this study, we have proposed a mechanism of DnaB loading on to ssDNA by DnaC protein. PMID:14715083
Quantitative analysis of alachlor protein adducts by gas chromatography-mass spectrometry.
Lambert, G R; Padgett, W T; George, M H; Kitchin, K T; Nesnow, S
This study examined the potential use of hemoglobin (Hb)- and serum-protein adducts of alachlor as potential biomarkers of alachlor exposure, a genotoxic and carcinogenic herbicide. The method developed was based on the observation that cleavage of S-cysteinyl alachlor-protein adducts by methanesulfonic acid gave the rearrangement product 3-(2',6'-diethylphenyl)-1, 3-thiazolidine-4-one (TZO). The structure of TZO was confirmed by mass spectroscopy, NMR spectroscopy, and independent synthesis. In the assay, treatment of alachlor-cysteinyl protein adducts by methanesulfonic acid was followed by extraction and analysis. TZO was detected and quantitated by electron-impact GC/MS in the single ion-monitoring mode. [ring-13C6]Alachlor-N-acetylcysteine was added as an internal standard prior to treatment and was converted to [ring-13C6]TZO, allowing response factors to be used to quantitate TZO concentrations. Incubations of alachlor (0-1000 microM) with human albumin and bovine serum albumin (BSA) resulted in linear adduct formation with both proteins. Maximal adduction levels of 613-1130 pmol alachlor-albumin adducts/mg protein were observed, with BSA binding close to twice that of human albumin. A linear concentration response of alachlor-Hb adducts was observed when whole blood from female CD rats was incubated with alachlor in vitro at concentrations up to 300 microM. Maximal binding was 1860 pmol alachlor-Hb adducts/mg globin. Male CD rats treated with alachlor at 150 mg/kg body wt/day ip for 0, 1, 2, and 3 days were sacrificed 4 days after final dosing. A maximal binding of 2250 pmol alachlor-Hb adducts/mg globin was observed. This assay provides a new approach for biomonitoring alachlor levels in experimental animals and has the potential for use in humans. PMID:10075819
Quantitative mass spectrometry measurements reveal stoichiometry of principal postsynaptic density proteins.
Lowenthal, Mark S; Markey, Sanford P; Dosemeci, Ayse
Quantitative studies are presented of postsynaptic density (PSD) fractions from rat cerebral cortex with the ultimate goal of defining the average copy numbers of proteins in the PSD complex. Highly specific and selective isotope dilution mass spectrometry assays were developed using isotopically labeled polypeptide concatemer internal standards. Interpretation of PSD protein stoichiometry was achieved as a molar ratio with respect to PSD-95 (SAP-90, DLG4), and subsequently, copy numbers were estimated using a consensus literature value for PSD-95. Average copy numbers for several proteins at the PSD were estimated for the first time, including those for AIDA-1, BRAGs, and densin. Major findings include evidence for the high copy number of AIDA-1 in the PSD (144 ▒ 30)-equivalent to that of the total GKAP family of proteins (150 ▒ 27)-suggesting that AIDA-1 is an element of the PSD scaffold. The average copy numbers for NMDA receptor sub-units were estimated to be 66 ▒ 18, 27 ▒ 9, and 45 ▒ 15, respectively, for GluN1, GluN2A, and GluN2B, yielding a total of 34 ▒ 10 NMDA channels. Estimated average copy numbers for AMPA channels and their auxiliary sub-units TARPs were 68 ▒ 36 and 144 ▒ 38, respectively, with a stoichiometry of ?1:2, supporting the assertion that most AMPA receptors anchor to the PSD via TARP sub-units. This robust, quantitative analysis of PSD proteins improves upon and extends the list of major PSD components with assigned average copy numbers in the ongoing effort to unravel the complex molecular architecture of the PSD. PMID:25874902
In-gel screening of phosphorus and copper, zinc and iron in proteins of yeast mitochondria by LA-ICP-MS and identification of phosphorylated protein structures by MALDI-FT-ICR-MS after separation with two-dimensional gel electrophoresis
J. Sabine Becker; Miroslav Zoriy; Udo Krause-Buchholz; J. Susanne Becker; Carola Pickhardt; Michael Przybylski; Gerhard Rodelb
A new screening technique using two-dimensional gels was developed in order to rapidly identify various elements in well-separated protein spots. Yeast mitochondrial proteins were separated using two-dimensional gel electrophoresis (blue native\\/SDS 2D-PAGE) and marked by silver staining. The 2D gels were systematically analyzed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) using a double-focusing sector field instrument. From more
A comparison of extracted proteins of isolates of Dermatophilus congolensis by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and western blotting
A. A Makinde; C. L Gyles
Antigenic diversity within a collection of 18 isolates of Dermatophilus congolensis from different Continents was examined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and by Western blotting with sera from cattle with clinical dermatophilosis using whole cell extracts obtained by three methods and one extract of extracellular products of D. congolensis. One of the methods involving the release of a
Quantitative Correlation Between the Protein Primary Sequences and Secondary Structures in Spider Dragline Silks
Jenkins, Janelle E.; Creager, Melinda S.; Lewis, Randolph V.; Holland, Gregory P.; Yarger, Jeffery L.
Synthetic spider silk holds great potential for use in various applications spanning medical uses to ultra lightweight armor, however producing synthetic fibers with mechanical properties comparable to natural spider silk has eluded the scientific community. Natural dragline spider silks are commonly made from proteins that contain highly repetitive amino acid motifs, adopting an array of secondary structures. Before further advances can be made in the production of synthetic fibers based on spider silk proteins, it is imperative to know the percentage of each amino acid in the protein that forms a specific secondary structure. Linking these percentages to the primary amino acid sequence of the protein will establish a structural foundation for synthetic silk. In this study, Nuclear Magnetic Resonance (NMR) techniques are used to quantify the percentage of Ala, Gly, and Ser that form both ?-sheet and helical secondary structures. The fraction of these three amino acids and their secondary structure are quantitatively correlated to the primary amino acid sequence for the proteins that comprise major and minor ampullate silk from the Nephila clavipes spider providing a blueprint for synthetic spider silks. PMID:20000730
Comparison of 4-plex to 8-plex iTRAQ quantitative measurements of proteins in human plasma samples.
Pottiez, Gwenael; Wiederin, Jayme; Fox, Howard S; Ciborowski, Pawel
Methods for isobaric tagging of peptides, iTRAQ or TMT, are commonly used platforms in mass spectrometry based quantitative proteomics. These two methods are very often used to quantitate proteins in complex samples, e.g., serum/plasma or CSF supporting biomarker discovery studies. The success of these studies depends on multiple factors, including the accuracy of ratios of reporter ions reflecting quantitative changes of proteins. Because reporter ions are generated during peptide fragmentation, the differences of chemical structure of iTRAQ balance groups may have an effect on how efficiently these groups are fragmented and thus how differences in protein expression will be measured. Because 4-plex and 8-plex iTRAQ reagents do have different structures of balanced groups, it has been postulated that indeed differences in protein identification and quantitation exist between these two reagents. In this study we controlled the ratios of tagged samples and compared quantitation of proteins using 4-plex versus 8-plex reagents in the context of a highly complex sample of human plasma using ABSciex 4800 MALDI-TOF/TOF mass spectrometer and ProteinPilot 4.0 software. We observed that 8-plex tagging provides more consistent ratios than 4-plex without compromising protein identification, thus allowing investigation of eight experimental conditions in one analytical experiment. PMID:22594965
Comparison of 4-plex to 8-plex iTRAQ Quantitative Measurements of Proteins in Human Plasma Samples
Methods for isobaric tagging of peptides, iTRAQ or TMT, are commonly used platforms in mass spectrometry based quantitative proteomics. These two methods are very often used to quantitate proteins in complex samples, e.g., serum/plasma or CSF supporting biomarker discovery studies. The success of these studies depends on multiple factors, including the accuracy of ratios of reporter ions reflecting quantitative changes of proteins. Because reporter ions are generated during peptide fragmentation, the differences of chemical structure of iTRAQ balance groups may have an effect on how efficiently these groups are fragmented and thus how differences in protein expression will be measured. Because 4-plex and 8-plex iTRAQ reagents do have different structures of balanced groups, it has been postulated that indeed differences in protein identification and quantitation exist between these two reagents. In this study we controlled the ratios of tagged samples and compared quantitation of proteins using 4-plex versus 8-plex reagents in the context of a highly complex sample of human plasma using ABSciex 4800 MALDI-TOF/TOF mass spectrometer and ProteinPilot 4.0 software. We observed that 8-plex tagging provides more consistent ratios than 4-plex without compromising protein identification, thus allowing investigation of eight experimental conditions in one analytical experiment. PMID:22594965
Investigation of Receptor interacting protein (RIP3)-dependent Protein Phosphorylation by Quantitative Phosphoproteomics*
Wu, Xiurong; Tian, Lili; Li, Jie; Zhang, Yingying; Han, Victor; Li, Yuanyue; Xu, Xiaozheng; Li, Hanjie; Chen, Xi; Chen, Jinan; Jin, Wenhai; Xie, Yongming; Han, Jiahuai; Zhong, Chuan-Qi
Receptor interacting protein 3 (RIP3) is a protein kinase that plays a key role in programmed necrosis. Despite the importance of RIP3-dependent necrosis in many pathological processes, current knowledge on the function of RIP3 is very limited. Here we present the results of a proteome-wide analysis of RIP3-regulated phosphorylation sites using cells from wildtype (RIP3+/+) and RIP3 knockout (RIP3?/?) mice. Because the activation of RIP3 requires stimulation by certain extracellular stimuli such as ligands of death receptors or Toll-like receptors, we compared the phosphorylation sites of lipopolysaccharide (LPS)-treated peritoneal macrophages from RIP3+/+ and RIP3?/? mice and the phosphorylation sites of tumor necrosis factor (TNF)-treated RIP3+/+ and RIP3?/? mouse embryonic fibroblast (MEF) cells. Stable isotope labeling by amino acids in cell culture and spike-in stable isotope labeling by amino acids in cell culture were used in the analyses of the MEFs and macrophages, respectively. Proteomic analyses using stable isotope labeling by amino acids in cell culture coupled with immobilized metal affinity chromatography-hydrophilic interaction liquid chromatography fractionation and nanoLC MS/MS identified 14,057 phosphopeptides in 4306 proteins from the macrophages and 4732 phosphopeptides in 1785 proteins from the MEFs. Analysis of amino acid sequence motifs among the phosphopeptides identified a potential motif of RIP3 phosphorylation. Among the phosphopeptides identified, 73 were found exclusively in RIP3+/+ macrophages, 121 were detected exclusively from RIP3+/+ MEFs, 286 phosphopeptides were induced more in RIP3+/+ macrophages than in RIP3?/? macrophages and 26 phosphopeptides had higher induction in RIP3+/+ MEFs than in RIP3?/? cells. Many of the RIP3 regulated phosphoproteins from the macrophages and MEF cells are functionally associated with the cell cycle; the rest, however, appear to have diverse functions in that a number of metabolism related proteins were phosphorylated in macrophages and development related phosphoproteins were induced in MEFs. The results of our phosphoproteomic analysis suggest that RIP3 might function beyond necrosis and that cell type specific function of RIP3 exists. PMID:22942356
Epithelium percentage estimation facilitates epithelial quantitative protein measurement in tissue specimens
Background The rapid advancement of high-throughput tools for quantitative measurement of proteins has demonstrated the potential for the identification of proteins associated with cancer. However, the quantitative results on cancer tissue specimens are usually confounded by tissue heterogeneity, e.g. regions with cancer usually have significantly higher epithelium content yet lower stromal content. Objective It is therefore necessary to develop a tool to facilitate the interpretation of the results of protein measurements in tissue specimens. Methods Epithelial cell adhesion molecule (EpCAM) and cathepsin L (CTSL) are two epithelial proteins whose expressions in normal and tumorous prostate tissues were confirmed by measuring staining intensity with immunohistochemical staining (IHC). The expressions of these proteins were measured by ELISA in protein extracts from OCT embedded frozen prostate tissues. To eliminate the influence of tissue heterogeneity on epithelial protein quantification measured by ELISA, a color-based segmentation method was developed in-house for estimation of epithelium content using H&E histology slides from the same prostate tissues and the estimated epithelium percentage was used to normalize the ELISA results. The epithelium contents of the same slides were also estimated by a pathologist and used to normalize the ELISA results. The computer based results were compared with the pathologistÆs reading. Results We found that both EpCAM and CTSL levels, measured by ELISA assays itself, were greatly affected by epithelium content in the tissue specimens. Without adjusting for epithelium percentage, both EpCAM and CTSL levels appeared significantly higher in tumor tissues than normal tissues with a p value less than 0.001. However, after normalization by the epithelium percentage, ELISA measurements of both EpCAM and CTSL were in agreement with IHC staining results, showing a significant increase only in EpCAM with no difference in CTSL expression in cancer tissues. These results were obtained with normalization by both the computer estimated and pathologist estimated epithelium percentage. Conclusions Our results show that estimation of tissue epithelium percentage using our color-based segmentation method correlates well with pathologists' estimation of tissue epithelium percentages. The epithelium contents estimated by color-based segmentation may be useful in immuno-based analysis or clinical proteomic analysis of tumor proteins. The codes used for epithelium estimation as well as the micrographs with estimated epithelium content are available online. PMID:24289299
Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein
Huang, Yao-Ming; Nayak, Sasmita; Bystroff, Christopher
Several versions of split green fluorescent protein (GFP) fold and reconstitute fluorescence, as do many circular permutants, but little is known about the dependence of reconstitution on circular permutation. Explored here is the capacity of GFP to fold and reconstitute fluorescence from various truncated circular permutants, herein called ōleave-one-outsö using a quantitative in vivo solubility assay and in vivo reconstitution of fluorescence. Twelve leave-one-out permutants are discussed, one for each of the 12 secondary structure elements. The results expand the outlook for the use of permuted split GFPs as specific and self-reporting gene encoded affinity reagents. PMID:21910151
Electrophoresis operations in space
NASA Technical Reports Server (NTRS)
Richman, D. W.
Application of electrophoresis in space processing is described. Spaceborne experiments in areas such as biological products and FDA approved drugs are discussed. These experiments will be carried on shuttle payloads.
Label-free quantitative mass spectrometry for analysis of protein antigens in a meningococcal group B outer membrane vesicle vaccine.
Dick, Lawrence W; Mehl, John T; Loughney, John W; Mach, Anna; Rustandi, Richard R; Ha, Sha; Zhang, Lan; Przysiecki, Craig T; Dieter, Lance; Hoang, Van M
The development of a multivalent outer membrane vesicle (OMV) vaccine where each strain contributes multiple key protein antigens presents numerous analytical challenges. One major difficulty is the ability to accurately and specifically quantitate each antigen, especially during early development and process optimization when immunoreagents are limited or unavailable. To overcome this problem, quantitative mass spectrometry methods can be used. In place of traditional mass assays such as enzyme-linked immunosorbent assays (ELISAs), quantitative LC-MS/MS using multiple reaction monitoring (MRM) can be used during early-phase process development to measure key protein components in complex vaccines in the absence of specific immunoreagents. Multiplexed, label-free quantitative mass spectrometry methods using protein extraction by either detergent or 2-phase solvent were developed to quantitate levels of several meningococcal serogroup B protein antigens in an OMV vaccine candidate. Precision was demonstrated to be less than 15% RSD for the 2-phase extraction and less than 10% RSD for the detergent extraction method. Accuracy was 70 to 130% for the method using a 2-phase extraction and 90-110% for detergent extraction. The viability of MS-based protein quantification as a vaccine characterization method was demonstrated and advantages over traditional quantitative methods were evaluated. Implementation of these MS-based quantification methods can help to decrease the development time for complex vaccines and can provide orthogonal confirmation of results from existing antigen quantification techniques. PMID:25997113
A quantitative autoradiographic method for the measurement of local rates of brain protein synthesis
Dwyer, B.E.; Donatoni, P.; Wasterlain, C.G.
We have developed a new method for measuring local rates of brain protein synthesis in vivo. It combines the intraperitoneal injection of a large dose of low specific activity amino acid with quantitative autoradiography. This method has several advantages: 1) It is ideally suited for young or small animals or where immobilizing an animal is undesirable. 2 The amino acid injection ''floods'' amino acid pools so that errors in estimating precursor specific activity, which is especially important in pathological conditions, are minimized. 3) The method provides for the use of a radioautographic internal standard in which valine incorporation is measured directly. Internal standards from experimental animals correct for tissue protein content and self-absorption of radiation in tissue sections which could vary under experimental conditions.
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction¢diffusion simulations, that the StrExp function can describe both, binding/barrier¢limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IBÆs). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IBÆs to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport. PMID:23148417
Quantitation of Human Metallothionein Isoforms: A Family of Small, Highly Conserved, Cysteine-rich Proteins*
Mehus, Aaron A.; Muhonen, Wallace W.; Garrett, Scott H.; Somji, Seema; Sens, Donald A.; Shabb, John B.
Human metallothioneins (MTs) are important regulators of metal homeostasis and protectors against oxidative damage. Their altered mRNA expression has been correlated with metal toxicity and a variety of cancers. Current immunodetection methods lack the specificity to distinguish all 12 human isoforms. Each, however, can be distinguished by the mass of its acetylated, cysteine-rich, hydrophilic N-terminal tryptic peptides. These properties were exploited to develop a bottom-up MALDI-TOF/TOF-MS-based method for their simultaneous quantitation. Key features included enrichment of N-terminal acetylated peptides by strong cation exchange chromatography, optimization of C18 reversed-phase chromatography, and control of methionine oxidation. Combinations of nine isoforms were identified in seven cell lines and two tissues. Relative quantitation was accomplished by comparing peak intensities of peptides generated from pooled cytosolic proteins alkylated with 14N- or 15N-iodoacetamide. Absolute quantitation was achieved using 15N-iodoacetamide-labeled synthetic peptides as internal standards. The method was applied to the cadmium induction of MTs in human kidney HK-2 epithelial cells expressing recombinant MT-3. Seven isoforms were detected with abundances spanning almost 2 orders of magnitude and inductions up to 12-fold. The protein-to-mRNA ratio for MT-1E was one-tenth that of other MTs, suggesting isoform-specific differences in protein expression efficiency. Differential expression of MT-1G1 and MT-1G2 suggested tissue- and cell-specific alternative splicing for the MT-1G isoform. Protein expression of MT isoforms was also evaluated in human breast epithelial cancer cell lines. Estrogen-receptor-positive cell lines expressed only MT-2 and MT-1X, whereas estrogen-receptor-negative cell lines additionally expressed MT-1E. The combined expression of MT isoforms was 38-fold greater in estrogen-receptor-negative cell lines than in estrogen-receptor-positive cells. These findings demonstrate that individual human MT isoforms can be accurately quantified in cells and tissues at the protein level, complementing and expanding mRNA measurement as a means for evaluating MTs as potential biomarkers for cancers or heavy metal toxicity. PMID:24493013
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation
Chongle Pan; Guruprasad H Kora; W. Hayes McDonald; David L. Tabb; Nathan C. VerBerkmoes; Gregory B. Hurst; Dale A. Pelletier; Nagiza F. Samatova; Robert L. Hettich
A profile likelihood algorithm is proposed for quantitative shotgun proteomics to infer the abundance ratios of proteins from the abundance ratios of isotopically labeled peptides derived from proteolysis. Previously, we have shown that the estimation variability and bias of peptide abundance ratios can be predicted from their profile signal-to-noise ratios. Given multiple quantified peptides for a protein, the profile likelihood
Real Time Quantitative PCR as a Method to Evaluate Simian Virus 40 Removal During Pharmaceutical Protein Purification
Liming Shi; Lenore A. Norling; Allen S. L. Lau; Sherrie Krejci; Alison J. Laney; Yuan Xu
Continuous cell lines used for pharmaceutical protein manufacturing have the potential to be contaminated by viruses. To ensure the safety of pharmaceutical proteins derived from continuous cell lines, validation of the ability of the manufacturing process to clear potential contaminating viruses is required for product registration. In this paper, a real time quantitative PCR method has been applied to the
Quantitative proteomic analysis of wheat grain proteins reveals differential effects of silencing of omega-5 gliadin genes in transgenic lines
Technology Transfer Automated Retrieval System (TEKTRAN)
Novel wheat lines with altered flour compositions can be used to decipher the roles of specific gluten proteins in flour quality. Grain proteins from transgenic wheat lines in which genes encoding the omega-5 gliadins were silenced by RNA interference (RNAi) were analyzed in detail by quantitative 2...
Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry
Dķbora Bonenfant; Tobias Schmelzle; Estela Jacinto; Josķ L. Crespo; Thierry Mini; Michael N. Hall; Paul Jenoe
Reversible protein phosphorylation plays an important role in many cellular processes. However, a simple and reliable method to measure changes in the extent of phosphorylation is lacking. Here, we present a method to quantitate the changes in phosphorylation occurring in a protein in response to a stimulus. The method consists of three steps: (i) enzymatic digestion in H216O or isotopically
Application of imaging capillary IEF for characterization and quantitative analysis of recombinant protein charge heterogeneity.
Sosic, Zoran; Houde, Damian; Blum, Andy; Carlage, Tyler; Lyubarskaya, Yelena
In this work several aspects of imaging capillary IEF (icIEF) application for charge heterogeneity analysis of recombinant proteins and monoclonal antibodies have been discussed. Advantages of the method as compared with traditional approaches for determination of biomolecule charge heterogeneity, such as gel and IEC, have been demonstrated. Correlation of icIEF-detected protein isoforms with the charge heterogeneity determined by IEC has been shown for a representative recombinant monoclonal antibody. Identification of charged variants collected from IEC has been performed by ESI-MS. Qualification of an icIEF method for use in quality control environment for quantitative analysis of recombinant protein charge heterogeneity and monitoring protein stability has also been discussed. The intermediate precision for determination of pI of main or main acidic species was =0.2% RSD. Relative % peak areas for acidic, main and basic species were reproducible within 1.9, 0.9 and 16.6% RSD, respectively. Based on the assay performance evaluation, icIEF assay has been shown to allow for fast method development, short analysis time and high sample throughput. Some aspects of the method specificity for use as an identity test in biopharmaceutical development have been discussed. PMID:19016565
Quantitative analysis of liver protein expression during hibernation in the golden-mantled ground squirrel.
Epperson, L Elaine; Dahl, Timothy A; Martin, Sandra L
Mammals that enter deep hibernation experience extreme reductions in body temperature and in metabolic, respiratory, and heart rates for several weeks at a time. Survival of these extremes likely entails a highly regulated network of tissue- and time-specific gene expression patterns that remain largely unknown. To date, studies to identify differentially-expressed genes have employed a candidate gene approach or in a few cases broader unbiased screens at the RNA level. Here we use a proteomic approach to compare and identify differentially expressed liver proteins from two seasonal stages in the golden-mantled ground squirrel (summer and entrance into torpor) using two-dimensional gels followed by MS/MS. Eighty-four two-dimensional gel spots were found that quantitatively alter with the hibernation season, 68 of which gave unambiguous identifications based on similarity to sequences in the available mammalian database. Based on what is known of these proteins from prior research, they are involved in a variety of cellular processes including protein turnover, detoxification, purine biosynthesis, gluconeogenesis, lipid metabolism and mobility, ketone body formation, cell structure, and redox balance. A number of the enzymes found to change seasonally are known to be either rate-limiting or first enzymes in a metabolic pathway, indicating key roles in metabolic control. Functional roles are proposed to explain the changes seen in protein levels and their potential influence on the phenotype of hibernation. PMID:15266006
Distinction of thioredoxin transnitrosylation and denitrosylation target proteins by the ICAT quantitative approach.
Wu, Changgong; Parrott, Andrew Myles; Liu, Tong; Jain, Mohit Raja; Yang, Yanfei; Sadoshima, Junichi; Li, Hong
S-Nitrosylation is a reversible PTM for regulating protein function. Thioredoxin-1 (Trx1) catalyzes either transnitrosylation or denitrosylation of specific proteins, depending on the redox status of the cysteines within its conserved oxidoreductase CXXC motif. With a disulfide bond formed between the two catalytic cysteines, Trx1 is not only inactive as a denitrosylase, but it may also be nitrosylated at Cys73 and serve as a transnitrosylating agent. Identification of Trx1-mediated transnitrosylation or denitrosylation targets will contribute to a better understanding of Trx1's function. Previous experimental approaches based on the attenuation of CXXC oxidoreductase activity cannot readily distinguish Trx1 transnitrosylation targets from denitrosylation targets. In this study, we used the ICAT method in conjunction with the biotin switch technique to differentiate Trx1 transnitrosylation targets from denitrosylation target proteins from neuroblastoma cells. We demonstrate that the ICAT approach is effective for quantitative identification of putative Trx1 transnitrosylation and denitrosylation target peptides. From these analyses, we confirmed reports that peroxiredoxin 1 is a Trx1 transnitrosylation, but not a denitrosylation target, and we found several other proteins, including cyclophilin A to be modulated in this manner. Unexpectedly, we found that many nitrosylation sites are reversibly regulated by Trx1, suggesting a more prominent role for Trx1 in regulating S-nitrosylation. PMID:21704743
Distinction of thioredoxin transnitrosylation and denitrosylation target proteins by the ICAT quantitative approach
Wu, Changgong; Parrott, Andrew Myles; Liu, Tong; Jain, Mohit Raja; Yang, Yanfei; Sadoshima, Junichi; Li, Hong
S-Nitrosylation is a reversible PTM for regulating protein function. Thioredoxin-1 (Trx1) catalyzes either transnitrosylation or denitrosylation of specific proteins, depending on the redox status of the cysteines within its conserved oxidoreductase CXXC motif. With a disulfide bond formed between the two catalytic cysteines, Trx1 is not only inactive as a denitrosylase, but it may also be nitrosylated at Cys73 and serve as a transnitrosylating agent. Identification of Trx1-mediated transnitrosylation or denitrosylation targets will contribute to a better understanding of Trx1Æs function. Previous experimental approaches based on the attenuation of CXXC oxidoreductase activity cannot readily distinguish Trx1 transnitrosylation targets from denitrosylation targets. In this study, we used the ICAT method in conjunction with the biotin switch technique to differentiate Trx1 transnitrosylation targets from denitrosylation target proteins from neuroblastoma cells. We demonstrate that the ICAT approach is effective for quantitative identification of putative Trx1 transnitrosylation and denitrosylation target peptides. From these analyses, we confirmed reports that peroxiredoxin 1 is a Trx1 transnitrosylation, but not a denitrosylation target, and we found several other proteins, including cyclophilin A to be modulated in this manner. Unexpectedly, we found that many nitrosylation sites are reversibly regulated by Trx1, suggesting a more prominent role for Trx1 in regulating S-nitrosylation. PMID:21704743
A quantitative comparison of sRNA-based and protein-based gene regulation
Pankaj Mehta; Sidhartha Goyal; Ned S. Wingreen
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in prokaryotes. sRNAs act post-transcriptionally via complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare and contrast sRNAs with conventional transcription factors (TFs) to better understand the advantages of each form of regulation. In particular, we calculate the steady-state behavior, noise properties, frequency-dependent gain (amplification), and dynamical response to large input signals of both forms of regulation. While the mean steady-state behavior of sRNA-regulated proteins exhibits a distinctive tunable threshold-linear behavior, our analysis shows that transcriptional bursting leads to significantly higher intrinsic noise in sRNA-based regulation than in TF-based regulation in a large range of expression levels and limits the ability of sRNAs to perform quantitative signaling. Nonetheless, we find that sRNAs are better than TFs at filtering noise in input signals. Additionally, we find that sRNAs allow cells to respond rapidly to large changes in input signals. These features suggest a niche for sRNAs in allowing cells to transition quickly yet reliably between distinct states. This functional niche is consistent with the widespread appearance of sRNAs in stress-response and quasi-developmental networks in prokaryotes.
Quantitative Characterization of Polymer¢Polymer, Protein¢Protein, and Polymer¢Protein Interaction via Tracer Sedimentation Equilibrium
Fodeke, Adedayo A.; Minton, Allen P.
Quantitative analysis of the composition dependence of the concentration gradient of each species of macromolecule within a solution mixture at sedimentation equilibrium permits the quantitative characterization of self- and heterointeractions between sedimenting solutes. Sedimentation equilibrium experiments were conducted on solutions containing a trace concentration of FITC-labeled BSA in varying concentrations of Ficoll 70 and on solutions containing a trace concentration of FITC-labeled Ficoll 70 in varying concentrations of BSA. The equilibrium gradient of each solute component in each mixture was measured independently. Analysis of the resulting gradients resulted in evaluation of the dependence of the activity coefficient of Ficoll upon the concentrations of Ficoll and BSA at concentrations of up to 100 g/L and the dependence of the activity coefficient of BSA upon the concentrations of Ficoll and BSA at concentrations of up to 100 g/L. The activity coefficients of both species increase significantly with increasing Ficoll and BSA concentration and do not vary with temperature, to within the precision of measurement, over the temperature range of 5¢37 ░C, indicating that the dominant interaction between Ficoll molecules and between BSA and Ficoll molecules is repulsive and probably due to steric volume exclusion. The measured dependences may be accounted for quantitatively by a simple model in which BSA and Ficoll 70 are represented by equivalent rigid particles. PMID:20677765
Single cell-level detection and quantitation of leaky protein expression from any strongly regulated bacterial system.
Arora, Kanika; Mangale, Sachin S; Guptasarma, Purnananda
Extremely low levels of "leaky" expression of genes in bacterial protein expression systems can severely curtail cell viability when expressed proteins are toxic. A general method for sensitive detection of such expression is lacking. Here, we present a method based on microscopic visualization of a fluorescent "reporter" protein (RFP-HU-A) constructed by fusing red fluorescent protein (RFP) to the N-terminus of a nucleoid-associated, histone-like DNA-binding protein, HU-A. Localization of RFP-HU-A within nucleoids facilitates detection, quantitation, and characterization of leaky expression at the single-cell level. PMID:26079706
Characterization of polyanionprotein complexes by frontal analysis continuous capillary electrophoresis and small angle
Dubin, Paul D.
electrophoresis and small angle neutron scattering: Effect of polyanion flexibility Toshiaki Hattori was measured by frontal analysis continuous capillary electrophoresis at pH values above the isoelectric point electrophoresis; Persistence length; Complex formation The elucidation of the interaction between proteins
Analysis by Capillary Electrophoresis of the Kinetics of Charge Ladder Formation for Bovine
Prentiss, Mara
Analysis by Capillary Electrophoresis of the Kinetics of Charge Ladder Formation for Bovine were synthesized and the relative abundances of the rungs analyzed by capillary electrophoresis by capillary electrophoresis (CE).5-7 In synthesizing charge ladders by acetylating various proteins, we have
Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling
Zhang, Haizhen; Brown, Roslyn N.; Qian, Wei-Jun; Monroe, Matthew E.; Purvine, Samuel O.; Moore, Ronald J.; Gritsenko, Marina A.; Shi, Liang; Romine, Margaret F; Fredrickson, James K.; PaÜa-Toli?, Ljiljana; Smith, Richard D.; Lipton, Mary S.
We report a mass spectrometry-based strategy for quantitative analysis of cell surface membrane proteome changes. The strategy includes enrichment of surface membrane proteins using a membrane-impermeable chemical probe followed by stable isotope 18O labeling and LC-MS analysis. We applied this strategy for enriching membrane proteins expressed by Shewanella oneidensis MR-1, a gram-negative bacterium with known metal-reduction capability via extracellular electron transfer between outer membrane proteins and extracellular electron receptors. LC/MS/MS analysis resulted in the identification of about 400 proteins with 79% of them being predicted to be membrane localized. Quantitative aspects of the membrane enrichment were shown by peptide level 16O and 18O labeling of proteins from wild-type and mutant cells (generated from deletion of a type II secretion protein, GspD) prior to LC-MS analysis. Using a chemical probe labeled pure protein as an internal standard for normalization, the quantitative data revealed reduced abundances in ?gspD mutant cells of many outer membrane proteins including the outer membrane c-cype cytochromes OmcA and MtrC, in agreement with previously investigation demonstrating that these proteins are substrates of the type II secretion system. PMID:20380418
Application of Microchip Electrophoresis for Clinical Tests
NASA Astrophysics Data System (ADS)
Yatsushiro, Shouki; Kataoka, Masatoshi
Microchip electrophoresis has recently attracted much attention in the field of nuclear acid analysis due to its high efficiency, ease of operation, low consumption of samples and reagents, and relatively low costs. In addition, the analysis has expanded to an analytical field like not only the analysis of DNA but also the analysis of RNA, the protein, the sugar chain, and the cellular function, etc. In this report, we showed that high-performance monitoring systems for human blood glucose levels and ?-amylase activity in human plasma using microchip electrophoresis.
Enzymatic assessment of cholesterol on electrophoresis gels for estimating HDL size distribution and plasma concentrations of HDL subclasses[S
Toledo-Ibelles, Paola; GarcĒa-Sßnchez, Cynthia; ┴vila-Vazzini, Nydia; Carre¾n-Torres, Elizabeth; Posadas-Romero, Carlos; Vargas-Alarc¾n, Gilberto; Pķrez-Mķndez, Oscar
The aim of this study was to develop an enzymatic cholesterol staining method to determine HDL subclasses in a polyacrylamide gradient gel electrophoresis, which further allows staining by protein in the same electrophoresis lane. HDLs from 120 healthy individuals were separated through nondenaturing PAGE. HDLs were stained for cholesterol using an enzymatic semisolid mixture. Once the gels were unstained, they were stained again for proteins with Coomassie blue. The proportions of HDL subclasses were determined by densitometry. HDL subclasses were transformed to concentrations using as reference HDL-cholesterol plasma levels. This method is comparable in linearity and reproducibility to Coomassie blue staining, although it provides quantitative data. As expected, HDL size distribution shifted toward larger particles when determined by cholesterol as compared with protein. With this method, we observed different proportions of HDL subclasses between men and women as compared with Coomassie blue staining. We described a method to determine HDL size distribution by enzymatic cholesterol staining on polyacrylamide gels. The method allows the quantification of the cholesterol plasma concentration of each HDL subclass with the possibility to further stain the protein in the same sample. The combination of HDL staining by cholesterol and protein on electrophoresis gels provides information that may have clinical relevance. PMID:20097938
Paris-Sud XI, Universitķ de
the #12;quantitative changes in serum proteins, lipids and cholestrol during the course of force feeding changes in serum proteins, lipids and cholestrol during the course of force feeding in geese. The effect by paper electrophoresis suggested by DiTThtER and ANrro (1965). The examination of the cholestrol was done
21 CFR 862.2485 - Electrophoresis apparatus for clinical use.
Code of Federal Regulations, 2010 CFR
...electrophoresis apparatus for clinical use is a device intended to separate molecules or particles, including plasma proteins, lipoproteins, enzymes, and hemoglobulins on the basis of their net charge in specified buffered media. This device is used in...
Kinetic, quantitative, and functional analysis of multiple forms of the vesicular stomatitis virus nucleocapsid protein in infected cells.
Peluso, R W
Multiple forms of the vesicular stomatitis virus nucleocapsid protein N have been detected in infected cells. One form is complexed with the viral NS protein in a 1:1 molar ratio, and the other forms are distinguished by their more rapid sedimentation rates on glycerol gradients. I performed a series of experiments designed to analyze the relationships between these forms of the N protein. Pulse-chase experiments demonstrate that the N protein is made first as the form which binds to the NS protein, forming a 1-to-1 molar complex, and that with increasing times of chase it is either assembled into nucleocapsids or converted to the two higher sedimenting forms. Using a newly developed quantitative immunoblotting procedure, I have quantitated the three differentially sedimenting species of the N protein and have shown that at later times postinfection (6 to 7 h), the faster-sedimenting forms of the N protein account for as much as 50% of the soluble N protein in the cell. The activity of these forms has been assessed, with only the 1-to-1 molar N-NS complex demonstrating the ability to support the replication and encapsidation of viral genomic RNA. A model for the conversion of the N protein from the active N-NS complex into the other forms of the protein is presented, and the possible function of the N-protein self-complexes is discussed. Images PMID:2839702
Subcellular quantitative proteomic analysis reveals host proteins involved in human cytomegalovirus infection.
Chai, Fan; Li, Hao-Yu; Wang, Wei; Zhu, Xiu-Juan; Li, Yang; Wang, Shaobo; Guo, Lin; Zhang, Lei-Ke; Xiao, Gengfu
Viral replication requires host cell macromolecules and energy, although host cells can alter their protein expression to restrict viral replication. To study the host cell response to human cytomegalovirus (HCMV) infection, a stable isotope labeling by amino acids in cell culture (SILAC)-based subcellular quantitative proteomic study of HCMV-infected human embryo lung fibroblast (HEL) cells was performed, and a total of 247 host proteins were identified as differentially regulated by HCMV. Western blotting and immunofluorescence confocal microscopy were performed to validate the data sets. Gene Ontology analysis indicated that cellular processes involving the metabolism, localization and immune system were regulated as a result of HCMV infection. Functional analysis of selected regulated proteins revealed that knockdown of HNRPD, PHB2 and UB2V2 can increase HCMV replication, while knockdown of A4 and KSRP resulted in decreased HCMV replication. Our study may improve our understanding of the dynamic interactions between HCMV and its host and provide multiple potential targets for anti-HCMV agent research. PMID:25910425
NSDL National Science Digital Library
Janice Stephens
In this experiment related to plant biotechnology, learners discover how to prepare and load an electrophoresis gel. They will then run the gels in an electrophoresis system to separate several dyes that are of different molecular sizes and carry different charges. This technique is fundamental to many of the procedures used in biotechnology. This lesson guide includes background information for the educator, safety precautions, and questions with answers for learners. For safety reasons, adult supervision is recommended. Modifications for use with younger learners are described in a related PDF (see related resource).
Capillary Electrophoresis and Capillary Electrophoresis¢Mass Spectrometry for Structural Analysis of N -Glycans Derived from Glycoproteins
Miyako Nakano; Kazuaki Kakehi; Naoyuki Taniguchi; Akihiro Kondo
\\u000a This chapter highlights recent developments in the analysis of proteins glycosylated of the amino groups (N) of asparagine residues (i.e., N-glycans) by capillary electrophoresis (CE) and capillary electrophoresis¢mass spectrometry (CE-MS). First, the analysis of\\u000a intact glycoproteins by CE and CE-MS is reviewed. In glycoform analysis of a heterogeneous protein due to different glycosylation,\\u000a multiforms are observed on CE. Second, to
Quantitative heterogeneous immunoassays in protein modified polydimethylsiloxane microfluidic channels for rapid detection of disease biomarkers.
Li, Peng
Conventional detection of disease biomarkers employs techniques such as lateral-flow assays or central laboratory-based enzyme-linked immunosorbent assays (ELISA). Miniaturization and performance improvement of such traditional immunoassays using microfluidic technologies has proved promising in producing rapid, sensitive and automated next-generation immunosensors for quantitative diagnoses in the point-of-care setting. In this article a poly(dimethylsiloxane) (PDMS)-based immunosensor is presented for rapid detection of C-reactive protein. PDMS is selected in part because of the vast popularity of using PDMS as a material for microfluidic devices and in part because of the challenge of obtaining a stable surface coating with PDMS for immunosensing applications. Practical procedures for fabrication, surface modification, and preservation of the microfluidic immuno-chips as well as detailed descriptions of performing the microfluidic heterogeneous assay are presented. PMID:23329452
Method for collecting and immobilizing individual cumulus cells enabling quantitative immunofluorescence analysis of proteins.
Appeltant, R; Maes, D; Van Soom, A
Most immunofluorescence methods rely on techniques dealing with a very large number of cells. However, when the number of cells in a sample is low (e.g., when cumulus cells must be analyzed from individual cumulus-oocyte complexes), specific techniques are required to conserve, fix, and analyze cells individually. We established and validated a simple and effective method for collecting and immobilizing low numbers of cumulus cells that enables easy and quick quantitative immunofluorescence analysis of proteins from individual cells. To illustrate this technique, we stained proprotein of a disintegrin and metalloproteinase with thrombospondin-like repeats-1 (proADAMTS-1) and analyzed its levels in individual porcine cumulus cells. PMID:25862082
IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins?
Breitwieser, Florian P.; Colinge, Jacques
The establishment of extremely powerful proteomics platforms able to map thousands of modification sites, e.g. phosphorylations or acetylations, over entire proteomes calls for equally powerful software tools to effectively extract useful and reliable information from such complex datasets. We present a new quantitative PTM analysis platform aimed at processing iTRAQ or Tandem Mass Tags (TMT) labeled peptides. It covers a broad range of needs associated with proper PTM ratio analysis such as PTM localization validation, robust ratio computation and statistical assessment, and navigable user report generation. IsobarPTM is made available as an R Bioconductor package and it can be run from the command line by non R specialists. Biological significance ōIsobarPTM is a new software tool facilitating the quantitative analysis of protein modification regulation streamlining important issues related to PTM localization and statistical modeling. Users are provided with a navigable spreadsheet report, which also annotate already public modification sites.ö This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations. PMID:23470796
Quantitative Proteomics Reveals the Temperature-Dependent Proteins Encoded by a Series of Cluster Genes in Thermoanaerobacter Tengcongensis*
Chen, Zhen; Wen, Bo; Wang, Quanhui; Tong, Wei; Guo, Jiao; Bai, Xue; Zhao, Jingjing; Sun, Yao; Tang, Qi; Lin, Zhilong; Lin, Liang; Liu, Siqi
Comprehensive and quantitative information of the thermophile proteome is an important source for understanding of the survival mechanism under high growth temperature. Thermoanaerobacter tengcongensis (T. tengcongensis), a typical anaerobic thermophilic eubacterium, was selected to quantitatively evaluate its protein abundance changes in response to four different temperatures. With optimized procedures of isobaric tags for relative and absolute quantitation quantitative proteomics (iTRAQ), such as peptide fractionation with high-pH reverse phase (RP) high performance liquid chromatography (HPLC), tandem MS acquisition mode in LTQ Orbitrap Velos MS, and evaluation of the quantification algorithms, high quality of the quantitative information of the peptides identified were acquired. In total, 1589 unique proteins were identified and defined 251 as the temperature-dependent proteins. Analysis of genomic locations toward the correspondent genes of these temperature-dependent proteins revealed that more than 30% were contiguous units with relevant biological functions, which are likely to form the operon structures in T. tengcongensis. The RNA sequencing (RNA-seq) data further demonstrated that these cluster genes were cotranscribed, and their mRNA abundance changes responding to temperature exhibited the similar trends as the proteomic results, suggesting that the temperature-dependent proteins are highly associated with the correspondent transcription status. Hence, the operon regulation is likely an energy-efficient mode for T. tengcongensis survival. In addition, evaluation to the functions of differential proteomes indicated that the abundance of the proteins participating in sulfur-respiration on the plasma membrane was decreased as the temperature increased, whereas the glycolysis-related protein abundance was increased. The energy supply in T. tengcongensis at high temperature is, therefore, speculated not mainly through the respiration chain reactions. PMID:23665590
Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis
Kramer, J.M. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)
X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs.
Quantitative Assessment of Effect of Preanalytic Cold Ischemic Time on Protein Expression in Breast Cancer Tissues
Background Companion diagnostic tests can depend on accurate measurement of protein expression in tissues. Preanalytic variables, especially cold ischemic time (time from tissue removal to fixation in formalin) can affect the measurement and may cause false-negative results. We examined 23 proteins, including four commonly used breast cancer biomarker proteins, to quantify their sensitivity to cold ischemia in breast cancer tissues. Methods A series of 93 breast cancer specimens with known time-to-fixation represented in a tissue microarray and a second series of 25 matched pairs of core needle biopsies and breast cancer resections were used to evaluate changes in antigenicity as a function of cold ischemic time. Estrogen receptor (ER), progesterone receptor (PgR), HER2 or Ki67, and 19 other antigens were tested. Each antigen was measured using the AQUA method of quantitative immunofluorescence on at least one series. All statistical tests were two-sided. Results We found no evidence for loss of antigenicity with time-to-fixation for ER, PgR, HER2, or Ki67 in a 4-hour time window. However, with a bootstrapping analysis, we observed a trend toward loss for ER and PgR, a statistically significant loss of antigenicity for phosphorylated tyrosine (P = .0048), and trends toward loss for other proteins. There was evidence of increased antigenicity in acetylated lysine, AKAP13 (P = .009), and HIF1A (P = .046), which are proteins known to be expressed in conditions of hypoxia. The loss of antigenicity for phosphorylated tyrosine and increase in expression of AKAP13, and HIF1A were confirmed in the biopsy/resection series. Conclusions Key breast cancer biomarkers show no evidence of loss of antigenicity, although this dataset assesses the relatively short time beyond the 1-hour limit in recent guidelines. Other proteins show changes in antigenicity in both directions. Future studies that extend the time range and normalize for heterogeneity will provide more comprehensive information on preanalytic variation due to cold ischemic time. PMID:23090068
Capillary Electrophoresis of DNA
Beatriz Sanchez-Vega
Capillary electrophoresis (CE) separations are carried out inside a capillary tube, which usually has a diameter of 50 Ąm to facilitate temperature control. The length of the capillary differs in different applications, but it is typically in the region of 20¢50 cm. The capillaries most widely used are fused silica covered with an external protective coating. A small portion of
Identification of Protein Network Alterations upon Retinal Ischemia-Reperfusion Injury by Quantitative Proteomics Using a Rattus norvegicus Model
Tian, Han; Wang, Leilei; Cai, Ruiqi; Zheng, Ling; Guo, Lin
Retinal ischemia is a common feature associated with several ocular diseases, including diabetic retinopathy. In this study, we investigated the effect of a retinal ischemia and reperfusion (I/R) injury on protein levels via a quantitative shotgun strategy using stable isotope dimethyl labeling combined with LC-MS/MS analysis. Based on the relative quantitation data of 1088 proteins, 234 proteins showed a greater than 1.5-fold change following I/R injury, 194 of which were up-regulated and 40 were down-regulated. Gene ontology analysis revealed that after I/R injury, there was an increase in the metabolic-process related proteins but a decline in cell communication, system process and transport-related proteins. A ribosome protein network and a secreted protein network consisting of many protease inhibitors were identified among the up-regulated proteins, despite a suppression of the mammalian target of rapamycin (mTOR) pathway following the I/R injury. A synaptic-related protein network was found to be significantly down-regulated, implicating a functional reduction of neurons following a retinal I/R injury. Our results provide new systems-biology clues for the study of retinal ischemia. PMID:25549249
The workflow for quantitative proteome analysis of chloroplast development and differentiation, chloroplast mutants, and protein interactions by spectral counting.
Friso, Giulia; Olinares, Paul Dominic B; van Wijk, Klaas J
This chapter outlines a quantitative proteomics workflow using a label-free spectral counting technique. The workflow has been tested on different aspects of chloroplast biology in maize and Arabidopsis, including chloroplast mutant analysis, cell-type specific chloroplast differentiation, and the proplastid-to-chloroplast transition. The workflow involves one-dimensional SDS-PAGE of the proteomes of leaves or chloroplast subfractions, tryptic digestions, online LC-MS/MS using a mass spectrometer with high mass accuracy and duty cycle, followed by semiautomatic data processing. The bioinformatics analysis can effectively select best gene models and deals with quantification of closely related proteins; the workflow avoids overidentification of proteins and results in more accurate protein quantification. The final output includes pairwise comparative quantitative analysis, as well as hierarchical clustering for discovery of temporal and spatial patterns of protein accumulation. A brief discussion about potential pitfalls, as well as the advantages and disadvantages of spectral counting, is provided. PMID:21863448
[Quantitative study of serum protein loss into the alimentary tract in patients with gastric cancer].
Nakatani, N
Quantitative study of serum protein loss into the alimentary tract from the tumor of gastric cancer using 111Indium-transferrin (111In-Tf) was performed. Gamma counting of 111In-Tf excreted in feces and 111In-Tf scintigram were performed in 24 patients with gastric cancer and 10 controls. Transferrin was labelled by incubating 111MBq (3mCi) of 111In chloride with approximately 13ml of patient plasma in vitro. After intravenous injection of 111In-Tf, an aliquot was weighed and its radioactivity was measured in a gamma-counter. Feces were collected every 24hrs up to 72hrs. Then 111In in the feces was calculated as a percentage of the injection dose. 111In excreted in the feces within 72hrs in patients with gastric cancer was 3.71 +/- 3.87% (mean +/- SD), which was significantly higher than the 0.48 +/- 0.26% in 10 controls. 111In in feces correlated the area of the tumor in the stomach (p < 0.001). In 18 patients positive scan was recognized and was localized the protein loss in the cavity of the stomach within 10 minutes. Positive scan was found to move along the intestine successively. 111In-Tf can be useful in assessing of hypoproteinemia of gastric cancer. PMID:7933636
Quantitative Description of a Protein Fitness Landscape Based on Molecular Features.
Meini, MarĒa-RocĒo; Tomatis, Pablo E; Weinreich, Daniel M; Vila, Alejandro J
Understanding the driving forces behind protein evolution requires the ability to correlate the molecular impact of mutations with organismal fitness. To address this issue, we employ here metallo-?-lactamases as a model system, which are Zn(II) dependent enzymes that mediate antibiotic resistance. We present a study of all the possible evolutionary pathways leading to a metallo-?-lactamase variant optimized by directed evolution. By studying the activity, stability and Zn(II) binding capabilities of all mutants in the preferred evolutionary pathways, we show that this local fitness landscape is strongly conditioned by epistatic interactions arising from the pleiotropic effect of mutations in the different molecular features of the enzyme. Activity and stability assays in purified enzymes do not provide explanatory power. Instead, measurement of these molecular features in an environment resembling the native one provides an accurate description of the observed antibiotic resistance profile. We report that optimization of Zn(II) binding abilities of metallo-?-lactamases during evolution is more critical than stabilization of the protein to enhance fitness. A global analysis of these parameters allows us to connect genotype with fitness based on quantitative biochemical and biophysical parameters. PMID:25767204
Serum Free Light Chains: An Alternative to the Urine Bence Jones Proteins Screening Test for Monoclonal Gammopathies
Peter G. Hill; Julia M. Forsyth; Baldeep Rai; Stewart Mayne
Background: Retrospective analyses have established the role of quantitative serum free light chains (FLCs) in the diagnosis of monoclonal light chain disorders. The aims of this study were to assess (a) whether the addition of serum FLCs to serum protein electrophoresis (SPEP) identified additional patients with monoclonal gammopathies; (b) whether serum FLC measurements could replace urinalysis for Bence Jones protein
Serum Free Light Chains: An Alternative Test to Urine Bence Jones Proteins When Screening for Monoclonal Gammopathies
Peter G. Hill; Julia M. Forsyth; Baldeep Rai; Stewart Mayne
Background: Retrospective analyses have established the role of quantitative serum free light chains (FLCs) in the diagnosis of monoclonal light chain disorders. The aims of this study were to assess (a) whether the addition of serum FLCs to serum protein electrophoresis (SPEP) identified additional patients with monoclonal gammopathies; (b) whether serum FLC measurements could replace urinalysis for Bence Jones protein
Analysis of protein composition of red wine in comparison with rose? and white wines by electrophoresis and high-pressure liquid chromatography-mass spectrometry (HPLC-MS).
Wigand, Petra; Tenzer, Stefan; Schild, Hansjoerg; Decker, Heinz
Wine proteins not only influence wine stability but are also being discussed as potential allergens. Proteins from red, rose?, and white wines were enriched by dialysis and lyophilization followed by separation by SDS-PAGE. Significant differences were detected in the protein compositions of the analyzed wine varieties, and the major protein bands were identified by mass spectrometry after in-gel digestion with trypsin. In German Portugieser red wine, a total of 121 tryptic peptides were identified, which were attributed to 12 grape proteins and 6 proteins derived from yeast. Among the identified constituents are several proteins considered to influence wine stability and previously described potential grape allergens. The pathogenesis-related proteins represent the main proteins in all of the wines, but only some red wines show a band with a molecular mass of 12 kDa, identified as a lipid transfer protein (LTP). The occurrence and distribution of LTP depend on the wine variety. PMID:19385597
Quantitative immunobinding assay for vitamin D-dependent calcium-binding protein (calbindin-D28k) using nitrocellulose filters
Varghese, S.; Christakos, S.
A sensitive dot immunobinding assay has been developed for the quantitative determination of vitamin D-dependent calcium-binding protein (calbindin-D28k; CaBP) in rat and human kidney and brain. Protein samples are spotted onto nitrocellulose sheets, fixed, and then rinsed with Tris-buffered saline. The remaining protein binding sites are blocked with bovine serum albumin, gelatin, or nonfat dry milk protein and the filters are then incubated sequentially with antiserum to calbindin-D28k (1:500 dilution) and /sup 125/I-protein A (200,000 cpm/ml). After washing, the radioactivity bound to each sample is quantitated by counting in a gamma counter. The sensitivity of the assay is such that 10 ng calbindin-D28k can be accurately quantitated. The highest levels of CaBP were detected in kidney (7.8 +/- 0.5 micrograms/mg protein) and cerebellum (22.1 +/- 1.4 micrograms/mg protein). Ten micrograms calmodulin, lactalbumin, or parvalbumin and 100 micrograms liver extract showed no reactivity in the assay. The assay is precise (intraassay variability, 4.0%) and reproducible (interassay variability, 8.8%). There was good agreement between the data in this assay and the data we obtained using radioimmunoassay (RIA). The assay has several advantages over the RIA. Iodination of pure antigen is not required and it is possible to detect membrane-bound and insoluble antigens using this assay. Also, the antiserum and /sup 125/I-protein A solutions can be saved and reused. This assay represents a major modification of the original immunobinding assays which used the less sensitive peroxidase stain. It is also an improvement over previous /sup 125/I immunobinding assays which were not quantitative but were used as antigen spot tests or which required iodination of the antibody.
Multifunctional Reagents for Quantitative Proteome-Wide Analysis of Protein Modification in Human Cells and Dynamic Profiling of Protein Lipidation During Vertebrate Development**
Broncel, Malgorzata; Serwa, Remigiusz A; Ciepla, Paulina; Krause, Eberhard; Dallman, Margaret J; Magee, Anthony I; Tate, Edward W
Novel multifunctional reagents were applied in combination with a lipid probe for affinity enrichment of myristoylated proteins and direct detection of lipid-modified tryptic peptides by mass spectrometry. This method enables high-confidence identification of the myristoylated proteome on an unprecedented scale in cell culture, and allowed the first quantitative analysis of dynamic changes in protein lipidation during vertebrate embryonic development. PMID:25807930
Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
Background Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli. Results In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression. Conclusion This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli. PMID:21513543
Quantitative proteomic analysis reveals proteins involved in the neurotoxicity of marine medaka Oryzias melastigma chronically exposed to inorganic mercury.
Wang, Yuyu; Wang, Dazhi; Lin, Lin; Wang, Minghua
Mercury is a ubiquitous environmental contaminant which exerts neurotoxicity upon animals. Nevertheless, the molecular mechanisms involved in inorganic mercury neurotoxicity are unknown. We investigated protein profiles of marine medaka, chronically exposed to mercuric chloride using two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS) analysis. The mercury accumulation and ultrastructure were also examined in the brain. The results showed that mercury was significantly accumulated in the treated brain, and subsequently caused a noticeable damage. The comparison of 2D-DIGE protein profiles between the control and treatment revealed that 16 protein spots were remarkably altered in abundance, which were further submitted for MALDI-TOF-TOF MS analysis. The identified proteins indicated that inorganic mercury may cause neurotoxicity through the induction of oxidative stress, cytoskeletal assembly dysfunction and metabolic disorders. Thus, this study provided a basis for a better understanding of the molecular mechanisms involved in mercury neurotoxicity. PMID:25460752
Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model
Liu, David R.
effect on conjugation is occlusion of the conjugative pilus by phage particles. This interaction model in which association between the pili and phage particles or g3p prevents transmission of an FInhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis
Use of non-porous reversed-phase high-performance liquid chromatography for protein profiling and isolation of proteins induced by temperature variations for Siberian permafrost bacteria with identification by matrix-assisted laser desorption\\/ionization time-of-flight mass spectrometry and capillary electrophoresis¢electrospray ionization mass spectrometry
Bathsheba E. Chong; Jeongkwon Kim; David M. Lubman; James M. Tiedje; Sohpia Kathariou
Non-porous reversed-phase high-performance liquid chromatography (NP-RP-HPLC) has been used to separate and isolate proteins from whole cell lysates of ED 7-3, a bacterium from the buried Siberian permafrost sediment. The proteins collected from the liquid eluent of this separation were then analyzed by matrix-assisted laser desorption\\/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis¢electrospray ionization mass spectrometry (CE¢ESI-MS). In order to
Quantitative analysis of aberrant protein glycosylation in liver cancer plasma by AAL-enrichment and MRM mass spectrometry.
Ahn, Yeong Hee; Shin, Park Min; Kim, Yong-Sam; Oh, Na Ree; Ji, Eun Sun; Kim, Kwang Hoe; Lee, Yeon Jung; Kim, Sung Ho; Yoo, Jong Shin
A lectin-coupled mass spectrometry (MS) approach was employed to quantitatively monitor aberrant protein glycosylation in liver cancer plasma. To do this, we compared the difference in the total protein abundance of a target glycoprotein between hepatocellular carcinoma (HCC) plasmas and hepatitis B virus (HBV) plasmas, as well as the difference in lectin-specific protein glycoform abundance of the target glycoprotein. Capturing the lectin-specific protein glycoforms from a plasma sample was accomplished by using a fucose-specific aleuria aurantia lectin (AAL) immobilized onto magnetic beads via a biotin-streptavidin conjugate. Following tryptic digestion of both the total plasma and its AAL-captured fraction of each HCC and HBV sample, targeted proteomic mass spectrometry was conducted quantitatively by a multiple reaction monitoring (MRM) technique. From the MRM-based analysis of the total plasmas and AAL-captured fractions, differences between HCC and HBV plasma groups in fucosylated glycoform levels of target glycoproteins were confirmed to arise from both the change in the total protein abundance of the target proteins and the change incurred by aberrant fucosylation on target glycoproteins in HCC plasma, even when no significant change occurs in the total protein abundance level. Combining the MRM-based analysis method with the lectin-capturing technique proved to be a successful means of quantitatively investigating aberrant protein glycosylation in cancer plasma samples. Additionally, it was elucidated that the differences between HCC and control groups in fucosylated biomarker candidates A1AT and FETUA mainly originated from an increase in fucosylation levels on these target glycoproteins, rather than an increase in the total protein abundance of the target glycoproteins. PMID:24027776
Applications of space-electrophoresis in medicine. [for cellular separations in molecular biology
NASA Technical Reports Server (NTRS)
Bier, M.
The nature of electrophoresis is reviewed and potential advances realizable in the field of biology and medicine from a space electrophoresis facility are examined. The ground-based applications of electrophoresis: (1) characterization of an ionized species; (2) determination of the quantitative composition of a complex mixture; and (3) isolation of the components of a mixture, separation achieved on the basis of the difference in transport rates is reviewed. The electrophoresis of living cells is considered, touching upon the following areas: the separation of T and B lymphocytes; the genetic influence on mouse lymphocyte mobilities; the abnormal production of specific and monoclonal immunoproteins; and the study of cancer. Schematic diagrams are presented of three types of electrophoresis apparatus: the column assembly for the static electrophoresis experiment on the Apollo-Soyuz mission, the continuous flow apparatus used in the same mission and a miniaturized electrophoresis apparatus.
Qualitative and Quantitative Characterization of Plasma Proteins When Incorporating Traveling Wave Ion Mobility into a Liquid Chromatography¢Mass Spectrometry Workflow for Biomarker Discovery: Use of Product Ion Quantitation As an Alternative Data Analysis Tool for Label Free Quantitation
Discovery of protein biomarkers in clinical samples necessitates significant prefractionation prior to liquid chromatography¢mass spectrometry (LC¢MS) analysis. Integrating traveling wave ion mobility spectrometry (TWIMS) enables in-line gas phase separation which when coupled with nanoflow liquid chromatography and data independent acquisition tandem mass spectrometry, confers significant advantages to the discovery of protein biomarkers by improving separation and inherent sensitivity. Incorporation of TWIMS leads to a packet of concentrated ions which ultimately provides a significant improvement in sensitivity. As a consequence of ion packeting, when present at high concentrations, accurate quantitation of proteins can be affected due to detector saturation effects. Human plasma was analyzed in triplicate using liquid-chromatography data independent acquisition mass spectrometry (LC-DIA-MS) and using liquid-chromatography ion-mobility data independent acquisition mass spectrometry (LC-IM-DIA-MS). The inclusion of TWIMS was assessed for the effect on sample throughput, data integrity, confidence of protein and peptide identification, and dynamic range. The number of identified proteins is significantly increased by an average of 84% while both the precursor and product mass accuracies are maintained between the modalities. Sample dynamic range is also maintained while quantitation is achieved for all but the most abundant proteins by incorporating a novel data interpretation method that allows accurate quantitation to occur. This additional separation is all achieved within a workflow with no discernible deleterious effect on throughput. Consequently, TWIMS greatly enhances proteome coverage and can be reliably used for quantification when using an alternative product ion quantification strategy. Using TWIMS in biomarker discovery in human plasma is thus recommended. PMID:24397486
Qualitative and quantitative characterization of plasma proteins when incorporating traveling wave ion mobility into a liquid chromatography-mass spectrometry workflow for biomarker discovery: use of product ion quantitation as an alternative data analysis tool for label free quantitation.
Daly, Charlotte E; Ng, Leong L; Hakimi, Amirmansoor; Willingale, Richard; Jones, Donald J L
Discovery of protein biomarkers in clinical samples necessitates significant prefractionation prior to liquid chromatography-mass spectrometry (LC-MS) analysis. Integrating traveling wave ion mobility spectrometry (TWIMS) enables in-line gas phase separation which when coupled with nanoflow liquid chromatography and data independent acquisition tandem mass spectrometry, confers significant advantages to the discovery of protein biomarkers by improving separation and inherent sensitivity. Incorporation of TWIMS leads to a packet of concentrated ions which ultimately provides a significant improvement in sensitivity. As a consequence of ion packeting, when present at high concentrations, accurate quantitation of proteins can be affected due to detector saturation effects. Human plasma was analyzed in triplicate using liquid-chromatography data independent acquisition mass spectrometry (LC-DIA-MS) and using liquid-chromatography ion-mobility data independent acquisition mass spectrometry (LC-IM-DIA-MS). The inclusion of TWIMS was assessed for the effect on sample throughput, data integrity, confidence of protein and peptide identification, and dynamic range. The number of identified proteins is significantly increased by an average of 84% while both the precursor and product mass accuracies are maintained between the modalities. Sample dynamic range is also maintained while quantitation is achieved for all but the most abundant proteins by incorporating a novel data interpretation method that allows accurate quantitation to occur. This additional separation is all achieved within a workflow with no discernible deleterious effect on throughput. Consequently, TWIMS greatly enhances proteome coverage and can be reliably used for quantification when using an alternative product ion quantification strategy. Using TWIMS in biomarker discovery in human plasma is thus recommended. PMID:24397486
Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics
Simpson, David C.; Smith, Richard D.
Throughout the field of global proteomics, ranging from simple organism studies to human medical applications, the high sample complexity creates demands for improved separations and analysis techniques. Furthermore, with increased organism complexity, the correlation between proteome and genome becomes less certain due to extensive mRNA processing prior to translation. In this way, the same DNA sequence can potentially code for regions in a number of distinct proteins; quantitative differences in expression (or abundance) between these often-related species are of significant interest. Well-established proteomics techniques, which use genomic information to identify peptides that originate from protease digestion, often cannot easily distinguish between such gene products; intact protein-level analyses are required to complete the picture, particularly for identifying post-translational modifications. While chromatographic techniques are currently better suited to peptide analysis, capillary electrophoresis (CE) in combination with mass spectrometry (MS) may become important for intact protein analysis. This review focuses on CE/MS instrumentation and techniques showing promise for such applications, highlighting those with greatest potential. Reference will also be made to developments relevant to peptide-level analyses for use in time- or sample-limited situations.
A chemiluminescent-western blot assay for quantitative detection of Plasmodium falciparum circumsporozoite protein.
Kumar, Sanjai; Zheng, Hong; Sangweme, Davison T; Mahajan, Babita; Kozakai, Yukiko; Pham, Phuong T; Morin, Merribeth J; Locke, Emily; Kumar, Nirbhay
Highly sensitive and reliable assays based on the quantitation of immunologically relevant component(s) in recombinant or whole parasite-based vaccines would facilitate pre-clinical and clinical phases and the monitoring of malaria vaccine deployment. Here we report a laboratory-grade Western Blot assay for quantitative detection of Plasmodium falciparum circumsporozoite protein (PfCSP) in P. falciparum sporozoite (PfSPZ) and in recombinant (rPfCSP) product. This assay is based on the immuno-reactivity of an anti-P. falciparum CSP monoclonal antibody (mAb 2A10) with the NANP-repeat units on PfCSP. The antigen-antibody complex is detected by reaction with a commercially obtained chemiluminescence-linked Immunodetection system. The linear range for detecting the recombinant P. falciparum CSP (rPfCSP) in this assay is 3-12pg (R(2)=0.9399). The range for detecting the day 15 salivary-gland PfSPZ is between 0.0625 and 1 parasite (R(2)=0.9448) and approximately 10.0pg of PfCSP was detected on each sporozoite. The assay was highly reproducible in measuring the PfCSP on PfSPZ. The inter-assay Coefficient of Variation (CV%) was 10.31% while the intra-assay CV% on three different days was 6.05%, 2.03% and 1.42% respectively. These results suggest that this ECL-WB assay is highly sensitive and robust with a low degree of inter-assay and intra-assay variations. To our knowledge, this is the most sensitive immunoassay for the detection of a recombinant or native malarial protein and may have a wider range of applications including the quantification of immunological component(s) in a vaccine formulation, determination of the antigenic integrity in adjuvanted-vaccine and in stability studies. In addition, this assay can be applied to measure the mosquito infectivity in malaria transmission areas and to determine the effects of intervention measures on malaria transmission. PMID:23399449
Quantitative modeling of DNA¢protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor
Man, Tsz-Kwong; Yang, Joshua SungWoo; Stormo, Gary D.
Understanding DNA¢protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple fluorescence, relative affinity (QuMFRA) assay, we determine the binding specificity of 11 different position 6 variants of the Mnt repressor for operators containing all 16 possible dinucleotides at operator positions 16 and 17. We show that the wild-type and all variant proteins interact with the two positions in a non-independent manner, but that a simple independent model provides a close approximation to the true binding affinities. The wild-type His at amino acid 6 is the only protein to prefer the AC sequence of the wild-type operator, whereas most of the variant proteins prefer TA. H6R is unique in having a strong preference for C at position 16. A comparison of the quantitative binding data for all of the protein variants with a model for recognition of the early growth response (EGR) zinc finger family suggests that interactions of Mnt with positions 16 and 17 are similar to interactions of EGR with positions 1 and 2, respectively. This information leads to an augmented model for the interaction of Mnt with its operator. PMID:15289576
Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-dimensional Gel Electrophoresis and HPLC-ESI-MS/MS
Xie, Xitao; Yi, Zhengping; Bowen, Benjamin; Wolf, Cassandra; Flynn, Charles R.; Sinha, Sandeep; Mandarino, Lawrence J.; Meyer, Christian
Abnormalities in adipocytes play an important role in various conditions, including the metabolic syndrome, type 2 diabetes mellitus and cardiovascular disease, but little is known about alterations at the protein level. We therefore sought to 1) comprehensively characterize the human adipocyte proteome for the first time, and 2) demonstrate feasibility of measuring adipocyte protein abundances by one-dimensional SDS-PAGE and High Performance Liquid Chromatography -Electron Spray Ionization - tandem Mass Spectrometry (HPLC-ESI-MS/MS). In adipocytes isolated from ~0.5 g subcutaneous abdominal adipose tissue of three healthy, lean subjects we identified a total of 1493 proteins. Triplicate analysis indicated a 22.5% coefficient of variation of protein abundances. Proteins ranged from 5.8 to 629 kDa and included a large number of proteins involved in lipid metabolism, such as fatty acid transport, fatty acid oxidation, lipid storage, lipolysis and lipid droplet maintenance. Furthermore, we found most glycolysis enzymes and numerous proteins associated with oxidative stress, protein synthesis and degradation as well as some adipokines. 22% of all proteins were of mitochondrial origin. These results provide the first detailed characterization of the human adipocyte proteome, suggest an important role of adipocyte mitochondria, and demonstrate feasibility of this approach to examine alterations of adipocyte protein abundances in human diseases. PMID:20812759
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles
The final, structure-determining step in the folding of membrane proteins involves the coalescence of preformed transmembrane helices to form the native tertiary structure. Here, we review recent studies on small peptide and protein systems that are providing quantitative data on the interactions that drive this process. Gel electrophoresis, analytical ultracentrifugation, and fluorescence resonance energy transfer (FRET) are useful methods for
Studies of muscle proteins in embryonic myocardial cells of cardiac lethal mutant mexican axolotls (Ambystoma mexicanum) by use of heavy meromyosin binding and sodium dodecyl sulfate polyacrylamide gel electrophoresis
In the Mexican axolotl Ambystoma mexicanum recessive mutant gene c, by way of abnormal inductive processes from surrounding tissues, results in an absence of embryonic heart function. The lack of contractions in mutant heart cells apparently results from their inability to form normally organized myofibrils, even though a few actin-like (60-A) and myosin-like (150-A) filaments are present. Amorphous "proteinaceous" collections are often visible. In the present study, heavy meromyosin (HMM) treatment of mutant heart tissue greatly increases the number of thin filaments and decorates them in the usual fashion, confirming that they are actin. The amorphous collections disappear with the addition of HMM. In addition, an analysis of the constituent proteins of normal and mutant embryonic hearts and other tissues is made by sodium dodecyl sulfate (SDS) gel electrophoresis. These experiments are in full agreement with the morphological and HMM binding studies. The gels show distinct 42,000-dalton bands for both normal and mutant hearts, supporting the presence of normal actin. During early developmental stages (Harrison's stage 34) the cardiac tissues in normal and mutant siblings have indistinguishable banding patterns, but with increasing development several differences appear. Myosin heavy chain (200,000 daltons) increases substantially in normal hearts during development but very little in mutants. Even so the quantity of 200,000-dalton protein in mutant hearts is significantly more than in any of the nonmuscle tissues studied (i.e. gut, liver, brain). Unlike normal hearts, the mutant hearts lack a prominent 34,000-dalton band, indicating that if mutants contain muscle tropomyosin at all, it is present in drastically reduced amounts. Also, mutant hearts retain large amounts of yolk proteins at stages when the platelets have virtually disappeared from normal hearts. The morphologies and electrophoresis patterns of skeletal muscle from normal and mutant siblings are identical, confirming that gene c affects only heart muscle differentiation and not skeletal muscle. The results of the study suggest that the precardiac mesoderm in cardiac lethal mutant axolotl embryos initiates but then fails to complete its differentiation into functional muscle tissue. It appears that this single gene mutation, by way of abnormal inductive processes, affects the accumulation and organization of several different muscle proteins, including actin, myosin, and tropomyosin. PMID:1107335
Investigation of Pokemon-regulated proteins in hepatocellular carcinoma using mass spectrometry-based multiplex quantitative proteomics.
Bi, Xin; Jin, Yibao; Gao, Xiang; Liu, Feng; Gao, Dan; Jiang, Yuyang; Liu, Hongxia
Pokemon is a transcription regulator involved in embryonic development, cellular differentiation and oncogenesis. It is aberrantly overexpressed in multiple human cancers including Hepatocellular carcinoma (HCC) and is considered as a promising biomarker for HCC. In this work, the isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy was used to investigate the proteomic profile associated with Pokemon in human HCC cell line QGY7703 and human hepatocyte line HL7702. Samples were labeled with four-plex iTRAQ reagents followed by two-dimensional liquid chromatography coupled with tandem mass spectrometry analysis. A total of 24 differentially expressed proteins were selected as significant. Nine proteins were potentially up-regulated by Pokemon while 15 proteins were potentially down-regulated and many proteins were previously identified as potential biomarkers for HCC. Gene ontology (GO) term enrichment revealed that the listed proteins were mainly involved in DNA metabolism and biosynthesis process. The changes of glucose-6-phosphate 1-dehydrogenase (G6PD, up-regulated) and ribonucleoside-diphosphate reductase large sub-unit (RIM1, down-regulated) were validated by Western blotting analysis and denoted as Pokemon's function of oncogenesis. We also found that Pokemon potentially repressed the expression of highly clustered proteins (MCM3, MCM5, MCM6, MCM7) which played key roles in promoting DNA replication. Altogether, our results may help better understand the role of Pokemon in HCC and promote the clinical applications. PMID:24261083
Determination of opium alkaloids in crude opium using non-aqueous capillary electrophoresis
Inga Bjornsdottir; Steen Honorķ Hansen
A method for the quantitative determination of the opium alkaloids morphine, codeine, thebaine, noscapine and papaverine in crude opium and in drug preparations based on non-aqueous capillary electrophoresis has been developed. The non-aqueous mode provides high separation selectivity and new possibilities for regulating the selectivity in capillary electrophoresis. The nature of the organic solvent, the acidity of the electrolytes as
Qualitative and quantitative changes in exoskeletal proteins synthesized throughout the molt cycle of the Bermuda land crab
Stringfellow, L.A.; Skinner, D.M.
During the premolt period in Crustacea, a single layer of epidermal cells that underlies the exoskeleton is thought to be responsible for the degradation of the old exoskeleton and synthesis of a new one. In order to identify molt-specific proteins and their temporal appearance, they cultured epidermis and associated integumentary tissue from the gill chambers of crab in vitro in the presence of one of three radiolabeled amino acids. Autoradiographs of (/sup 35/S)Met-labeled tissues indicate a low level of synthesis in epidermal cells of intermolt animals; synthesis increases during premolt and stage B of postmolt. Label is also found in the innermost layer of the old exoskeleton while it is being degraded and in new exoskeletal layers during their synthesis. Fluorographs of gels of integumentary proteins show marked quantitative changes in 44 and 56 kD proteins late in premolt. Qualitative changes include synthesis of 46 and 48 kD proteins during late premolt and three proteins (all of approx. 170 kD) detectable only in postmolt. Solubilized gel slices of (/sup 3/H)Leu-labeled proteins indicate maximum synthesis at an earlier premolt stage than seen in Met-labeled proteins. Other proteins of 20, 24, 29, 32, and 96 kD are synthesized in a stage-dependent manner while (/sup 3/H)Tyr labels small proteins that appear only in late premolt.
Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction
Wang, Li; Carnegie, Graeme K.
Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells. BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction. PMID:23979513
Identification of the Hepatic Protein Targets of Reactive Metabolites of Acetaminophen in Vivo in Mice Using Two-dimensional Gel Electrophoresis and Mass Spectrometry
Yongchang Qiu; Leslie Z. Benet; Alma L. Burlingame
Liver toxicity following an overdose of acetamino- phen is frequently considered a model for drug-induced hepatotoxicity. Extensive studies over many years have established that such toxicity is well correlated with liver protein arylation by acetaminophen metabolites. Identification of protein targets for covalent modifica- tions is a challenging but necessary step in understand- ing how covalent binding could lead to liver
A 1Hour Enzyme-Linked Immunosorbent Assay for Quantitation of Acrolein and Hydroxynonenal-Modified Proteins by Epitope-Bound Casein Matrix Method
Kimihiko Satoh; Satoshi Yamada; Yukiko Koike; Yasuo Igarashi; Shinya Toyokuni; Takayuki Kumano; Takenori Takahata; Makoto Hayakari; Shigeki Tsuchida; Koji Uchida
A simple and rapid enzyme-linked immunosorbent assay (ELISA) method for quantitation of acrolein and 4-hydroxy-2-nonenal (HNE)-modified proteins was developed. Microtiter plate wells were precoated and blocked simultaneously with epitope-bound bovine caseins as matrix proteins, and aldehyde-modified proteins were quantitated by a competition assay with a monoclonal antibody specific for acrolein-modified lysine or HNE-modified histidine epitopes. Minimal reaction times required for
Multiplexed capillary electrophoresis system
Yeung, Edward S. (Ames, IA); Li, Qingbo (Ames, IA); Lu, Xiandan (Ames, IA)
The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.
Multiplexed capillary electrophoresis system
Yeung, Edward S. (Ames, IA); Chang, Huan-Tsang (Silver Spring, MD); Fung, Eliza N. (Ames, IA); Li, Qingbo (Ames, IA); Lu, Xiandan (Ames, IA)
The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.
Multiplexed capillary electrophoresis system
Yeung, E.S.; Li, Q.; Lu, X.
The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.
Multiplexed capillary electrophoresis system
Yeung, E.S.; Chang, H.T.; Fung, E.N.; Li, Q.; Lu, X.
The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.
odium dodecyl sulfate polyacry-lamide gel electrophoresis (SDS-
Lebendiker, Mario
been attributed to three innovations that permit- ted the correlation of electrophoretic mobil- ity) and reducing agents to denature pro- teins (7). SDS binds strongly to proteins at an approximate ratio of 1-Cl 10 inNovations 13 Preparation of protein samples for SDS-polyacrylamide gel electrophoresis
Improved Methodical Approach for Quantitative BRET Analysis of G Protein Coupled Receptor Dimerization
Szalai, Bence; Hoffmann, Pķter; Prokop, Susanne; Erdķlyi, Lßszl¾; Vßrnai, Pķter; Hunyady, Lßszl¾
G Protein Coupled Receptors (GPCR) can form dimers or higher ordered oligomers, the process of which can remarkably influence the physiological and pharmacological function of these receptors. Quantitative Bioluminescence Resonance Energy Transfer (qBRET) measurements are the gold standards to prove the direct physical interaction between the protomers of presumed GPCR dimers. For the correct interpretation of these experiments, the expression of the energy donor Renilla luciferase labeled receptor has to be maintained constant, which is hard to achieve in expression systems. To analyze the effects of non-constant donor expression on qBRET curves, we performed Monte Carlo simulations. Our results show that the decrease of donor expression can lead to saturation qBRET curves even if the interaction between donor and acceptor labeled receptors is non-specific leading to false interpretation of the dimerization state. We suggest here a new approach to the analysis of qBRET data, when the BRET ratio is plotted as a function of the acceptor labeled receptor expression at various donor receptor expression levels. With this method, we were able to distinguish between dimerization and non-specific interaction when the results of classical qBRET experiments were ambiguous. The simulation results were confirmed experimentally using rapamycin inducible heterodimerization system. We used this new method to investigate the dimerization of various GPCRs, and our data have confirmed the homodimerization of V2 vasopressin and CaSR calcium sensing receptors, whereas our data argue against the heterodimerization of these receptors with other studied GPCRs, including type I and II angiotensin, ?2 adrenergic and CB1 cannabinoid receptors. PMID:25329164
Continuous Signal Enhancement for Sensitive Aptamer Affinity Probe Electrophoresis Assay Using Electrokinetic Concentration
Cheow, Lih Feng; Han, Jongyoon
We describe an electrokinetic concentration-enhanced aptamer affinity probe electrophoresis assay to achieve highly sensitive and quantitative detection of protein targets in a microfluidic device. The key weaknesses of aptamer as a binding agent (weak binding strength/fast target dissociation) were counteracted by continuous injection of fresh sample while band-broadening phenomena were minimized due to self-focusing effects. With 30 minutes of continuous signal enhancement, we can detect 4.4 pM of human immunoglobulin E (IgE) and 9 pM of human immunodifficiency virus 1 reverse transcriptase (HIV-1 RT), which is among the lowest limit of detection (LOD) reported. IgE was detected in serum sample with LOD of 39 pM due to nonspecific interactions between aptamers and serum proteins. The method presented in this paper also has broad applicability to improve sensitivities of various other mobility shift assays. PMID:21809885
High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis Reveals a Glucose-Response Protein of 65 kDa in Pancreatic Islet Cells
Heather Weik Collins; Carol Buettger; Franz Matschinsky
High-resolution two-dimensional PAGE was used to search for glucose-response proteins in isolated pancreatic islets that were labeled with [35S]methionine at ambient glucose concentrations of 0-18 mM. A 65-kDa protein, isoelectric focusing point of approximately 6.6-7.0, was discovered that showed at least a 20-fold stimulation of radiolabeling when glucose in the labeling medium was increased from 3 to 18 mM, in
Detection of phosphorylated forms of Moloney murine leukemia virus major capsid protein p30 by immunoprecipitation and two-dimensional gel electrophoresis.
Ikuta, K; Luftig, R B
We detected phosphorylation of the major Moloney murine leukemia virus (M-MuLV) capsid polypeptide, p30, by using 32Pi-labeled virions. This was observed both on two-dimensional polyacrylamide gels directly or on one-dimensional gels of viral lysates that had been immunoprecipitated with monospecific goat anti-p30 serum. The phosphorylation event had been difficult to detect because pp12 the major virion phosphoprotein incorporates almost all of the 32P label added to infected cells (Y. Yoshinaka and R. B. Luftig, Virology 116:181-195, 1982). When immunoprecipitates from M-MuLV lysates labeled with 32Pi were compared with those labeled with [35S]methionine, it was calculated that the degree of phosphorylation at the p30 domain of Pr65gag was only 0.22 to 0.54% relative to phosphorylation at the p12 domain. Two-dimensional gel electrophoresis of the 32P-labeled p30 immunoprecipitates showed that there were three phosphorylated p30 forms with isoelectric points (pIs) of 5.7, 5.8, and 6.0. These forms were generally more acidic than the [35S]methionine-labeled p30 forms, which had pIs of 6.0, 6.1, 6.3 (the major constituent with greater than 80% of the label), and 6.6. The predominant phosphoamino acid of the major phosphorylated p30 form (pI 5.8) was phosphoserine. Further, tryptic peptide analysis of this p30 form showed that only one peptide was predominantly phosphorylated. Based on a comparison of specific labeling of p30 tryptic peptides with [14C]serine, [35S]methionine, and 32Pi, we tentatively assigned the phosphorylation site to a 2.4-kilodalton NH2-terminal peptide containing triple tandem serines spanning the region from amino acids 4 to 24. Images PMID:3334749
Protein Quantitation using Fluorescence Total protein content is a measurement common to many applications in basic science and
Raizada, Manish N.
purified or different samples are being compared. Regardless of the method of protein determination, Vermont 05404-0998 USA COPYRIGHT ® 2006 TEL: 888-451-5171 FAX: 802-655-7941 Outside the USA: 802-655 instructions (2). After dilution of the protein sample, the protein solution was incubated for 10 minutes at 95
A new approach to electrophoresis in space
NASA Technical Reports Server (NTRS)
Snyder, Robert S.; Rhodes, Percy H.
Previous electrophoresis experiments performed in space are reviewed. There is sufficient data available from the results of these experiments to show that they were designed with incomplete knowledge of the fluid dynamics of the process including electrohydrodynamics. Redesigning laboratory chambers and operating procedures developed on Earth for space without understanding both the advantages and disadvantages of the microgravity environment has yielded poor separations of both cells and proteins. However, electrophoreris is still an important separation tool in the laboratory and thermal convection does limit its performance. Thus, there is a justification for electrophoresis but the emphasis of future space experiments must be directed toward basic research with model experiments to understand the microgravity environment and fluid analysis to test the basic principles of the process.
Quantitative changes in yolk protein and other components in the ovary and testis of the sea urchin Pseudocentrotus depressus.
Unuma, T; Yamamoto, T; Akiyama, T; Shiraishi, M; Ohta, H
Both male and female sea urchins accumulate the major yolk protein (MYP; the most abundant yolk granule protein in sea urchin eggs) in the nutritive phagocytes of immature gonads before gametogenesis. In this study, quantitative changes in MYP as well as in other biochemical components in the ovary and testis were examined in the course of gametogenesis in Pseudocentrotus depressus. Before gametogenesis, both the ovary and testis contained large quantities of proteins, lipids and polysaccharides. MYP reached about 80% of total protein in both sexes. In the testis, MYP decreased rapidly as spermatogenesis proceeded, and the fully mature testis contained little MYP; the levels of lipids and polysaccharides also decreased. In contrast, the levels of nucleic acids and proteins other than MYP increased markedly. In the ovary, MYP decreased gradually as oogenesis proceeded, and the fully mature ovary contained less than half of the initial amount of MYP. Polysaccharides also decreased, whereas proteins other than MYP increased. These results, taken together with those from other studies, suggest that MYP serves as a protein reserve that accumulates before gametogenesis and is used as material for synthesizing new substances constituting gametes in both male and female sea urchins. PMID:12477906
Capillary electrophoresis in clinical chemistry
Rainer Lehmann; Wolfgang Voelter; Hartmut M. Liebich
Since its introduction, capillary electrophoresis has diversified, spreading out into different specialized fields covering solutions for almost any analytical questions arising in research laboratories. In the context of clinical chemistry, results must be provided at low costs and in a clinically relevent time frame; however, the attributes which have made capillary electrophoresis such a successful tool in basic research are
Fluorogenic Tagging of Peptide and Protein 3-Nitrotyrosine with 4-(Aminomethyl)-benzenesulfonic Acid for Quantitative Analysis of Protein Tyrosine Nitration.
Sharov, Victor S; Dremina, Elena S; Galeva, Nadezhda A; Gerstenecker, Gary S; Li, Xiaobao; Dobrowsky, Rick T; Stobaugh, John F; Sch÷neich, Christian
Protein 3-nitrotyrosine (3-NT) has been recognized as an important biomarker of nitroxidative stress associated with inflammatory and degenerative diseases, and biological aging. Analysis of protein-bound 3-NT continues to represent a challenge since in vivo it frequently does not accumulate on proteins in amounts detectable by quantitative analytical methods. Here, we describe a novel approach of fluorescent tagging and quantitation of peptide-bound 3-NT residues based on the selective reduction to 3-AT followed by reaction with 4-(amino-methyl)benzenesulfonic acid (ABS) in the presence of K(3)Fe(CN)(6) to form a highly fluorescent 2-phenylbenzoxazole product. Synthetic 3-NT peptide (0.005-1 ?M) upon reduction with 10 mM sodium dithionite and tagging with 2 mM ABS and 5 ?M K(3)Fe(CN)(6) in 0.1 M Na(2)HPO(4) buffer (pH 9.0) was converted with yields >95% to a single fluorescent product incorporating two ABS molecules per 3-NT residue, with fluorescence excitation and emission maxima at 360 ▒ 2 and 490 ▒ 2 nm, respectively, and a quantum yield of 0.77 ▒ 0.08, based on reverse-phase LC with UV and fluorescence detection, fluorescence spectroscopy and LC-MS-MS analysis. This protocol was successfully tested for quantitative analysis of in vitro Tyr nitration in a model protein, rabbit muscle phosphorylase b, and in a complex mixture of proteins from C2C12 cultured cells exposed to peroxynitrite, with a detection limit of ca. 1 pmol 3-NT by fluorescence spectrometry, and an apparent LOD of 12 and 40 pmol for nitropeptides alone or in the presence of 100 ?g digested cell proteins, respectively. LC-MS-MS analysis of ABS tagged peptides revealed that the fluorescent derivatives undergo efficient backbone fragmentations, allowing for sequence-specific characterization of protein Tyr nitration in proteomic studies. Fluorogenic tagging with ABS also can be instrumental for detection and visualization of protein 3-NT in LC and gel-based protein separations. PMID:20703364
Fluorogenic Tagging of Peptide and Protein 3-Nitrotyrosine with 4-(Aminomethyl)-benzenesulfonic Acid for Quantitative Analysis of Protein Tyrosine Nitration
Sharov, Victor S.; Dremina, Elena S.; Galeva, Nadezhda A.; Gerstenecker, Gary S.; Li, Xiaobao; Dobrowsky, Rick T.; Stobaugh, John F.
Protein 3-nitrotyrosine (3-NT) has been recognized as an important biomarker of nitroxidative stress associated with inflammatory and degenerative diseases, and biological aging. Analysis of protein-bound 3-NT continues to represent a challenge since in vivo it frequently does not accumulate on proteins in amounts detectable by quantitative analytical methods. Here, we describe a novel approach of fluorescent tagging and quantitation of peptide-bound 3-NT residues based on the selective reduction to 3-AT followed by reaction with 4-(amino-methyl)benzenesulfonic acid (ABS) in the presence of K3Fe(CN)6 to form a highly fluorescent 2-phenylbenzoxazole product. Synthetic 3-NT peptide (0.005¢1 ?M) upon reduction with 10 mM sodium dithionite and tagging with 2 mM ABS and 5 ?M K3Fe(CN)6 in 0.1 M Na2HPO4 buffer (pH 9.0) was converted with yields >95% to a single fluorescent product incorporating two ABS molecules per 3-NT residue, with fluorescence excitation and emission maxima at 360 ▒ 2 and 490 ▒ 2 nm, respectively, and a quantum yield of 0.77 ▒ 0.08, based on reverse-phase LC with UV and fluorescence detection, fluorescence spectroscopy and LC¢MS¢MS analysis. This protocol was successfully tested for quantitative analysis of in vitro Tyr nitration in a model protein, rabbit muscle phosphorylase b, and in a complex mixture of proteins from C2C12 cultured cells exposed to peroxynitrite, with a detection limit of ca. 1 pmol 3-NT by fluorescence spectrometry, and an apparent LOD of 12 and 40 pmol for nitropeptides alone or in the presence of 100 ?g digested cell proteins, respectively. LC¢MS¢MS analysis of ABS tagged peptides revealed that the fluorescent derivatives undergo efficient backbone fragmentations, allowing for sequence-specific characterization of protein Tyr nitration in proteomic studies. Fluorogenic tagging with ABS also can be instrumental for detection and visualization of protein 3-NT in LC and gel-based protein separations. PMID:20703364
Direct real-time quantitative PCR for measurement of host-cell residual DNA in therapeutic proteins.
Peper, Grit; Fankhauser, Alexander; Merlin, Thomas; Roscic, Ana; Hofmann, Matthias; Obrdlik, Petr
Real-time quantitative PCR (qPCR) is important for quantification of residual host cell DNA (resDNA) in therapeutic protein preparations. Typical qPCR protocols involve DNA extraction steps complicating sample handling. Here, we describe a "direct qPCR" approach without DNA extraction. To avoid interferences of DNA polymerase with a therapeutic protein, proteins in the samples were digested with proteinase K (PK) in the presence of sodium dodecyl sulfate (SDS). Tween 20 and NaCl were included to minimize precipitation of therapeutic proteins in the PK/SDS mix. After PK treatment, the solution was applied directly for qPCR. Inhibition of DNA polymerase by SDS was prevented by adding 2% (v/v) of Tween 20 to the final qPCR mix. The direct qPCR approach was evaluated for quantification of resDNA in therapeutic proteins manufactured in Chinese hamster ovary (CHO) host cells. First, direct qPCR was compared with qPCR applied on purified DNA ("extraction qPCR"). For both qPCRs, the same CHO-specific primers and probes were used. Comparable residual DNA levels were detected with both PCR approaches in purified and highly concentrated drug proteins as well as in in-process-control samples. Finally, the CHO-specific direct qPCR protocol was validated according to ICH guidelines and applied for 25 different therapeutic proteins. The specific limits of quantification were 0.1-0.8ppb for 24 proteins, and 2.0ppb for one protein. General applicability of the direct qPCR was demonstrated by applying the sample preparation protocol for quantification of resDNA in therapeutic proteins manufactured in other hosts such as Escherichia coli and mouse cells. PMID:25151232
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation
Pan, Chongle [ORNL; Kora, Guruprasad H [ORNL; McDonald, W Hayes [ORNL; Tabb, Dave L [ORNL; Verberkmoes, Nathan C [ORNL; Hurst, Gregory {Greg} B [ORNL; Pelletier, Dale A [ORNL; Samatova, Nagiza F [ORNL; Hettich, Robert {Bob} L [ORNL
A profile likelihood algorithm is proposed for quantitative shotgun proteomics to infer the abundance ratios of proteins from the abundance ratios of isotopically labeled peptides derived from proteolysis. Previously, we have shown that the estimation variability and bias of peptide abundance ratios can be predicted from their profile signal-to-noise ratios. Given multiple quantified peptides for a protein, the profile likelihood algorithm probabilistically weighs the peptide abundance ratios by their inferred estimation variability, accounts for their expected estimation bias, and suppresses contribution from outliers. This algorithm yields maximum likelihood point estimation and profile likelihood confidence interval estimation of protein abundance ratios. This point estimator is more accurate than an estimator based on the average of peptide abundance ratios. The confidence interval estimation provides an "error bar" for each protein abundance ratio that reflects its estimation precision and statistical uncertainty. The accuracy of the point estimation and the precision and confidence level of the interval estimation were benchmarked with standard mixtures of isotopically labeled proteomes. The profile likelihood algorithm was integrated into a quantitative proteomics program, called ProRata, freely available at www.MSProRata.org.
A quantitative method for detecting deposits of amyloid A protein in aspirated fat tissue of patients with arthritis
Hazenberg, B.; Limburg, P.; Bijzet, J.; van Rijswijk, M. H
OBJECTIVEŚTo describe a new, quantitative, and reproducible method for detecting deposits of amyloid A protein in aspirated fat tissue and to compare it with smears stained with Congo red.?METHODSŚAfter extraction of at least 30Āmg of abdominal fat tissue in guanidine, the amyloid A protein concentration was measured by a monoclonal antibody-based sandwich ELISA.?RESULTSŚThe concentrations in 24Āpatients with arthritis and AA amyloidosis (median 236,Ārange 1.1-8530 ng/mg tissue) were higher (p<0.001) than in non-arthritic controls, uncomplicated rheumatoid arthritis, and other types of systemic amyloidosis (median 1.1,Ārange 1.1-11.6 ng/mg tissue). Patients with extensive deposits, according to Congo red staining, had higher concentrations than patients with minute deposits.?CONCLUSIONŚThis is a new, quantitative, and reproducible method for detecting deposits of amyloid A protein in aspirated fat tissue of patients with arthritis, even when minute deposits are present as detected in smears stained with Congo red.?? Keywords: amyloid A protein; fat tissue; arthritis PMID:10343524
Measurement of local rates of brain protein synthesis by quantitative autoradiography: validation with L-(/sup 3/H)valine
Dwyer, B.E.; Donatoni, P.; Wasterlain, C.G.
Following the injection of 4-day old rats with 150 mM L-(3,4-/sup 3/H)valine (10 mumol/g, IP) the incorporation of /sup 3/H into protein was linear 2 hours. Valine specific activity in the brain acid-soluble fraction was constant between 30 and 120 min after injection with a mean value of 82.3% of the injectate. Significant amounts of tritated metabolites accumulated in the brain acid-soluble fraction (41.4% of radioactivity at 120 min) but do not prove an impediment to measuring rates of protein synthesis. The rate of protein synthesis in cerebral cortex of the 4-day old rat was measured by quantitative autoradiography using (/sup 3/H)valine and /sup 3/H-sensitive film. The measured rate shows excellent agreement with that found previously using L-(1-/sup 14/C)valine. Our results suggest that (/sup 3/H)valine can be a useful precursor to measure local rates of brain protein synthesis by quantitative autoradiography.
High throughput microchip-based separation and quantitation of high-molecular-weight glutenin subunits
L. Rhazi; A.-L. Bodard; B. Fathollahi; T. Aussenac
Knowledge of glutenin subunit composition is important for the prediction of the genetic potential of breeding lines as these proteins are known to be responsible for the main differences in bread-making quality. In this study, a commercial high throughput microchip capillary electrophoresis-sodium dodecyl sulfate (microchip CE) platform, LabChip 90, was evaluated for qualitative and quantitative analyses of HMW-GS. 130 French
Serum globulin electrophoresis
... blood sample is needed. At the lab, the technician places the blood sample on special paper and applies an electric current. The proteins move on the paper and form bands that show the amount of each protein.
Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis
Alexander Krah; Frank Schmidt; Dorte Becher; Monika Schmid; Dirk Albrecht; Axel Rack; Knut Buttner; Peter R. Jungblut
Helicobacter pylori is a causative agent of severe dis- eases of the gastric tract ranging from chronic gastritis to gastric cancer. Cellular proteins of H. pylori were sepa- rated by high resolution two-dimensional gel electro- phoresis. A dataset of 384 spots was automatically picked, digested, spotted, and analyzed by matrix-as- sisted laser desorption ionization mass spectrometry peptide mass fingerprint in
Static continuous electrophoresis device
NASA Technical Reports Server (NTRS)
Rhodes, P. H. (inventor)
An apparatus is disclosed for carrying out a moving wall type electrophoresis process for separation of cellular particles. The apparatus includes a water-tight housing containing an electrolytic buffer solution. A separation chamber in the housing is defined by spaced opposed moving walls and spaced opposed side walls. Substrate assemblies, which support the moving wall include vacuum ports for positively sealing the moving walls against the substrate walls. Several suction conduits communicate with the suction ports and are arranged in the form of valleys in a grid plate. The raised land portion of the grid plat supports the substrate walls against deformation inwardly under suction. A cooling chamber is carried on the back side of plate. The apparatus also has tensioner means including roller and adjustment screws for maintaining the belts in position and a drive arrangement including an electric motor with a gear affixed to its output shaft. Electrode assemblies are disposed to provide the required electric field.
Development of a chip-based capillary gel electrophoresis method for quantification of a half-antibody in immunoglobulin G4 samples.
Vasilyeva, Elena; Woodard, James; Taylor, Frederick R; Kretschmer, Matthias; Fajardo, Hans; Lyubarskaya, Yelena; Kobayashi, Kazumi; Dingley, Amy; Mhatre, Rohin
A method based on microfluidic technology was developed to support quantitative analysis of recombinant monoclonal immunoglobulin G4 (IgG4) antibody samples. The assay was performed on an Agilent 2100 Bioanalyzer in combination with the Protein 200 Plus LabChip Kit and the Protein 200 Plus assay software. Capillary electrophoresis principles have been transferred to a chip format that integrates all separation, staining, virtual destaining, and detection steps. The method is referred to in this paper as chip-based capillary gel electrophoresis (GelChip-CE method). The GelChip-CE method under nonreducing conditions proved to be a quantitative test for half-antibody determination in IgG4 samples. Similar to the traditional nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method, the GelChip-CE method includes a denaturing step prior to separation. We showed that denaturing the sample by heating resulted in an artificial increase in the amount of half-antibody detected, which could be prevented by addition of N-ethylmaleimide to the sample buffer. The GelChip-CE method allowed for analysis of IgG4 samples with more accuracy, higher precision, and a faster turnaround time than SDS-PAGE and reversed-phase high-performance liquid chromatography (RP-HPLC). PMID:15565674
Quantitative feature extraction reveals the status quo of protein fibrillation in the cell nucleus.
Arnhold, Florian; von Mikecz, Anna
Stepwise fibrillation of otherwise soluble proteins to insoluble amyloid-like protein aggregates is a hallmark of neurodegenerative protein-misfolding diseases including Alzheimer's, polyglutamine diseases, and the prion encephalopathies. Investigation of protein aggregation mechanisms has considerably advanced in vitro due to recent technical innovation, whereas the development of analyses tools for intracellular protein fibrillation remains a major challenge. Here, we introduce a method that enables monitoring of the protein fibrillation status in the cell nucleus. We show that the amyloid indicator Congo red can be induced to bind to distinct nucleoplasmic microdomains that are describable by application of discrete mathematics on the image information. Since formation of Congo red-binding nuclear microdomains (CRBDs) correlates with increased amyloid formation and decreased solubility of endogenous proteins with homopolymeric polyglutamine (polyQ) stretches we introduce the idea that different protein fibrillation steps can be characterized intracellularly by graph theory-aided pattern recognition. PMID:21687851
Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
Zhou, Kang
Background: Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. ...
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein
Liu, Jiajian; Stormo, Gary D
Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely true, an additive model over the DNA positions can be a good approximation, at least for some proteins. Much less information is available about whether the protein positions contribute additively to the interaction. Results Using EGR zinc finger proteins, we measure the binding affinity of six different variants of the protein to each of six different variants of the consensus binding site. Both the protein and binding site variants include single and double mutations that allow us to assess how well additive models can account for the data. For each protein and DNA alone we find that additive models are good approximations, but over the combined set of data there are context effects that limit their accuracy. However, a small modification to the purely additive model, with only three additional parameters, improves the fit significantly. Conclusion The additive model holds very well for every DNA site and every protein included in this study, but clear context dependence in the interactions was detected. A simple modification to the independent model provides a better fit to the complete data. PMID:16014175
Diversity and systematics of Deschampsia sensu lato ( Poaceae ), inferred from karyotypes, protein electrophoresis, total genomic DNA hybridization and chloroplast DNA analysis
R. Garcia-Suarez; C. Alonso-Blanco; M. C. Fernandez-Carvajal; J. A. Fernandez-Prieto; A. Roca; R. Giraldez
We have analyzed the C-banding karyotypes, electrophoretic mobility of isozymes and seed proteins, total genomic DNA hybridization and chloroplast DNA ofAristavena setacea, Deschampsia cespitosa, D. media, Avenella flexuosa andA. stricta, which had been previously considered as belonging to the genusDeschampsiaBeauv. s. l., in order to determine their taxonomic relationships. The results obtained with these different approaches indicate thatAvenella diverges substantially
Polygonum hydropiper crude root extract mimics estrogenic properties in females: Evidence of uterine protein profiles studied by sodium dodecyl sulfate polyacrylamide gel electrophoresis
Ajit Hazarika; Hirendra N. Sarma
Polygonum hydropiper is a widely grown weed in the north-eastern states of India. In the present study, estrogenic effects of the crude root extract\\u000a (CRE) ofPolygonum hydropiper on uterine protein was tested in ovary-intact and ovariectomized (OVX) female albino rats. The methanolic crude extract ofPolygonum hydropiper was given to adult ovary-intact and OVX female albino rat in a dose of
Comparative and quantitative proteomic analysis of normal and degenerated human annulus fibrosus cells.
Ye, Dongping; Liang, Weiguo; Dai, Libing; Zhou, Longqiang; Yao, Yicun; Zhong, Xin; Chen, Honghui; Xu, Jiake
Degeneration of the intervertebral disc (IVD) is a major chronic medical condition associated with back pain. To better understand the pathogenesis of IVD degeneration, we performed comparative and quantitative proteomic analyses of normal and degenerated human annulus fibrosus (AF) cells and identified proteins that are differentially expressed between them. Annulus fibrosus cells were isolated and cultured from patients with lumbar disc herniation (the experimental group, degenerated AF cells) and scoliosis patients who underwent orthopaedic surgery (the control group, normal AF cells). Comparative proteomic analyses of normal and degenerated cultured AF cells were carried out using 2-D electrophoresis, mass spectrometric analyses, and database searching. Quantitative analyses of silver-stained 2-D electrophoresis gels of normal and degenerated cultured AF cells identified 10 protein spots that showed the most altered differential expression levels between the two groups. Among these, three proteins were decreased, including heat shock cognate 71-kDa protein, glucose-6-phosphate 1-dehydrogenase, and protocadherin-23, whereas seven proteins were increased, including guanine nucleotide-binding protein G(i) subunit ?-2, superoxide dismutase, transmembrane protein 51, adenosine receptor A3, 26S protease regulatory subunit 8, lipid phosphate phosphatase-related protein, and fatty acyl-crotonic acid reductase 1. These differentially expressed proteins might be involved in the pathophysiological process of IVD degeneration and have potential values as biomarkers of the degeneration of IVD. PMID:25739836
Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action
Wang, Pengcheng; Xue, Liang; Batelli, Giorgia; Lee, Shinyoung; Hou, Yueh-Ju; Van Oosten, Michael J.; Zhang, Huiming; Tao, W. Andy; Zhu, Jian-Kang
Sucrose nonfermenting 1 (SNF1)-related protein kinase 2s (SnRK2s) are central components of abscisic acid (ABA) signaling pathways. The snrk2.2/2.3/2.6 triple-mutant plants are nearly completely insensitive to ABA, suggesting that most of the molecular actions of ABA are triggered by the SnRK2s-mediated phosphorylation of substrate proteins. Only a few substrate proteins of the SnRK2s are known. To identify additional substrate proteins of the SnRK2s and provide insight into the molecular actions of ABA, we used quantitative phosphoproteomics to compare the global changes in phosphopeptides in WT and snrk2.2/2.3/2.6 triple mutant seedlings in response to ABA treatment. Among the 5,386 unique phosphorylated peptides identified in this study, we found that ABA can increase the phosphorylation of 166 peptides and decrease the phosphorylation of 117 peptides in WT seedlings. In the snrk2.2/2.3/2.6 triple mutant, 84 of the 166 peptides, representing 58 proteins, could not be phosphorylated, or phosphorylation was not increased under ABA treatment. In vitro kinase assays suggest that most of the 58 proteins can serve as substrates of the SnRK2s. The SnRK2 substrates include proteins involved in flowering time regulation, RNA and DNA binding, miRNA and epigenetic regulation, signal transduction, chloroplast function, and many other cellular processes. Consistent with the SnRK2 phosphorylation of flowering time regulators, the snrk2.2/2.3/2.6 triple mutant flowered significantly earlier than WT. These results shed new light on the role of the SnRK2 protein kinases and on the downstream effectors of ABA action, and improve our understanding of plant responses to adverse environments. PMID:23776212
Identification of O-linked N-Acetylglucosamine Proteins in Rat Skeletal Muscle Using Two-dimensional Gel Electrophoresis and Mass Spectrometry
Caroline Cieniewski-Bernard; Bruno Bastide; Tony Lefebvre; Yvonne Mounier; Jean-Claude Michalski
O-linked N-acetylglucosaminylation (O-GlcNAc) is a reg- ulatory post-translational modification of nucleo-cyto- plasmic proteins that has a complex interplay with phos- phorylation. O-GlcNAc has been described as a nutritional sensor, the level of UDP-GlcNAc that serves as a donor for the uridine diphospho-N-acetylglucosamine:polypep- tide -N-acetyl-glucosaminyltransferase being regulated by the cellular fate of glucose. Because muscular contrac- tion is both dependent on
Quantitative analysis of human cerebrospinal fluid proteins using a combination of cysteine tagging and amine-reactive isobaric labeling.
Giron, Priscille; Dayon, Lo'c; Turck, Natacha; Hoogland, Christine; Sanchez, Jean-Charles
Highly complex and dynamic protein mixtures are hardly comprehensively resolved by direct shotgun proteomic analysis. As many proteins of biological interest are of low abundance, numerous analytical methodologies have been developed to reduce sample complexity and go deeper into proteomes. The present work describes an analytical strategy to perform cysteinyl-peptide subset enrichment and relative quantification through successive cysteine and amine-isobaric tagging. A cysteine-reactive covalent capture tag (C│T) allowed derivatization of cysteines and specific isolation on a covalent capture (CC) resin. The 6-plex amine-reactive tandem mass tags (TMT) served for relative quantification of the targeted peptides. The strategy was first evaluated on a model protein mixture with increasing concentrations to assess the specificity of the enrichment and the quantitative performances of the workflow. It was then applied to human cerebrospinal fluid (CSF) from post-mortem and ante-mortem samples. These studies confirmed the specificity of the C│T and the CC technique to cysteine-containing peptides. The model protein mixture analysis showed high precision and accuracy of the quantification with coefficients of variation and mean absolute errors of less than 10% on average. The CSF experiments demonstrated the potential of the strategy to study complex biological samples and identify differential brain-related proteins. In addition, the quantification data were highly correlated with a classical TMT experiment (i.e., without C│T cysteine-tagging and enrichment steps). Altogether, these results legitimate the use of this quantitative C│T strategy to enrich and relatively quantify cysteine-containing peptides in complex mixtures. PMID:20973565
Optimization of capillary electrophoresis?inductively coupled plasma mass spectrometry for species analysis of metallothionein-like proteins extracted from liver tissues of Elbe-bream and Roe deer
NASA Astrophysics Data System (ADS)
Pr÷frock, Daniel; Prange, Andreas; Schauml÷ffel, Dirk; Ruck, Wolfgang
Species analysis of metallothionein-like proteins (MLP) in liver tissues from Elbe-Bream ( Abramis brama L.) and Roe Deer ( Capreolus capreolus L.) using capillary electrophoresis (CE) combined with inductively coupled plasma mass spectrometry detection is described. In order to allow systematic development of the method, commercially available metallothionein (MT) preparations of rabbit liver were used. Optimum separation efficiency was obtained by investigating the influence of parameters such as voltage, capillary temperature, buffer concentration, buffer pH and the use of different buffer systems. Instrumental parameters such as CE capillary position, interface adjustment and contamination problems are also discussed. Separation was performed using uncoated fused silica capillaries with 75 ?m i.d. and 70 cm length. The optimum conditions were found to be: Separation voltage 30 kV, positive polarity, capillary temperature 288.15 K and a buffer concentration of 100 mmol l -1 Tricine-NH 3 adjusted to pH 7.2. Sample preparation was performed so as to minimize oxidation and heavy metal contamination of the samples. The high molecular mass protein matrix was reduced by acetonitrile precipitation. For commercial MT preparations the relative standard deviations (R.S.D) in the retention times were 0.9% for MT-1 and 1.9% for MT-2; the R.S.D.'s in the peak areas were less than 6% for MT-1 and 16% for MT-2, respectively. Under optimized conditions the MLPs in the real samples could be separated efficiently in less than 10 min. By comparison with the migration times of commercially available MT preparations, two of the observed peaks could be assigned to MT-1 and MT-2.
A capillary electrophoresis-tandem mass spectrometry methodology for the determination of non-protein amino acids in vegetable oils as novel markers for the detection of adulterations in olive oils.
Sßnchez-Hernßndez, Laura; Marina, Maria Luisa; Crego, Antonio L
A new analytical methodology based on capillary electrophoresis-mass spectrometry (CE-MS(2)) is presented in this work, enabling the identification and determination of six non-protein amino acids (ornithine, ?-alanine, GABA, alloisoleucine, citrulline and pyroglutamic acid) in vegetable oils. This methodology is based on a previous derivatization with butanol and subsequent separation using acidic conditions followed by on-line coupling to an ion trap analyzer for MS(2) detection established through an electrospray-coaxial sheath flow interface. The electrophoretic and interface parameters were optimized obtaining the separation of all compounds in less than 15 min and with resolutions higher than 5. The proposed method was validated by assessing its accuracy, precision (RSD<7% for corrected peak areas), LODs and LOQs (between 0.04-0.19 ng/g and 0.06-0.31 ng/g, respectively) and linearity range (R(2)>0.99), and it was used in order to identify the selected non-protein amino acids in soybean oils, sunflower oils, corn oils and extra virgin olive oils. MS(2) experiments performed the fingerprint fragmentation of these compounds allowing to corroborate ornithine and alloisoleucine in seed oils but not in olive oils. The method was applied to identify and quantify olive oil adulterations with soybean oil detecting in a single run the amino acids in mixtures up to 2% (w/w). The results showed a high potential in using these compounds as novel markers for the detection of adulterations of extra virgin olive oils with seed oils. Thus, the developed method could be considered a simple, rapid and reliable method for the quality evaluation of extra virgin olive oil permitting its authentication. PMID:21306720
Investigation of Protein-tyrosine Phosphatase 1B Function by Quantitative Proteomics
Philipp Mertins; H. Christian Eberl; Jorg Renkawitz; Jesper V. Olsen; Michel L. Tremblay; Matthias Mann; Axel Ullrich; Henrik Daub
Because of their antagonistic catalytic functions, protein- tyrosine phosphatases (PTPs) and protein-tyrosine ki- nases act together to control phosphotyrosine-mediated signaling processes in mammalian cells. However, unlike for protein-tyrosine kinases, little is known about the cel- lular substrate specificity of many PTPs because of the lack of appropriate methods for the systematic and de- tailed analysis of cellular PTP function. Even
Cytokine Analysis by Immunoaffinity Capillary Electrophoresis
Mendonca, Mark; Kalish, Heather
Immunoaffinity capillary electrophoresis (ICE) is a powerful tool used to detect and quantify target proteins of interest in complex biological fluids. The target analyte is captured and bound to antibodies immobilized onto the wall of a capillary, labeled in situ with a fluorescent dye, eluted and detected online using laser-induced fluorescence following electrophoretic separation. Here, we illustrate how to construct an immunoaffinity capillary and utilize it to run ICE in order to capture and quantify target cytokines and chemokines from a clinical sample. PMID:22976107
A quantitative proteomic analysis of the tegumental proteins from Schistosoma mansoni schistosomula reveals novel potential therapeutic targets.
Sotillo, Javier; Pearson, Mark; Becker, Luke; Mulvenna, Jason; Loukas, Alex
The tegument of Schistosoma mansoni plays an integral role in host-parasite interactions, particularly during the transition from the free-living cercariae to the intra-mammalian schistosomula stages. This developmental period is characterised by the transition from a trilaminate surface to a heptalaminate tegument that plays key roles in immune evasion, nutrition and excretion. Proteins exposed at the surface membranes of newly transformed schistosomula are therefore thought to be prime targets for the development of new vaccines and drugs for schistosomiasis. Using a combination of tegumental labelling and high-throughput quantitative proteomics, more than 450 proteins were identified on the apical membrane of S. mansoni schistosomula, of which 200 had significantly regulated expression profiles at different stages of schistosomula development in vitro, including glucose transporters, sterols, heat shock proteins, antioxidant enzymes and peptidases. Current vaccine antigens were identified on the apical membrane (Sm-TSP-1, calpain) or sub-tegumental (Sm-TSP-2, Sm29) fractions of the schistosomula, displaying localisation patterns that, in some cases, differ from that in the adult stage fluke. This work provides the first known in-depth proteomic analysis of the surface-exposed proteins in the schistosomula tegument, and some of the proteins identified are clear targets for the generation of new vaccines and drugs against schistosomiasis. PMID:25910674
iTRAQ-Based Quantitative Proteomic Analysis on S100 Calcium Binding Protein A2 in Metastasis of Laryngeal Cancer
Zha, Cong; Jiang, Xue Hua; Peng, Shi Fang
Laryngeal cancer is the most frequent neoplasm in the head and neck region, with the vast majority of tumors originating from squamous cells. The survival rate of patients with laryngeal cancer has not improved substantially over the past 25 years. To acquire further knowledge regarding the molecules responsible for laryngeal cancer oncogenesis and, in turn, to improve target therapy?iTRAQ and mass spectrometry analysis were utilized to detect differences in protein expression from 15 paired laryngeal cancer and adjacent non-cancerous tissue samples. Using mass spectrometry analysis, the expression levels of 100 proteins in laryngeal cancer samples were distinct from the non-tumor, non-cancerous samples. Further validation of the differentially expressed proteins S100A2, KRT16, FGB and HSPB1 were carried out using quantitative real-time RT-PCR, immunoblot and immunohistochemistry. Functional analysis of one of the highly expressed proteins, S100 calcium binding protein A2 (S100A2), was performed using RNA interference. As a consequence, attenuated S100A2 expression enhanced the ability of HEp-2 cell lines to migrate and invade in vitro. Our investigation complements the current understanding of laryngeal cancer progression. Furthermore, this study supports the concept that enhanced expression of S100A2 may be a promising strategy in developing novel cancer therapeutic drugs. PMID:25874882
Quantitation of low concentrations of polysorbates in high protein concentration formulations by solid phase extraction and cobalt-thiocyanate derivatization.
Kim, Justin; Qiu, Jinshu
A spectrophotometric method was developed to quantify low polysorbate (PS) levels in biopharmaceutical formulations containing high protein concentrations. In the method, Oasis HLB solid phase extraction (SPE) cartridge was used to extract PS from high protein concentration formulations. After loading a sample, the cartridge was washed with 4M guanidine HCl and 10% (v/v) methanol, and the retained PS was eluted by acetonitrile. Following the evaporation of acetonitrile, aqueous cobalt-thiocyanate reagent was added to react with the polyoxyethylene oxide chain of polysorbates to form a blue colored PS-cobaltothiocyante complex. This colored complex was then extracted into methylene chloride and measured spectrophotometrically at 620 nm. The method performance was evaluated on three products containing 30-40 mg L(-1) PS-20 and PS-80 in ?70 g L(-1) protein formulations. The method was specific (no matrix interference identified in three types of protein formulations), sensitive (quantitation limit of 10 mg L(-1) PS) and robust with good precision (relative standard deviation ?6.4%) and accuracy (spike recoveries from 95% to 101%). The linear range of the method for both PS-20 and PS-80 was 10 to 80 mg L(-1) PS. By diluting samples with 6M guanidine HCl and/or using different methylene chloride volumes to extract the colored complexes of standards and samples, the method could accurately and precisely quantify 40 mg L(-1) PS in up to 300 g L(-1) protein formulations. PMID:24331050
Quantitative analysis of the mitochondrial and plastid proteomes of the moss Physcomitrella patens reveals protein macrocompartmentation and microcompartmentation.
Mueller, Stefanie J; Lang, Daniel; Hoernstein, Sebastian N W; Lang, Erika G E; Schuessele, Christian; Schmidt, Anton; Fluck, Melanie; Leisibach, Desirķe; Niegl, Christina; Zimmer, Andreas D; Schlosser, Andreas; Reski, Ralf
Extant eukaryotes are highly compartmentalized and have integrated endosymbionts as organelles, namely mitochondria and plastids in plants. During evolution, organellar proteomes are modified by gene gain and loss, by gene subfunctionalization and neofunctionalization, and by changes in protein targeting. To date, proteomics data for plastids and mitochondria are available for only a few plant model species, and evolutionary analyses of high-throughput data are scarce. We combined quantitative proteomics, cross-species comparative analysis of metabolic pathways, and localizations by fluorescent proteins in the model plant Physcomitrella patens in order to assess evolutionary changes in mitochondrial and plastid proteomes. This study implements data-mining methodology to classify and reliably reconstruct subcellular proteomes, to map metabolic pathways, and to study the effects of postendosymbiotic evolution on organellar pathway partitioning. Our results indicate that, although plant morphologies changed substantially during plant evolution, metabolic integration of organelles is largely conserved, with exceptions in amino acid and carbon metabolism. Retargeting or regulatory subfunctionalization are common in the studied nucleus-encoded gene families of organelle-targeted proteins. Moreover, complementing the proteomic analysis, fluorescent protein fusions revealed novel proteins at organelle interfaces such as plastid stromules (stroma-filled tubules) and highlight microcompartments as well as intercellular and intracellular heterogeneity of mitochondria and plastids. Thus, we establish a comprehensive data set for mitochondrial and plastid proteomes in moss, present a novel multilevel approach to organelle biology in plants, and place our findings into an evolutionary context. PMID:24515833
New capillary electrophoresis method for the determination of furosine in dairy products.
Vallejo-Cordoba, Belinda; Mazorra-Manzano, Miguel A; Gonzßlez-C¾rdova, Aar¾n F
A new capillary electrophoresis (CE) method was established for the quantitative determination of furosine in dairy products. Sample preparation and suitable electrophoretic conditions allowed accurate and reproducible quantitation of furosine in dairy products. Sample preparation consisted of drying hydrolyzed samples, redissolving them in 0.2 M NaOH, and purifying them by solid-phase extraction. The electrophoretic separation was carried out in an uncoated capillary maintained at 30 degrees C using 0.1 M phosphate buffer containing the additive hexadecyl trimethylammonium bromide (HDTAB, 1.2 mM) (pH 7.0) under 10 kV voltage and reverse polarity. Coefficients of variation of less than 2.25% for migration time and 5.80% for peak areas indicated that the technique was reproducible. The calibration curve followed a linear relationship with a highly significant (p < 0.01) coefficient of multiple determination (R (2) = 0.997). The limit of quantitation was 0.5 ppm, a concentration that corresponds to 4.5 mg/100 g of protein in milk samples. Furosine concentration (mg/100 g of protein) ranges of different dairy products (raw, pasteurized, UHT, and evaporated milks and yogurt) agreed with ranges previously reported. Therefore, the CE method presented is a suitable technique for the routine assessment of furosine in dairy products. PMID:15366821
Quantitative mRNA expression profiling of heat-shock protein families in rainbow trout cells
Nobuhiko Ojima; Michiaki Yamashita; Shugo Watabe
We isolated multiple HSPs from rainbow trout Oncorhynchus mykiss RTG-2 cells and quantitatively compared their mRNA levels between unstressed and heat-shocked cells using real-time RT-PCR analysis. Consequently, we isolated nine cDNAs encoding HSPs from heat-shocked RTG-2 cells, namely, Hsp90?a, Hsp90?b, Grp78, Hsp70a, Hsc70a, Hsc70b, Cct8, Hsp47, and DnaJ homolog. Quantitative RT-PCR analyses, in which Hsp70b isolated previously was included, showed
Production and use of stable isotope-labeled proteins for absolute quantitative proteomics.
Lebert, Dorothķe; Dupuis, Alain; Garin, Jķr¶me; Bruley, Christophe; Brun, Virginie
In the field of analytical chemistry, stable isotope dilution assays are extensively used in combination with liquid chromatography-mass spectrometry (LC-MS) to provide confident quantification results. Over the last decade, the principle of isotope dilution has been adopted by the proteomic community in order to accurately quantify proteins in biological samples. In these experiments, a protein's concentration is deduced from the ratio between the MS signal of a tryptic peptide and that of a stable isotope-labeled analog, which serves as an internal standard. The first isotope dilution standards introduced in proteomics were chemically synthesized peptides incorporating a stable isotope-tagged amino acid. These isotopically labeled peptide standards, which are currently widely used, are generally added to samples after protein isolation and digestion. Thus, if protein enrichment is necessary, they do not allow correction for protein losses that may occur during sample pre-fractionation, nor do they allow the tryptic digestion yield to be taken into account. To reduce these limitations we have developed the PSAQ (Protein Standard Absolute Quantification) strategy using full-length stable isotope-labeled proteins as quantification standards. These standards and the target proteins share identical biochemical properties. This allows standards to be spiked into samples at an early stage of the analytical process. Thanks to this possibility, the PSAQ method provides highly accurate quantification results, including for samples requiring extensive biochemical pre-fractionation. In this chapter, we describe the production of full-length stable isotope-labeled proteins (PSAQ standards) using cell-free expression devices. The purification and quality control of protein standards, crucial for good-quality and accurate measurements, are also detailed. Finally, application of the PSAQ method to a typical protein quantification assay is presented. PMID:21604118
Copolymers For Capillary Gel Electrophoresis
Liu, Changsheng (State College, PA); Li, Qingbo (State College, PA)
This invention relates to an electrophoresis separation medium having a gel matrix of at least one random, linear copolymer comprising a primary comonomer and at least one secondary comonomer, wherein the comonomers are randomly distributed along the copolymer chain. The primary comonomer is an acrylamide or an acrylamide derivative that provides the primary physical, chemical, and sieving properties of the gel matrix. The at least one secondary comonomer imparts an inherent physical, chemical, or sieving property to the copolymer chain. The primary and secondary comonomers are present in a ratio sufficient to induce desired properties that optimize electrophoresis performance. The invention also relates to a method of separating a mixture of biological molecules using this gel matrix, a method of preparing the novel electrophoresis separation medium, and a capillary tube filled with the electrophoresis separation medium.
DNA typing by capillary electrophoresis
Zhang, N.
Capillary electrophoresis is becoming more and more important in nucleic acid analysis including DNA sequencing, typing and disease gene measurements. This work summarized the background of DNA typing. The recent development of capillary electrophoresis was also discussed. The second part of the thesis showed the principle of DNA typing based on using the allelic ladder as the absolute standard ladder in capillary electrophoresis system. Future work will be focused on demonstrating DNA typing on multiplex loci and examples of disease diagnosis in the on-line format of PCR-CE. Also capillary array electrophoresis system should allow high throughput, fast speed DNA typing. Only the introduction and conclusions for this report are available here. A reprint was removed for separate processing.
Electrophoresis 1994, IS, 591-615 Capillary electrophoresis of DNA in ultradilute polymer solutions 597 Annelise E. Barron
Barron, Annelise E.
Electrophoresis 1994, IS, 591-615 Capillary electrophoresis of DNA in ultradilute polymer solutions electrophoresis in ultradilute polymer solutions Using capillary electrophoresis, large DNA molecules (2 separations in such dilute polymer solutions. Electrophoresis experiments employing solutions of both small
Quantitative Characterization of Temperature-Independent and Temperature-Dependent Protein¢Protein Interactions in Highly Nonideal Solutions
Fodeke, Adedayo A.; Minton, Allen P.
The interaction among each of three dilute ōtracerö proteins (bovine serum albumin, superoxide dismutase, and ovomucoid) at a concentration of 2 mg/mL and each of two ōcrowderö proteins (ovomucoid and BSA) at concentrations up to 100 mg/mL was characterized by analysis of dependence of the equilibrium gradients of both tracer and crowder upon the concentration of crowder. The equilibrium gradients of both crowder proteins were found to be independent of temperature over the range 5¢37 ░C. The equilibrium gradients of tracer BSA and ovomucoid in the complementary crowder species were likewise found to be independent of temperature over this range, indicating that interaction among these tracers and crowders is predominantly repulsive and essentially entirely entropic in nature. The equilibrium gradient of tracer SOD in BSA was also found to be independent of temperature over this range, but the gradient of tracer SOD in ovomucoid depended significantly upon temperature in a manner indicating a significant enthalpic (attractive) component of the overall interaction between SOD and ovomucoid. The experimental data are analyzed using model-free expansions of the thermodynamic activity coefficients of tracer and crowder in powers of the concentration of crowder and using approximate statistical thermodynamic models based upon highly simplified descriptions of molecular structure and interactions. Detailed analysis of the results indicates a relatively small contribution of nonspecific attraction to the total protein¢protein interaction, which is dominated by steric repulsion. PMID:21846103
Quantitation of secreted proteins using mCherry fusion constructs and a fluorescent microplate reader.
Duellman, Tyler; Burnett, John; Yang, Jay
Traditional assays for secreted proteins include methods such as Western blot and enzyme-linked immunosorbent assay (ELISA) detection of the protein in the cell culture medium. We describe a method for the detection of a secreted protein based on fluorescent measurement of an mCherry fusion reporter. This microplate reader-based mCherry fluorescence detection method has a wide dynamic range of 4.5 orders of magnitude and a sensitivity that allows detection of 1 to 2fmol fusion protein. Comparison with the Western blot detection method indicated greater linearity, wider dynamic range, and a similar lower detection threshold for the microplate-based fluorescent detection assay of secreted fusion proteins. An mCherry fusion protein of matrix metalloproteinase-9 (MMP-9), a secreted glycoprotein, was created and expressed by transfection of human embryonic kidney (HEK) 293 cells. The cell culture medium was assayed for the presence of the fluorescent signal up to 32 h after transfection. The secreted MMP-9-mCherry fusion protein was detected 6h after transfection with a linear increase in signal intensity over time. Treatment with chloroquine, a drug known to inhibit the secretion of many proteins, abolished the MMP-9-mCherry secretion, demonstrating the utility of this method in a biological experiment. PMID:25542417
Supporting Information: A quantitative comparison of sRNA-based and protein-based gene regulation
Mehta, Pankaj
of proteins; s (m) is the average rate of transcription of sRNAs (mRNAs); p is the average rate of translation extensively considered in the literature2Ł5 . The kinetics of ordinary transcription and translation in a cell of mRNA molecules, p the average number of proteins, m the average rate of transcription, p the average
Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress
Mustafa, Ghazala; Komatsu, Setsuko
Flooding stress has a negative impact on soybean cultivation because it severely impairs growth and development. To understand the flooding responsive mechanism in early stage soybeans, a glycoproteomic technique was used. Two-day-old soybeans were treated with flooding for 2 days and roots were collected. Globally, the accumulation level of glycoproteins, as revealed by cross-reaction with concanavalin A decreased by 2 days of flooding stress. Glycoproteins were enriched from total protein extracts using concanavalin A lectin resin and analyzed using a gel-free proteomic technique. One-hundred eleven and 69 glycoproteins were identified without and with 2 days of flooding stress, respectively. Functional categorization of these identified glycoproteins indicated that the accumulation level of proteins related to protein degradation, cell wall, and glycolysis increased, while stress-related proteins decreased under flooding stress. Also the accumulation level of glycoproteins localized in the secretory pathway decreased under flooding stress. Out of 23 common glycoproteins between control and flooding conditions, peroxidases and glycosyl hydrolases were decreased by 2 days of flooding stress. mRNA expression levels of proteins in the endoplasmic reticulum and N-glycosylation related proteins were downregulated by flooding stress. These results suggest that flooding might negatively affect the process of N-glycosylation of proteins related to stress and protein degradation; however glycoproteins involved in glycolysis are activated. PMID:25477889
Quantitation of influenza A virus in the presence of extraneous protein using electrochemical impedance spectroscopy
Walid Mohamed Hassen; Valķrie Duplan; Eric Frost; Jan J. Dubowski
In an attempt to provide an insight into detection of specific viruses in biological samples, we report on quantitation of influenza A virus (IAV) in samples containing large amounts of extraneous bovine serum albumin (BSA), foetal bovine serum (FBS) and hepatitis B virus (HBV) vaccine. Detection was carried out using electrochemical impedance spectroscopy (EIS) with an antibody-neutravidin-thiol architecture immobilized on
Quantitative analysis of residual protein contamination of podiatry instruments reprocessed through local and central decontamination units
Background The cleaning stage of the instrument decontamination process has come under increased scrutiny due to the increasing complexity of surgical instruments and the adverse affects of residual protein contamination on surgical instruments. Instruments used in the podiatry field have a complex surface topography and are exposed to a wide range of biological contamination. Currently, podiatry instruments are reprocessed locally within surgeries while national strategies are favouring a move toward reprocessing in central facilities. The aim of this study was to determine the efficacy of local and central reprocessing on podiatry instruments by measuring residual protein contamination of instruments reprocessed by both methods. Methods The residual protein of 189 instruments reprocessed centrally and 189 instruments reprocessed locally was determined using a fluorescent assay based on the reaction of proteins with o-phthaldialdehyde/sodium 2-mercaptoethanesulfonate. Results Residual protein was detected on 72% (n = 136) of instruments reprocessed centrally and 90% (n = 170) of instruments reprocessed locally. Significantly less protein (p < 0.001) was recovered from instruments reprocessed centrally (median 20.62 ?g, range 0 - 5705 ?g) than local reprocessing (median 111.9 ?g, range 0 - 6344 ?g). Conclusions Overall, the results show the superiority of central reprocessing for complex podiatry instruments when protein contamination is considered, though no significant difference was found in residual protein between local decontamination unit and central decontamination unit processes for Blacks files. Further research is needed to undertake qualitative identification of protein contamination to identify any cross contamination risks and a standard for acceptable residual protein contamination applicable to different instruments and specialities should be considered as a matter of urgency. PMID:21219613
A quantitative model of odor deactivation based on the redox shift of the pheromone-binding protein im moth antennae.
Kaissling, K E
Recent in vitro experiments with homogenates of isolated olfactory hairs of Antheraea polyphemus suggest that the pheromone-binding protein (PBP) is involved not only in pheromone solubilization and transport but also in pheromone deactivation. PBP occurs in a reduced form with one or two disulfide bridges (PBP(red)) and in the oxidized form with three bridges (PBP(ox)). From kinetic experiments it was concluded that the pheromone is first bound to PBP(red). This complex activates the receptor molecules and then turns into the oxidized form which--according to our working hypothesis--is unable to activate further receptor molecules. Apparently, the pheromone bound to the PBP (both forms) is protected from enzymatic degradation into nonexcitatory metabolites. A quantitative kinetic model of pheromone deactivation was developed (in collaboration with J. Thorson, Oxford) in which the receptor molecules are considered to act as enzymes catalyzing the redox shift of the binding protein. PMID:10049225
Quantitative analysis of Nipah virus proteins released as virus-like particles reveals central role for the matrix protein
Patch, Jared R; Crameri, Gary; Wang, Lin-Fa; Eaton, Bryan T; Broder, Christopher C
Background Nipah virus (NiV) is an emerging paramyxovirus distinguished by its ability to cause fatal disease in both animal and human hosts. Together with Hendra virus (HeV), they comprise the genus Henipavirus in the Paramyxoviridae family. NiV and HeV are also restricted to Biosafety Level-4 containment and this has hampered progress towards examining details of their replication and morphogenesis. Here, we have established recombinant expression systems to study NiV particle assembly and budding through the formation of virus-like particles (VLPs). Results When expressed by recombinant Modified Vaccinia virus Ankara (rMVA) or plasmid transfection, individual NiV matrix (M), fusion (F) and attachment (G) proteins were all released into culture supernatants in a membrane-associated state as determined by sucrose density gradient flotation and immunoprecipitation. However, co-expression of F and G along with M revealed a shift in their distribution across the gradient, indicating association with M in VLPs. Protein release was also altered depending on the context of viral proteins being expressed, with F, G and nucleocapsid (N) protein reducing M release, and N release dependent on the co-expression of M. Immunoelectron microscopy and density analysis revealed VLPs that were similar to authentic virus. Differences in the budding dynamics of NiV proteins were also noted between rMVA and plasmid based strategies, suggesting that over-expression by poxvirus may not be appropriate for studying the details of recombinant virus particle assembly and release. Conclusion Taken together, the results indicate that NiV M, F, and G each possess some ability to bud from expressing cells, and that co-expression of these viral proteins results in a more organized budding process with M playing a central role. These findings will aid our understanding of paramyxovirus particle assembly in general and could help facilitate the development of a novel vaccine approach for henipaviruses. PMID:17204159
Quantitative proteome analyses identify PrfA-responsive proteins and phosphoproteins in Listeria monocytogenes.
Misra, Sandeep Kumar; Moussan Dķsirķe Akķ, Francine; Wu, Zongfu; Milohanic, Eliane; Cao, Thanh Nguyen; Cossart, Pascale; Deutscher, Josef; Monnet, Vķronique; Archambaud, Cristel; Henry, Cķline
Protein phosphorylation is a major mechanism of signal transduction in bacteria. Here, we analyzed the proteome and phosphoproteome of a wild-type strain of the food-borne pathogen Listeria monocytogenes that was grown in either chemically defined medium or rich medium containing glucose. We then compared these results with those obtained from an isogenic prfA* mutant that produced a constitutively active form of PrfA, the main transcriptional activator of virulence genes. In the prfA* mutant grown in rich medium, we identified 256 peptides that were phosphorylated on serine (S), threonine (T), or tyrosine (Y) residues, with a S/T/Y ratio of 155:75:12. Strikingly, we detected five novel phosphosites on the virulence protein ActA. This protein was known to be phosphorylated by a cellular kinase in the infected host, but phosphorylation by a listerial kinase had not previously been reported. Unexpectedly, SILAC experiments with the prfA* mutant grown in chemically defined medium revealed that, in addition to previously described PrfA-regulated proteins, several other proteins were significantly overproduced, among them were several proteins involved in purine biosynthesis. This work provides new information for our understanding of the correlation among protein phosphorylation, virulence mechanisms, and carbon metabolism. PMID:25383790
Quantitation of Total Protein using OPA Total protein content is a measurement common to many applications in basic science and
Raizada, Manish N.
is of particular importance when proteins are being purified or different samples are being compared. Regardless 05404-0998 USA COPYRIGHT ® 2006 TEL: 888-451-5171 FAX: 802-655-7941 Outside the USA: 802-655-4740 E.4 as the diluent. Samples and standards were placed in microplate wells (10 ml per well) and 300 ml of OPA reagent
Quantitative proteomics analysis of differential protein expression and oxidative modification of specific proteins in the brains of old mice
H. Fai Poon; Radhika A. Vaishnav; Thomas V. Getchell; Marilyn L. Getchell; D. Allan Butterfield
The brain is susceptible to oxidative stress, which is associated with age-related brain dysfunction, because of its high content of peroxidizable unsaturated fatty acids, high oxygen consumption per unit weight, high content of key components for oxidative damage, and the relative scarcity of antioxidant defense systems. Protein oxidation, which results in functional disruption, is not random but appears to be
Lights, Camera, Action! Systematic Variation in Difference Gel Electrophoresis
Lights, Camera, Action! ┬Ł Systematic Variation in Difference Gel Electrophoresis Kimberly F variation, including that caused by the apparatus used for imaging proteins (location of the camera). The conventional 2DE method is attractive because of its resolving power, sensitivity, and the low equipment cost
Filamin C, a dysregulated protein in cancer revealed by label-free quantitative proteomic analyses of human gastric cancer cells
Xu, Lei-Lei; Chen, Si-Jie; Yao, Jun; Jiang, Ying-Hua; Peng, Gang; Fang, Cai-Yun
Gastric cancer (GC) is the fourth and fifth most common cancer in men and women, respectively. We identified 2,750 proteins at false discovery rates of 1.3% (protein) and 0.03% (spectrum) by comparing the proteomic profiles of three GC and a normal gastric cell lines. Nine proteins were significantly dysregulated in all three GC cell lines, including filamin C, a muscle-specific filamin and a large actin-cross-linking protein. Downregulation of filamin C in GC cell lines and tissues were verified using quantitative PCR and immunohistochemistry. Data-mining using public microarray datasets shown that filamin C was significantly reduced in many human primary and metastasis cancers. Transient expression or silencing of filamin C affected the proliferation and colony formation of cancer cells. Silencing of endogenous filamin C enhanced cancer cell migration and invasion, whereas ectopic expression of filamin C had opposing effects. Silencing of filamin C increased the expression of matrix metallopeptidase 2 and improved the metastasis of prostate cancer in a zebrafish model. High filamin C associated with better prognosis of prostate cancer, leukemia and breast cancer patients. These findings establish a functional role of filamin C in human cancers and these data will be valuable for further study of its mechanisms. PMID:25577646
Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin.
Schulz, Melanie; Brandner, Stefanie; Eberhagen, Carola; Eckardt-Schupp, Friederike; Larsen, Martin R; Andrae, Ulrich
A comprehensive quantitative analysis of changes in protein phosphorylation preceding or accompanying transcriptional activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 5L rat hepatoma cells was performed using the SILAC approach. Following exposure of the cells to DMSO or 1 nM TCDD for 0.5 to 2 h, 5648 phosphorylated peptides corresponding to 2156 phosphoproteins were identified. Eight peptides exhibited a statistically significantly altered phosphorylation because of TCDD exposure and 22 showed a regulation factor of ? 1.5 in one of the experiments per time point. The vast majority of the TCCD-induced phosphorylation changes had not been reported before. The transcription factor ARNT, the obligate partner for gene activation by the TCDD-bound Ah receptor, exhibited an up-regulation of its Ser77 phosphorylation, a modification known to control the differential binding of ARNT homodimers and heterodimers to different enhancers suggesting that this phosphorylation represents a novel mechanism contributing to the alteration of gene expression by TCDD. Other proteins with altered phosphorylation included, among others, various transcriptional coregulators previously unknown to participate in TCDD-induced gene activation, regulators of small GTPases of the Ras superfamily, UBX domain-containing proteins and the oncogenic protein LYRIC. The results open up new directions for research on the molecular mechanisms of dioxin action and toxicity. PMID:23298284
Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology.
Hennig, Janosch; Sattler, Michael
RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence-specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross-linking immuno-precipitation (CLIP) and other recently developed high-throughput methods provide comprehensive, genome-wide maps of protein-RNA interactions in the cell. Structural biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high-throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein-RNA recognition in gene regulation, as we review in this article. PMID:26059946
In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are
Tsien, Roger Y.
synapses in the circuit, a process known as "experience-dependent plasticity" (1). When animals controlled protein availability is highlighted in studies of neuro- logical diseases, which often result from
Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth*
Zhang, Hongtao; Zhou, Houjiang; Berke, Lidija; Heck, Albert J. R.; Mohammed, Shabaz; Scheres, Ben; Menke, Frank L. H.
Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined 15N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, AUXIN RESPONSE FACTOR2 (ARF2), SUPPRESSOR OF AUXIN RESISTANCE 3 (SAR3), and SORTING NEXIN1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach. PMID:23328941
Quantitative partition of protein, carbohydrate and fat pools in growing pigs.
Chwalibog, A; Thorbek, G
A model combining data from balance experiments with data from oxidation of nutrients demonstrating the pools of protein, carbohydrate and fat and their partition in the body was presented. Data from more than 200 experiments with growing pigs were used to fill up the "black boxes" in the model and to discuss the pattern between catabolic and anabolic processes of the different nutrients. With a ME-intake of 1.3 MJ/kg0.75 the proportion of retained protein from the protein pool varied from 50 to 75% depending on the age of animals and the protein quality. At a low protein intake and ME of 0.6 MJ/kg0.75 the utilization of protein was reduced to about 25% as a substantial part of the protein pool was oxidized. The carbohydrate group from the protein sources constituted less than 5% of the carbohydrate pool. The oxidation of carbohydrates was between 50-75% of the pool in all experiments, while the rest was used for lipogenesis. Even on a low feeding level the pattern occurred indicating a requirement for specific substances formed in the body. Lipogenesis constituted 46-96% of the fat pool depending of the amount on digested fat in the different experiments. No oxidation of fat was observed in experiments with pigs (30-90 kg LW) on a high feeding level in spite of the broad variation in the amount of digested fat, indicating a complete storage of the fat pool into body fat. In experiments with piglets (3-9 kg LW) on the same energy intake fat oxidation of about 30% occurred, probably caused by the high energy requirement of the piglets.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8526731
Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions
Parikesit, Arli A.; Stadler, Peter F.; Prohaska, Sonja J.
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. PMID:24710298
Evolution and quantitative comparison of genome-wide protein domain distributions.
Parikesit, Arli A; Stadler, Peter F; Prohaska, Sonja J
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. PMID:24710298
High efficiency and quantitatively reproducible protein digestion by trypsin-immobilized magnetic microspheres
Sun, Liangliang; Li, Yihan; Yang, Ping; Zhu, Guijie; Dovichi, Norman J.
Aldehyde- and NHS-activated magnetic microspheres were used to immobilize trypsin (CHO-trypsin and NHS-trypsin), and their performance for protein digestion was evaluated by reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry using an LTQ Orbitrap Velos instrument. NHS-trypsin provided greater sequence coverage and identified more peptides for the digestion of bovine serum albumin. A one-minute digestion at room temperature using the immobilized trypsin also identified more peptides (96 ▒ 6 vs. 48 ▒ 1) and produced higher sequence coverage (90 ▒ 2% vs. 75 ▒ 2%) than traditional free trypsin digestion for 12 hours at 37 ░C. Analysis of 15 nM (0.001 mg/mL) BSA digested by NHS-trypsin in 1 min. at room temperature consistently yielded one detected peptide; 150 nM BSA generated 22 peptides. Peptide intensity and protein spectral count were used to evaluate the run-to-run digestion reproducibility of NHS-trypsin with a three-protein-mixture. Three high intensity peptides for each protein generated intensity ratios from 0.70 to 1.09 and spectral count ratios from 0.78 to 1.18. Finally, RAW 264.7 cell lysates were digested by NHS-trypsin for 10 min. and 30 min. at room temperature; 604 and 697 protein groups, respectively, were identified by RPLC-ESI-MS/MS, with a peptide false discovery rate of less than 1%. Digestion by solution phase trypsin for 12 hours at 37 ░C resulted in identification of 878 protein groups. PMID:22176736
Peptide Production and Decay Rates Affect the Quantitative Accuracy of Protein Cleavage Isotope Dilution Mass Spectrometry (PC-IDMS)*
Shuford, Christopher M.; Sederoff, Ronald R.; Chiang, Vincent L.; Muddiman, David C.
No consensus has been reached on the proper time to add stable-isotope labeled (SIL) peptides in protein cleavage isotope dilution mass spectrometry workflows. While quantifying 24 monolignol pathway enzymes in the xylem tissue of Populus trichocarpa, we compared the protein concentrations obtained when adding the SIL standard peptides concurrently with the enzyme or after quenching of the digestion (i.e. postdigestion) and observed discrepancies for nearly all tryptic peptides investigated. In some cases, greater than 30-fold differences were observed. To explain these differences and potentially correct for them, we developed a mathematical model based on pseudo-first-order kinetics to account for the dynamic production and decay (e.g. degradation and precipitation) of the native peptide targets in conjunction with the decay of the SIL peptide standards. A time course study of the digests confirmed the results predicted by the proposed model and revealed that the discrepancy between concurrent and postdigestion introduction of the SIL standards was related to differential decay experienced by the SIL peptide and the native peptide in each method. Given these results, we propose concurrent introduction of the SIL peptide is most appropriate, though not free from bias. Mathematical modeling of this method reveals that overestimation of protein quantities would still result when rapid peptide decay occurs and that this bias would be further exaggerated by slow proteolysis. We derive a simple equation to estimate the bias for each peptide based on the relative rates of production and decay. According to this equation, nearly half of the peptides evaluated here were estimated to have quantitative errors greater than 10% and in a few cases over 100%. We conclude that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification. PMID:22595788
The Influence of Free 3-Nitrotyrosine and Saliva on the Quantitative Analysis of Protein-Bound 3-Nitrotyrosine in Sputum
Ueshima, Kazuhito; Minakata, Yoshiaki; Sugiura, Hisatoshi; Yanagisawa, Satoru; Ichikawa, Tomohiro; Akamatsu, Keiichirou; Hirano, Tsunahiko; Nakanishi, Masanori; Matsunaga, Kazuto; Yamagata, Toshiyuki; Ichinose, Masakazu
Background: We have recently developed a new technique for quantitatively measuring protein-bound 3-nitrotyrosine (3-NT), a footprint of nitrosative stress, utilizing high-performance liquid chromatography with an electrochemical detection (HPLC-ECD) system. Using this system, we showed that 3-NT formation was upregulated in the sputum of both COPD and asthmatic patients. However, in order to improve the accuracy of the measurement system, We have to resolve some problems which were the influence of free amino acid form of 3-NT and of salivary contamination. Objectives: We initially investigated the amount of the free amino acid form of 3-NT in induced sputum and compared with that of protein-bound 3-NT. Next, we evaluated the concentration of protein-bound 3-NT in saliva and compared with that in induced sputum by means of HPLC-ECD. Methods: Five male COPD patients were enrolled. Induced sputum and saliva were obtained from the patients. The free amino acid form of 3-NT in sputum and saliva was measured by HPLC-ECD, and the protein-bound 3-NT and tyrosine in sputum and saliva were enzymatically hydrolyzed by Streptomyces griseus Pronase and measured for the protein hydrolysate by HPLC-ECD. Results: The mean value of the amount of protein-bound 3-NT was 65.0 fmol (31.2 to 106.4 fmol). On the other hand, the amount of the free amino acid form of 3-NT was under the detection limit (<10 fmol). The levels of both 3-NT (sputum: 0.55 ▒ 0.15 pmol/ml, saliva: 0.02 ▒ 0.01 pmol/ml, p < 0.01) and tyrosine (sputum: 0.81 ▒ 0.43 ?mol/ml, saliva: 0.07 ▒ 0.04 ?mol/ml, p < 0.01) in saliva were significantly lower than in sputum. The percentage of 3-NT in saliva to that in sputum was about 3.1%, and that of tyrosine was about 9.0%. Conclusion: The free amino acid form of 3-NT does not affect the measurement of protein-bound 3-NT. Furthermore, the influence of salivary contamination on the measurement of protein-bound 3-NT in induced sputum by means of HPLC-ECD was very small and could be negligible. PMID:19662171
The authors are characterizing toxicant-induced injury to the nervous system by measuring nervous system cell-type specific proteins together with accompanying changes in morphology and behavior. In the present study, cerebellar neurotoxicity was assessed in the Gunn rat an autos...
UV Resonance Raman-Selective Amide Vibrational Enhancement: Quantitative Methodology for Determining Protein Secondary Structure
Asher, Sanford A.
, such as CD, VCD, and absorption spectroscopy. In addition, the spectra are immune to the light-scattering artifacts that plague CD, VCD, and IR absorption measurements. Thus, it will be possible to examine proteins, such as CD, VCD, and IR absorption spectroscopy (12-18). We show here that the ability of this UV Raman
Analysis of disease-associated protein expression using quantitative proteomics-fibulin-5 is expressed in association with hepatic fibrosis.
Bracht, Thilo; Schweinsberg, Vincent; Trippler, Martin; Kohl, Michael; Ahrens, Maike; Padden, Juliet; Naboulsi, Wael; Barkovits, Katalin; Megger, Dominik A; Eisenacher, Martin; Borchers, Christoph H; Schlaak, J÷rg F; Hoffmann, Andreas-Claudius; Weber, Frank; Baba, Hideo A; Meyer, Helmut E; Sitek, Barbara
Hepatic fibrosis and cirrhosis are major health problems worldwide. Until now, highly invasive biopsy remains the diagnostic gold standard despite many disadvantages. To develop noninvasive diagnostic assays for the assessment of liver fibrosis, it is urgently necessary to identify molecules that are robustly expressed in association with the disease. We analyzed biopsied tissue samples from 95 patients with HBV/HCV-associated hepatic fibrosis using three different quantification methods. We performed a label-free proteomics discovery study to identify novel disease-associated proteins using a subset of the cohort (n = 27). Subsequently, gene expression data from all available clinical samples were analyzed (n = 77). Finally, we performed a targeted proteomics approach, multiple reaction monitoring (MRM), to verify the disease-associated expression in samples independent from the discovery approach (n = 68). We identified fibulin-5 (FBLN5) as a novel protein expressed in relation to hepatic fibrosis. Furthermore, we confirmed the altered expression of microfibril-associated glycoprotein 4 (MFAP4), lumican (LUM), and collagen alpha-1(XIV) chain (COL14A1) in association to hepatic fibrosis. To our knowledge, no tissue-based quantitative proteomics study for hepatic fibrosis has been performed using a cohort of comparable size. By this means, we add substantial evidence for the disease-related expression of the proteins examined in this study. PMID:25807371
Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants
Rodrigues, Silas P.; Ventura, Josķ A.; Aguilar, Clemente; Nakayasu, Ernesto S.; Choi, HyungWon; Sobreira, Tiago J. P.; Nohara, Lilian L.; Wermelinger, Luciana S.; Almeida, Igor C.; Zingali, Russolina B.; Fernandes, Patricia M. B.
Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifersÆ regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses. PMID:22465191
Internal standards in the quantitative determination of protein biopharmaceuticals using liquid chromatography coupled to mass spectrometry.
Bronsema, Kees J; Bischoff, Rainer; van de Merbel, Nico C
Following the increase in development of protein biopharmaceuticals, there is a growing demand for the sensitive and reliable quantification of these proteins in complex biological matrices such as plasma and serum to support (pre)-clinical research. In this field, ligand binding assays (LBAs) are currently the standard analytical technique, but in recent years, there is a trend towards the use of liquid chromatography hyphenated with (tandem) mass spectrometry (LC-MS/MS). One of the reasons for this trend is the possibility to use internal standards to correct for analytical variability and thus improve the precision and accuracy of the results. In the LC-MS/MS bioanalysis of small molecules, internal standardization is quite straightforward: either a stable-isotope labeled (SIL) form of the analyte or a structural analogue is used. For the quantification of biopharmaceutical proteins, the situation is more complex. Since the protein of interest is digested to a mixture of peptides, one of which is subsequently used for quantification, there are more options for internal standardization. A SIL form or a structural analogue of either the intact protein or the signature peptide can be used. In addition, a modified form of the SIL-peptide internal standard, containing one or more cleavable groups is a possibility, and an internal standard can be generated during the analysis by using differential derivatization techniques. In this paper we provide an overview of the different options for internal standardization in the field of absolute targeted quantification of protein biopharmaceuticals using LC-MS/MS, based on literature from 2003 to 2011. The advantages and disadvantages of the different approaches are evaluated both with regard to the correction they provide for the variability of the different steps of the analysis and with regard to their generic availability. As most of the approaches used lead to acceptable results in terms of accuracy and precision, we conclude that there currently is no clear preferable method for internal standardization in the field of protein quantification by LC-MS/MS. It is essential, however, that any step in the analysis that is not covered by the internal standard chosen, should be carefully optimized and controlled. PMID:22426285
Quantitative mRNA expression profiling of heat-shock protein families in rainbow trout cells.
Ojima, Nobuhiko; Yamashita, Michiaki; Watabe, Shugo
We isolated multiple HSPs from rainbow trout Oncorhynchus mykiss RTG-2 cells and quantitatively compared their mRNA levels between unstressed and heat-shocked cells using real-time RT-PCR analysis. Consequently, we isolated nine cDNAs encoding HSPs from heat-shocked RTG-2 cells, namely, Hsp90betaa, Hsp90betab, Grp78, Hsp70a, Hsc70a, Hsc70b, Cct8, Hsp47, and DnaJ homolog. Quantitative RT-PCR analyses, in which Hsp70b isolated previously was included, showed that the mRNA accumulation levels of Hsp70a, Hsp70b, Hsc70a, Hsc70b, and Hsp47 were significantly increased after heat shock, and the increased levels of two Hsp70s, Hsp70a, and Hsp70b, were most conspicuous. In the case of Hsc70s, the increased level of Hsc70b was more remarkable than that of Hsc70a. These results demonstrate the importance of a comprehensive expression analysis of HSPs for better understanding of the cellular stress response in fish, especially in tetraploid species such as rainbow trout. PMID:15721272
Characterization of antibodies for quantitative determination of spiggin protein levels in male and female three-spined stickleback (Gasterosteus aculeatus)
Berg, HÕkan; Scherbak, Nikolai; Liimatta, Harri; Hoffmann, Erik; Karlsson, Johnny; Olsson, Per-Erik
Spiggin is an adhesive glycoprotein produced in the kidney of sticklebacks during the breeding season and is subsequently secreted into the urinary bladder from where it is employed for nest building. Since the production of the protein has been shown to be under androgenic control, spiggin has been suggested to be a useful biomarker for androgenic substances in the environment. In this study, two polyclonal spiggin antibodies based on synthetic peptides and one polyclonal antibody directed against native spiggin have been characterized. The antibodies ability to identify spiggin was investigated by quantitative immunoassay. For both peptide antibodies the quantification range was determined to be between 1 and 80 ng spiggin and determination of renal spiggin levels from immature and mature males displayed a 15-fold increase in total spiggin content of the kidney resulting in a 6-fold increase in male kidney weight due to hypertrophy. The kidney somatic index (KSI) was found to correlate well with the total renal spiggin content and therefore it appears that KSI in sticklebacks could be used as an initial method to identify substances displaying androgenic effects. Furthermore, western blot analysis revealed that the polyclonal antibodies recognize different spiggin isoforms and that spiggin can be detected in the urinary bladder and kidney of both males and female sticklebacks. In order to develop a quantitative detection method for native spiggin it is necessary to produce a standard that can be used in a bioassay. Due to the adhesive and polymerization characteristics of spiggin the protein is difficult to use as a standard in bioassays. So far spiggin has been shown to exist in at least 14 isoforms, all of which contain polymerization domains. To overcome the solubility problem we have produced recombinant spiggin gamma, with only one polymerization domain, that can be expressed in E. coli. Western blot analysis demonstrated that the polyclonal antibodies were able to detect recombinant spiggin gamma protein in bacterial cell lysate, suggesting that it may be developed into a useful source of standard spiggin to be used for quantitative determination of androgen induced spiggin production in sticklebacks. PMID:19442269
8-Plex Quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for AlzheimerÆs disease
Choe, Leila; DÆAscenzo, Mark; Relkin, Norman R.; Pappin, Darryl; Ross, Phil; Williamson, Brian; Guertin, Steven; Pribil, Patrick; Lee, Kelvin H.
An 8-plex version of an isobaric reagent for the quantitation of proteins using shotgun methods is presented. The 8-plex version of the reagent relies on amine-labeling chemistry of peptides similar to 4-plex reagents. MS/MS reporter ions at 113, 114, 115, 116, 117, 118, 119, and 121 m/z are used to quantify protein expression. This technology which was first applied to a test mixture consisting of 8 proteins and resulted in accurate quantitation, has the potential to increase throughput of analysis for quantitative shotgun proteomics experiments when compared to 2-plex and 4-plex methods. The technology was subsequently applied to a longitudinal study of cerebrospinal fluid proteins from subjects undergoing intravenous immunoglobulin treatment for AlzheimerÆs disease. Results from this study identify a number of protein expression changes that occur in cerebrospinal fluid after 3 and 6 months of treatment compared to a baseline and compared to a drug washout period. A visualization tool was developed for this dataset and is presented. The tool can aid in the identification of key peptides and measurements. One conclusion aided by the visualization tool is that there are differences in considering peptide-based observations versus protein-based observations from quantitative shotgun proteomics studies. PMID:17880003
Electrophoresis experiment, experiment MA-014
NASA Technical Reports Server (NTRS)
Hannig, K.; Wirth, H.
A continuous, free flow electrophoresis study was conducted during the Apollo Soyuz Test Project mission to investigate and evaluate the increase in sample flow rate and sample resolution achievable in space. The electrophoresis equipment was designed for the separation of four mixtures of biological cells with variable sample flow rates, buffer flow rates, and electric field gradients. Separation quality was assessed by measuring the light from a quartz lamp through the electrophoresis channel and on to a photodiode system. The preliminary results indicate that all monitored systems operated correctly during the experiment. The optical system produced a light that was too bright to discern true cell distributions, but data were received that show a distribution of separated cells.
Electrophoresis experiment. Experiment MA-014
NASA Technical Reports Server (NTRS)
Hannig, K. H.
A continuous free-flow electrophoresis study was conducted during the Apollo-Soyuz Test Project Mission to investigate and evaluate the increase in sample flow rate and sample resolution achievable in space. The electrophoresis equipment was designed for the separation of four mixtures of biological cells with variable sample flow rates, buffer flow rates, and electric field gradients. Separation quality was assessed by measuring the light from a quartz lamp through the electrophoresis channel and onto a photodiode system. The data evaluation indicates that all monitored systems operated correctly during the experiment. The optical system produced a light that was too bright to discern true cell distributions, but final analysis of scientific data by computer processing shows the expected distribution of separated cells.
Determination of pharmaceutical and personal care products in wastewater by capillary electrophoresis with UV detection
Stephen E. Gibbons; Chuan Wang; Yinfa Ma
Capillary electrophoresis (CE) offers a fast and cost-effective alternative analytical technique to LC-MS\\/MS for separation and quantitation of many PPCP compounds in wastewater. In this study, we have developed a method that can simultaneously analyze eight different PPCP compounds in untreated wastewater (ibuprofen, triclosan, carbamazepine, caffeine, acetaminophen, sulfamethoxazole, trimethoprim, and lincomycin), using capillary electrophoresis with UV detection (CE-UV). The method
Development of a quinoxaline-based fluorescent probe for quantitative estimation of protein binding site polarity.
Kudo, Kentaro; Momotake, Atsuya; Kanna, Yoko; Nishimura, Yoshinobu; Arai, Tatsuo
The compound 2-[(1E)-2-(1H-pyrrol-2-yl)ethenyl]-quinoxaline (PQX) is a promising fluorescent chromophore for the estimation of protein binding site polarity, due to its full-color solvatochromic fluorescence. A linear relationship was obtained between the peak emission wavenumber and E(T)(N) (normalized solvent polarity). The BSA binding site polarity was estimated from the solvatochromic plot. PMID:21331415
Quantitative capillary reversed passive latex agglutination test for C-reactive protein (CRP) in the dog
K. Tagata; S. Yokoyama; T. Ginbo; M. Honda; T. Okimura; M. Odakura; M. Nomura; S. Yamamoto
A capillary reversed passive latex agglutination test (capillary RPLA) was developed which allows quantification of serum C-reactive protein (CRP) within approximately 15 min. The logarithmic regression line (calibration curve) obtained after measuring each CRP concentration three times in twofold dilutions of a standard canine serum containing 222 Ąg\\/ml of CRP was y=6.394+0.030x (r=0.995). Capillary RPLA permitted quantification of CRP in
Quantitative mass spectrometry-based assay development and validation: from small molecules to proteins.
Bo×ovi?, Andrea; Kulasingam, Vathany
Mass spectrometry (MS) has emerged as a powerful analytical tool for the identification, characterization and quantification of various biomolecules (small molecules, drug metabolites and proteins) in biological specimens. The use of mass spectrometers in the clinical diagnostic laboratories have gained popularity due to its ease of development of new assays, ability to measure multiple analytes in a single analytical run, low volume requirements and low reagent costs. Novel technological advancements in ionization sources, instrumentation and software have increased the popularity of these platforms. Consequently, a number of home-brew assays, utilizing the power of MS, are being developed and validated for clinical diagnostic use. In this review, we will discuss the two phases that precede method implementation: method development and validation for both small molecule analysis and protein quantification using liquid chromatography tandem mass spectrometry (LC-MS/MS). Some of the challenges facing protein quantification will be highlighted and an outlook for the future of laboratory medicine and MS will be provided. PMID:23041077
Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings
Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad
Three-bond 3JC?C? and 3JHNH? couplings in peptides and proteins both are functions of the intervening backbone torsion angle ?. In well ordered regions, 3JHNH? is tightly correlated with 3JC?C?, but the presence of large ? angle fluctuations differentially affects the two types of couplings. Assuming the ? angles to follow a Gaussian distribution, the width of this distribution can be extracted from 3JC?C? and 3JHNH?, as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of 3JC?C? and 3JHNH couplings at very high precision, and impact of factors other than the intervening torsion angle on 3J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of ?-synuclein yields rather homogeneous widths of 69▒6░ for the ? angle distributions, and 3JC?C? values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and 1H-1H NOEs. Data are consistent with a modest (? 30%) population of the polyproline II region. PMID:25590347
Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism
NASA Astrophysics Data System (ADS)
Rajendra, Jascindra; Damianoglou, Angeliki; Hicks, Matthew; Booth, Paula; Rodger, P. Mark; Rodger, Alison
The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC 4), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ▒ 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC 4 and rhodamine B to determine the polarisations of their long wavelength transitions.
Quantitative and qualitative analysis of cellular prion protein (PrP(C)) expression in bovine somatic tissues.
Peralta, Oscar A; Eyestone, Willard H
The host encoded cellular prion protein (PrP(C)) is an N-linked glycoprotein tethered to the cell membrane by a glycophosphatidylinositol (GPI) anchor. Under certain conditions, PrP(C) can undergo conversion into a conformationally-altered isoform (PrP(Sc)) widely believed to be the pathogenic agent of transmissible spongiform encephalopathies (TSEs). Understanding the tissue-specific expression of PrP(C) is crucial considering that cells expressing high levels of PrP(C) bear a risk for conversion and accumulation of PrP(Sc). In the present study, fifteen bovine somatic tissues were analyzed for PrP(C) expression by quantitative western blot and immunohistochemistry. Quantitative western blot analysis revealed highest expression of PrP(C) in cerebellum, obex and spinal cord. Intermediate levels were detected in thymus, intestine, nerve, heart and spleen, and lower levels in lung, muscle, kidney, lymph node, skin, pancreas and liver. Immunohistochemical analysis detected intense cellular-specific PrP(C) staining in neurons, thymocytes and lymphocytes. PrP(C) was also detected in the enteric wall, pancreatic islets of langerhans, myocardium, pulmonary alveolar sacs, renal glomeruli and dermal epithelial cells. This study demonstrated the quantitatively varied, wide-spread, tissue- and cell-specific expression pattern of PrP(C) in bovine somatic tissues. The importance of this study is to lay the foundation for understanding the tissue-specific expression of PrP(C) and to consider the potential participation of more bovine tissues in the transmission of BSE infection. PMID:19806026
Identification, purification, and characterization of subunits of cAMP-dependent protein kinase in human testis. Reverse mobilities of human RII alpha and RII beta on sodium dodecyl sulfate-polyacrylamide gel electrophoresis compared with rat and bovine RIIs.
SkÕlhegg, B S; Landmark, B; Foss, K B; Lohmann, S M; Hansson, V; Lea, T; Jahnsen, T
We have previously identified and characterized regulatory (R) subunits of cyclic AMP-dependent protein kinase, particularly the RII subunits in rat tissues (Jahnsen, T., Lohmann, S. M., Walter, U., Hedin, L., and Richards, J. S. (1985) J. Biol. Chem. 260, 15980-15987; Jahnsen, T., Hedin, L., Lohmann, S. M., Walter, U., and Richards, J. S. (1986) J. Biol. Chem. 261, 6637-6639; Jahnsen, T., Hedin, L., Kidd, V. J., Beattie, W. G., Lohmann, S. M., Walter, U., Durica, J., Schulz, T. Z., Schiltz, E., Browner, M., Lawrence, C. B., Goldman, D., Ratoosh, S. L., and Richards, J. S. (1986) J. Biol. Chem. 261, 12352-12361). These studies showed that rat RII alpha and RII beta had apparent molecular masses of 54 and 52 kDa, respectively. The aim of the present study was to purify and characterize cAMP-dependent protein kinase R subunits in human testis and to examine which of the subunits (mRNAs and proteins) are present in this tissue. Our results show that human testis contains mRNAs for five out of the seven known subunits of cAMP-dependent protein kinase. We observed strong expression of mRNAs for RI alpha (1.5 and 3.2 kilobases (kb)), RII alpha (2.2, 2.4, and 7.0 kb), and RII beta (3.3 kb). We also demonstrated mRNAs for two of the three catalytic subunits, C alpha (2.7 kb) and C gamma (1.7 kb). Purification of R subunits by DEAE-cellulose and cAMP affinity chromatography revealed three distinct forms with apparent molecular masses of 49, 51, and 53 kDa, respectively. Characterization of these R subunits by their 8-azido-cAMP photoaffinity labeling and immunoreactivity, as well as by a phosphorylation-dependent mobility shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), indicated subunit sizes of RII beta (53 kDa) greater than RII alpha dephosphoform (51 kDa) greater than RI alpha (49 kDa). This conclusion was verified by the analysis of RII subunits produced by in vitro transcription/translation of full-length cDNAs for both human RII alpha and RII beta in wheat germ lysates. The in vitro translated products were the same size as the purified human testis subunits, and only the smallest RII subunit (RII alpha) revealed a distinct mobility shift on SDS-PAGE after phosphorylation/dephosphorylation. This study supports the conclusion that the mobilities of human RII subunits (RII alpha, RII beta) on SDS-PAGE are reversed in contrast with those of other species such as rat and bovine.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1544918
Derivation of quantitative removal efficiency of protein stain from K/S value of washing test fabric soiled with hemoglobin.
Kurono, Rie; Nishio, Naoki; Oya, Masaru
We have improved a previous method for the preparation of hemoglobin-soiled fabrics in order to facilitate quantitative calculation of the efficiency with which protein stains can be removed from such materials. We then evaluated the sensitivity of surface reflectance as a method for stain quantification. Test fabrics were made by spotting a white fabric with a certain amount of hemoglobin solution and drying it. We observed a large difference between the percentage stain removal as measured by surface reflectance when compared with chemical analysis. Deformities in the surface of the soiled fabric caused by capillary action in the drying process likely contributed to this difference. Quantitative removal percentage could be predicted easily from the K/S values of test fabrics that were dry-heated without steam, although soil adhesion was too weak to evaluate the washing power of commercial detergent. Overall, we found that practical test fabrics with adequate soil adhesion properties can be prepared by adopting a steam heating process after dry heating. PMID:23535309
Quantitative expression patterns of peroxisome proliferator-activated receptor-{beta}/{delta} (PPAR{beta}/{delta}) protein in mice
Girroir, Elizabeth E. [Department of Veterinary and Biomedical Sciences, Center of Molecular Toxicology and Carcinogenesis, Pennsylvania State University, 312 Life Sciences Building, University Park, PA 16802 (United States); Hollingshead, Holly E. [Department of Veterinary and Biomedical Sciences, Center of Molecular Toxicology and Carcinogenesis, Pennsylvania State University, 312 Life Sciences Building, University Park, PA 16802 (United States); Graduate Program in Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, PA 16802 (United States); He Pengfei; Zhu Bokai; Perdew, Gary H. [Department of Veterinary and Biomedical Sciences, Center of Molecular Toxicology and Carcinogenesis, Pennsylvania State University, 312 Life Sciences Building, University Park, PA 16802 (United States); Peters, Jeffrey M. [Department of Veterinary and Biomedical Sciences, Center of Molecular Toxicology and Carcinogenesis, Pennsylvania State University, 312 Life Sciences Building, University Park, PA 16802 (United States); Graduate Program in Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, PA 16802 (United States)], E-mail: email@example.com
The expression patterns of PPAR{beta}/{delta} have been described, but the majority of these data are based on mRNA data. To date, there are no reports that have quantitatively examined the expression of PPAR{beta}/{delta} protein in mouse tissues. In the present study, a highly specific PPAR{beta}/{delta} antibody was developed, characterized, and used to examine tissue expression patterns of PPAR{beta}/{delta}. As compared to commercially available anti-PPAR{beta}/{delta} antibodies, one of six polyclonal anti-PPAR{beta}/{delta} antibodies developed was significantly more effective for immunoprecipitation of in vitro-translated PPAR{beta}/{delta}. This antibody was used for quantitative Western blot analysis using radioactive detection methods. Expression of PPAR{beta}/{delta} was highest in colon, small intestine, liver, and keratinocytes as compared to other tissues including heart, spleen, skeletal muscle, lung, brain, and thymus. Interestingly, PPAR{beta}/{delta} expression was localized in the nucleus and RXR{alpha} can be co-immunoprecipitated with nuclear PPAR{beta}/{delta}. Results from these studies demonstrate that PPAR{beta}/{delta} expression is highest in intestinal epithelium, liver, and keratinocytes, consistent with significant biological roles in these tissues.
Influence of ignored and well-known zone distortions on the separation performance of proteins in capillary free zone electrophoresis with special reference to analysis in polyacrylamide-coated fused silica capillaries in various buffers. I. Theoretical studies.
Hjertķn, Stellan; Mohabbati, Sheila; Westerlund, Douglas
Distortion of the starting zone upon its electrophoretic migration toward the detection window gives rise to both symmetrical zones caused by diffusion, sedimentation in the horizontal section of the capillary and the curvature of the capillary, and asymmetrical zones having their origin in Joule heating, sedimentation in the vertical section of the capillary, pH and conductivity differences between the sample zone and the surrounding buffer, solute adsorption onto the capillary wall, and association-dissociation of complexes between the analyte and a buffer constituent or between analytes. Interestingly and importantly a theoretical study shows that moderate pH and conductivity differences as well as adsorption and all of the above interactions when they are characterized by a fast on/off kinetics do not increase the zone broadening (or only slightly), because the sharpening of one boundary of the zone is about the same as the broadening of the other boundary. In addition the peak symmetry caused by a conductivity difference is in most experiments counteracted by a pH difference. The experimentally determined plate numbers in the absence of electroosmosis exceeded one million per meter in some experiments (Part II). These plate numbers are among the highest reported [Z. Zhao, A. Malik, M.L. Lee, Anal. Chem. 65 (1993) 2747; M. Gilges, K. Kleemiss, G. Schomburg, Anal. Chem. 66 (1994) 2038; H. Wan, M. Ohman, L.G. Blomberg, J. Chromatogr. A 924 (2001) 591 (plate numbers determined in the presence of electroosmosis may be higher, although the width of the zone in the capillary may be larger) [p. 680 in S. Hjertķn, Electrophoresis 11 (1990) 665]). Capillary free zone electrophoresis is perhaps the only separation method, which, under optimum conditions, gives a plate number not far from the theoretical limit. A prerequisite for this high performance is that the polyacrylamide-coated capillary is washed with 2 M HCl between the runs and stored in water over night (Part II). The difference between the experimentally determined total variance and the sum of the calculated variances originating from the width of the starting zone, longitudinal diffusion, Joule heating, sedimentation in the vertical section of the capillary, curvature of the capillary (i.e., the sum of all other variances) was in our most successful experiments about 28% of the variance of diffusion. The zone broadening, 2sigma, caused by diffusion was estimated at 0.77 mm. The total zone width (2sigma) calculated from the experimentally determined plate number was as small as 1 mm when the migration distance was 40 cm. Accordingly, the only efficient way to reduce drastically the total zone width is to decrease the analysis time and, thereby, the diffusional broadening. An important finding was that the variance originating from the loops of the capillary is not always negligible in high-performance runs. Therefore, one should employ straight capillaries and avoid CE apparatus with cartridges that require a strong curvature of the capillary, common in most commercial instruments. Mathematical formulas have been derived for the sedimentation of the solute zone, the enrichment factor, and the migration time in experiments where the solute is dissolved in a dilute running buffer. This zone sharpening method gave very narrow starting zones (0.04-0.4 mm). However, upon high dilution of the buffer the enrichment becomes so strong that part of the sample zone probably sediments out of the capillary; the almost inevitable change in pH may decrease the mobility of the proteins and, thus, cause the enrichment factor to become still lower than expected. Diffusion of the protein in the very narrow starting zone (located close to the tip of the capillary) and sometimes the thermal expansion of the buffer in the capillary contributes to additional loss of protein in the enrichment step. In some buffers, the interaction between the protein and the buffer constituents is so slow that the peaks become broad. Therefore, different types of buffers should be tested when high resolu
Quantitative measurement of epidermal growth factor receptor-mitogen-activated protein kinase signal transduction using a nine-plex, peptide-based immunoassay.
Rauh-Adelmann, Christine; Moskow, John M; Graham, James R; Yen, Lucy G; Boucher, Jeffrey I; Murphy, Cheryl E; Nadler, Timothy K; Gordon, Neal F; Radding, Jeffrey A
Aberrant epidermal growth factor receptor (EGFR, ErbB1) signaling is implicated in cell transformation, motility, and invasion in a variety of cell types, and EGFR is the target of several anticancer drugs. However, the kinetics of EGFR signaling and the individual contributions of site-specific phosphorylation events remain largely unknown. A peptide-based, multiplex immunoassay approach was developed to simultaneously measure both total and phosphorylated protein in a single sample. The approach involves the proteolytic digestion of proteins prior to the isolation and quantitation of site-specific phosphorylation events within an individual protein. Quantitation of phosphorylated and total proteins, in picomolar to nanomolar concentrations, were interpolated from standard curves generated with synthetic peptides that correspond to the peptide targets used in the immunoassays. In this study, a bead-based, nine-plex immunoassay measuring total and phosphorylated protein was constructed to measure temporal, site-specific phosphorylation of key members of the EGFR pathway (ErbB1 receptor, MEK1, MEK2, ERK1, and ERK2) in A431 cells stimulated with epidermal growth factor. The effect of MEK inhibition on this pathway was determined using a known MEK kinase inhibitor, SL327. The results reported herein are the first quantitative measurements of site-specific phosphorylation events and total proteins in a single sample, at the same time representing a new paradigm for standardized protein and phosphorylation analysis using multiplexed, peptide-based, sandwich immunoassays. PMID:18275835
Investigating the Cellular Distribution and Interactions of HIV-1 Nucleocapsid Protein by Quantitative Fluorescence Microscopy
Anton, Halina; Taha, Nedal; Boutant, Emmanuel; Richert, Ludovic; Khatter, Heena; Klaholz, Bruno; Rondķ, Philippe; Rķal, Elķonore; de Rocquigny, Hugues; Mķly, Yves
The nucleocapsid protein (NCp7) of the Human immunodeficiency virus type 1 (HIV-1) is a small basic protein containing two zinc fingers. About 2000 NCp7 molecules coat the genomic RNA in the HIV-1 virion. After infection of a target cell, the viral core enters into the cytoplasm, where NCp7 chaperones the reverse transcription of the genomic RNA into the proviral DNA. As a consequence of their much lower affinity for double-stranded DNA as compared to single-stranded RNAs, NCp7 molecules are thought to be released in the cytoplasm and the nucleus of infected cells in the late steps of reverse transcription. Yet, little is known on the cellular distribution of the released NCp7 molecules and on their possible interactions with cell components. Hence, the aim of this study was to identify potential cellular partners of NCp7 and to monitor its intracellular distribution and dynamics by means of confocal fluorescence microscopy, fluorescence lifetime imaging microscopy, fluorescence recovery after photobleaching, fluorescence correlation and cross-correlation spectroscopy, and raster imaging correlation spectroscopy. HeLa cells transfected with eGFP-labeled NCp7 were used as a model system. We found that NCp7-eGFP localizes mainly in the cytoplasm and the nucleoli, where it binds to cellular RNAs, and notably to ribosomal RNAs which are the most abundant. The binding of NCp7 to ribosomes was further substantiated by the intracellular co-diffusion of NCp7 with the ribosomal protein 26, a component of the large ribosomal subunit. Finally, gradient centrifugation experiments demonstrate a direct association of NCp7 with purified 80S ribosomes. Thus, our data suggest that NCp7 molecules released in newly infected cells may primarily bind to ribosomes, where they may exert a new potential role in HIV-1 infection. PMID:25723396
Investigating the cellular distribution and interactions of HIV-1 nucleocapsid protein by quantitative fluorescence microscopy.
Anton, Halina; Taha, Nedal; Boutant, Emmanuel; Richert, Ludovic; Khatter, Heena; Klaholz, Bruno; Rondķ, Philippe; Rķal, Elķonore; de Rocquigny, Hugues; Mķly, Yves
The nucleocapsid protein (NCp7) of the Human immunodeficiency virus type 1 (HIV-1) is a small basic protein containing two zinc fingers. About 2000 NCp7 molecules coat the genomic RNA in the HIV-1 virion. After infection of a target cell, the viral core enters into the cytoplasm, where NCp7 chaperones the reverse transcription of the genomic RNA into the proviral DNA. As a consequence of their much lower affinity for double-stranded DNA as compared to single-stranded RNAs, NCp7 molecules are thought to be released in the cytoplasm and the nucleus of infected cells in the late steps of reverse transcription. Yet, little is known on the cellular distribution of the released NCp7 molecules and on their possible interactions with cell components. Hence, the aim of this study was to identify potential cellular partners of NCp7 and to monitor its intracellular distribution and dynamics by means of confocal fluorescence microscopy, fluorescence lifetime imaging microscopy, fluorescence recovery after photobleaching, fluorescence correlation and cross-correlation spectroscopy, and raster imaging correlation spectroscopy. HeLa cells transfected with eGFP-labeled NCp7 were used as a model system. We found that NCp7-eGFP localizes mainly in the cytoplasm and the nucleoli, where it binds to cellular RNAs, and notably to ribosomal RNAs which are the most abundant. The binding of NCp7 to ribosomes was further substantiated by the intracellular co-diffusion of NCp7 with the ribosomal protein 26, a component of the large ribosomal subunit. Finally, gradient centrifugation experiments demonstrate a direct association of NCp7 with purified 80S ribosomes. Thus, our data suggest that NCp7 molecules released in newly infected cells may primarily bind to ribosomes, where they may exert a new potential role in HIV-1 infection. PMID:25723396
Quantitative assessment of regulatory proteins in blood as markers of radiation effects in the late period after occupational exposure.
Kirillova, Evgenia N; Zakharova, Maria L; Muksinova, Klara N; Drugova, Elena D; Pavlova, Olga S; Sokolova, Svetlana N
The objective of this research was quantitative assessment of serum and membrane regulatory proteins in blood from nuclear workers as markers of radiation-induced alterations in immune homeostasis in the late period after protracted exposure of nuclear workers with different doses. The effector and regulatory lymphocytes were measured using a flow cytofluorometer in workers from the main facilities of the Mayak PA (aged ?60 y up to 80 y) in the late period after combined exposure to external gamma-rays and internal alpha-radiation from incorporated 239Pu. The control group included non-occupationally exposed members of the Ozyorsk population matched by gender and age to the group of Mayak workers. Thirty serum proteins involved in regulation of immune homeostasis, such as growth factors, multifunctional interleukins, pro- and anti-inflammatory cytokines, and their receptors, were measured using ELISA in blood serum specimens from the Radiobiology Human Tissue Repository. The dosimetry estimates were obtained using Doses-2005. The correlation analysis revealed a statistically significant direct relationship of T-killers and plutonium body burden and a decreasing level of T-helpers with accumulated external dose in exposed individuals. There were differences in expression of membrane markers in young regulatory cells (double null T-lymphocytes, NKT-lymphocytes, regulatory T-cells, and an increase of activated forms of T-lymphocytes), which indicated an active role of regulatory cells in maintaining immune homeostasis in terms of protracted exposure. The assessment of regulatory proteins in blood indicated that growth factors (EGF, TGF-?1, PDGF), multifunctional interleukins (IL-17A, IL-18), and pro-inflammatory cytokines (IL-1? and INF-?) could be potential markers of radiation-induced alterations in protein status. An imbalance of pro- and antiinflammatory proteins in blood and variations of protein profiles at the lower exposure levels (gamma-ray dose <1 Gy, plutonium body burden <0.74 kBq) in the late period after protracted exposure were less pronounced than at the higher exposure levels, which was probably explained by compensatory-adaptive responses in the late period among senile individuals with polypathology. PMID:22647909
Intensity range based quantitative FRET data analysis to localize protein molecules in live cell nuclei.
Chen, Ye; Periasamy, Ammasi
F÷rster (fluorescence) resonance energy transfer (FRET) is an ideal technique to estimate the distance between interacting protein molecules in live specimens using intensity-based microscopy. The spectral overlap of donor and acceptor- essential for FRET-also generates a contamination of the FRET signal. There are a number of algorithms available to remove this spectral bleedthrough (SBT) contamination and in this paper we compare two popular algorithms to estimate the SBT element and to calculate a more precise level of energy transfer efficiency, and with that a more accurate distance estimate. PMID:16397825
Insulin stacking for capillary electrophoresis
Z. K Shihabi; M Friedberg
Stacking methods are very important in overcoming the poor detection limits in capillary electrophoresis. Human insulin, a polypeptide, was concentrated on the capillary (stacked) based on three different and simple treatment methods to the sample: dilute buffers, high salt content, and acetonitrile (66%) were added to the sample to induce stacking. A dilute buffer in the sample caused a limited
Capillary electrophoresis in food analysis
Yiyang Dong
Unlike other chromatographic methods such as gas chromatography and high performance liquid chromatography which were routinely used in almost all food labs, capillary electrophoresis is relatively a novice in food science, the detection limits and low process sample volume is the AchillesÆ heel of this technique. Nevertheless, with ease of its high resolving power, rapid method development, easy sample preparation
Quantitation of fluorescence energy transfer between cell surface proteins via fluorescence donor photobleaching kinetics.
Young, R M; Arnette, J K; Roess, D A; Barisas, B G
We describe practical aspects of photobleaching fluorescence energy transfer measurements on individual living cells. The method introduced by T. M. Jovin and co-workers (see, most recently, Kubitscheck et al. 1993. Biophys. J. 64:110) is based on the reduced rate of irreversible photobleaching of donor fluorophores when acceptor fluorophores are present. Measuring differences in donor photobleaching rates on cells labeled with donor only (fluorescein isothiocyanate-conjugated proteins) and with both donor and acceptor (tetramethylrhodamine-conjugated proteins) allows calculation of the fluorescence energy transfer efficiency. We assess possible methods of data analysis in light of the underlying processes of photobleaching and energy transfer and suggest optimum strategies for this purpose. Single murine B lymphocytes binding various ratios of donor and acceptor conjugates of tetravalent concanavalin A (Con A) and divalent succinyl Con A were examined for interlectin energy transfer by these methods. For Con A, a maximum transfer efficiency of 0.49 +/- 0.02 was observed. Under similar conditions flow cytometric measurements of donor quenching yielded a value of 0.54 +/- 0.03. For succinyl Con A, the maximum transfer efficiency was 0.36. To provide concrete examples of quantities arising in such energy transfer determinations, we present examples of individual cell data and kinetic analyses, population rate constant distributions, and error estimates for the various quantities involved. PMID:7948701
Hyperoxia-Induced Protein Alterations in Renal Rat Tissue: A Quantitative Proteomic Approach to Identify Hyperoxia-Induced Effects in Cellular Signaling Pathways
Hinkelbein, Jochen; B÷hm, Lennert; Spelten, Oliver; Sander, David; Soltķsz, Stefan; Braunecker, Stefan
Introduction. In renal tissue as well as in other organs, supranormal oxygen pressure may lead to deleterious consequences on a cellular level. Additionally, hyperoxia-induced effect in cells and related free radicals may potentially contribute to renal failure. The aim of this study was to analyze time-dependent alterations of rat kidney protein expression after short-term normobaric hyperoxia using proteomics and bioinformatic approaches. Material and Methods. N = 36 Wistar rats were randomized into six different groups: three groups with normobaric hyperoxia (exposure to 100% oxygen for 3?h) and three groups with normobaric normoxia (NN; room air). After hyperoxia exposure, kidneys were removed immediately, after 3 days and after 7 days. Kidney lysates were analyzed by two-dimensional gel electrophoresis followed by peptide mass fingerprinting using tandem mass spectrometry. Statistical analysis was performed with DeCyder 2D software (p < 0.01). Biological functions of differential regulated proteins were studied using functional network analysis (Ingenuity Pathways Analysis and PathwayStudio). Results. Expression of 14 proteins was significantly altered (p < 0.01): eight proteins (MEP1A_RAT, RSSA_RAT, F16P1_RAT, STML2_RAT, BPNT1_RAT, LGMN_RAT, ATPA_RAT, and VDAC1_RAT) were downregulated and six proteins (MTUS1_RAT, F16P1_RAT, ACTG_RAT, ACTB_RAT, 2ABA_RAT, and RAB1A_RAT) were upregulated. Bioinformatic analyses revealed an association of regulated proteins with inflammation. Conclusions. Significant alterations in renal protein expression could be demonstrated for up to 7 days even after short-term hyperoxia. The identified proteins indicate an association with inflammation signaling cascades. MEP1A and VDAC1 could be promising candidates to identify hyperoxic injury in kidney cells.
Quantitative multi-agent models for simulating protein release from PLGA bioerodible nano- and microspheres.
Barat, Ana; Crane, Martin; Ruskin, Heather J
Using poly(lactide-co-glycolide) (PLGA) particles for drug encapsulation and delivery has recently gained considerable popularity for a number of reasons. An advantage in one sense, but a drawback of PLGA use in another, is that drug delivery systems made of this material can provide a wide range of dissolution profiles, due to their internal structure and properties related to particles' manufacture. The advantages of enriching particulate drug design experimentation with computer models, are evident with simulations used to predict and optimize design, as well as indicate choice of best manufacturing parameters. In the present work, we seek to understand the phenomena observed for PLGA micro- and nanospheres, through Cellular Automata (CA) agent-based Monte Carlo (MC) models. Systems are studied both over large temporal scales (capturing slow erosion of PLGA) and for various spatial configurations (capturing initial as well as dynamic morphology). The major strength of this multi-agent approach is to observe dissolution directly, by monitoring the emergent behaviour: the dissolution profile manifested, as a sphere erodes. Different problematic aspects of the modelling process are discussed in details in this paper. The models were tested on experimental data from literature, demonstrating very good performance. Quantitative discussion is provided throughout the text in order to make a demonstration of the use in practice of the proposed model. PMID:18436414
Electrokinetic motion of polarizable particles Dielectrophoresis, induced-charge electrophoresis, electrophoresis of the second kind.
Bazant, Martin Z.
-charge electrophoresis, electrophoresis of the second kind. Definition The electrokinetic motion of polarizable particles results from electro-osmotic flow (induced- charge electrophoresis) of the first of second kind, in addition to electrostatic forces (dielectrophoresis). Overview The classical theory of electrophoresis
Quantitative proteomic dissection of a native 14-3-3? interacting protein complex associated with hepatocellular carcinoma.
Bai, Chen; Tang, Siwei; Bai, Chen; Chen, Xian
The 14-3-3 proteins regulate diverse biological processes that are implicated in cancer development, and seven 14-3-3 isoforms were identified with isoform-specific roles in different human tumors. In our previous work, we dissected the interactome of 14-3-3? formed during the DNA damage response in a hepatocellular carcinoma (HCC) cell using an AACT/SILAC-based quantitative proteomic approach. In this study, we used a similar proteomic approach to profile/identify the 14-3-3? interactome formed in native HCC cells. Functional categorization and data-dependent network analysis of the native HCC-specific 14-3-3? interactome revealed that 14-3-3? is involved in the regulation of multiple biological processes (BPs)/pathways, including cell cycle control, apoptosis, signal transduction, transport, cell adhesion, carbohydrate metabolism, and nucleic acid metabolism. Biological validation further supports that 14-3-3?, via association with multiple BP/pathway-specific proteins, coordinates the regulation of proliferation, survival, and metastasis of HCC. The findings in this study, together with those of our previous study, provide an extensive profile of the 14-3-3? interaction network in HCC cells, which should be valuable for understanding the pathology of HCC and HCC therapy. PMID:24363202
Optimization of Turn Geometries for Microchip Electrophoresis
Santiago, Juan G.
Optimization of Turn Geometries for Microchip Electrophoresis Joshua I. Molho,* Amy E. Herr, Bruce the performance of miniaturized electrophoresis systems that utilize dispersion-introduc- ing turns-chip capillary electrophoresis (CE) is an important separation technique for microfluidic devices.1 Several
Techniques For Focusing In Zone Electrophoresis
NASA Technical Reports Server (NTRS)
Sharnez, Rizwan; Twitty, Garland E.; Sammons, David W.
In two techniques for focusing in zone electrophoresis, force of applied electrical field in each charged particle balanced by restoring force of electro-osmosis. Two techniques: velocity-gradient focusing (VGF), suitable for rectangular electrophoresis chambers; and field-gradient focusing (FGF), suitable for step-shaped electrophoresis chambers.
Quantitative In Vivo Fluorescence Cross-Correlation Analyses Highlight the Importance of Competitive Effects in the Regulation of Protein-Protein Interactions
Sadaie, Wakako; Harada, Yoshie; Matsuda, Michiyuki
Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)¢Ras¢extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction. PMID:24958104
Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effects in the regulation of protein-protein interactions.
Sadaie, Wakako; Harada, Yoshie; Matsuda, Michiyuki; Aoki, Kazuhiro
Computer-assisted simulation is a promising approach for clarifying complicated signaling networks. However, this approach is currently limited by a deficiency of kinetic parameters determined in living cells. To overcome this problem, we applied fluorescence cross-correlation spectrometry (FCCS) to measure dissociation constant (Kd) values of signaling molecule complexes in living cells (in vivo Kd). Among the pairs of fluorescent molecules tested, that of monomerized enhanced green fluorescent protein (mEGFP) and HaloTag-tetramethylrhodamine was most suitable for the measurement of in vivo Kd by FCCS. Using this pair, we determined 22 in vivo Kd values of signaling molecule complexes comprising the epidermal growth factor receptor (EGFR)-Ras-extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway. With these parameters, we developed a kinetic simulation model of the EGFR-Ras-ERK MAP kinase pathway and uncovered a potential role played by stoichiometry in Shc binding to EGFR during the peak activations of Ras, MEK, and ERK. Intriguingly, most of the in vivo Kd values determined in this study were higher than the in vitro Kd values reported previously, suggesting the significance of competitive bindings inside cells. These in vivo Kd values will provide a sound basis for the quantitative understanding of signal transduction. PMID:24958104
Identification and Characterization of Species of the Family Bacteriodaceae by Polyacrylamide Gel Electrophoresis
Ann Strom; J. K. Dyer; Connell Marsh; Jack L. Tribble
A method is described for identifying and characterizing microorganisms of the family Bacteroidaceae by their protein profiles. Protein profiles of six species and several strains of this family were compared using gradient polyacrylamide gel electrophoresis in the slab form. The protein profiles were sufficiently distinct and reproducible to allow identification of species, subspecies, and even minor strain differences. This technique
Craft, George E; Chen, Anshu; Nairn, Angus C
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including ParkinsonÆs disease and AlzheimerÆs disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders. PMID:23623823
Novel absorption detection techniques for capillary electrophoresis
Xue, Y.
Capillary electrophoresis (CE) has emerged as one of the most versatile separation methods. However, efficient separation is not sufficient unless coupled to adequate detection. The narrow inner diameter (I.D.) of the capillary column raises a big challenge to detection methods. For UV-vis absorption detection, the concentration sensitivity is only at the {mu}M level. Most commercial CE instruments are equipped with incoherent UV-vis lamps. Low-brightness, instability and inefficient coupling of the light source with the capillary limit the further improvement of UV-vis absorption detection in CE. The goals of this research have been to show the utility of laser-based absorption detection. The approaches involve: on-column double-beam laser absorption detection and its application to the detection of small ions and proteins, and absorption detection with the bubble-shaped flow cell.
abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes
Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC¢MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were expressed in the respective Flp-In HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed that the expression level of SH-GFP was ?50% lower than that of SH-TBK1_MOUSE. Subsequently, the input material was normalized to obtain a similar quantity of purified SH-tagged proteins. Optimization of the release of protein complexes from the anti-HA-agarose with different eluting agents was then assessed. With respect to the total number of protein groups identified in the purified complexes, elution with 2% SDS surpassed both 100 mM glycine and 100 mM formic acid. Relative quantitation of the purified protein complexes using TMT 6-plex reagents confirmed the higher efficiency of the 2% SDS elution followed by filter-aided sample preparation (FASP). The data presented in this study provide a new application of FASP to quantitative MS analysis of affinity-purified protein complexes. We have termed the approach abFASP-MS, or affinity-based filter-aided sample preparation mass spectrometry. PMID:24400740
Irreversible effects of dichloromethane on the brain after long term exposure: a quantitative study of DNA and the glial cell marker proteins S-100 and GFA
L E Rosengren; P Kjellstrand; A Aurell; K G Haglid
Two astroglial proteins S-100 and GFA, as well as DNA, were quantitatively determined in different regions of the gerbil brain after continuous long term exposure to moderate concentrations of dichloromethane. The intention of the experiment was to expose three groups of animals at three different solvent concentrations (210, 350, or 700 ppm) for three months. Because of the high mortality
Quantitative method for the assignment of hinge and shear mechanism in protein domain movements
Taylor, Daniel; Cawley, Gavin; Hayward, Steven
Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a æhingeÆ mechanism and those with a æshearÆ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term æshearÆ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/. Contact: email@example.com. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25078396
Quantitative Determination of Site-Specific Conformational Distributions in an Unfolded Protein by Solid State Nuclear Magnetic Resonance
Hu, Kan-Nian; Havlin, Robert H.; Yau, Wai-Ming; Tycko, Robert
Summary Solid state nuclear magnetic resonance (NMR) techniques are used to investigate the structure of the 35-residue villin headpiece subdomain (HP35) in folded, partially denatured, and fully denatured states. Experiments are carried out in frozen glycerol/water solutions, with chemical denaturation by guanidine hydrochloride (GdnHCl). Without GdnHCl, two-dimensional solid state 13C NMR spectra of samples prepared with uniform 13C labeling of selected residues show relatively sharp crosspeaks at chemical shifts that are consistent with the known three-helix bundle structure of folded HP35. At high GdnHCl concentrations, most crosspeaks broaden and shift, qualitatively indicating disruption of the folded structure and development of static conformational disorder in the frozen denatured state. Conformational distributions at one residue in each helical segment are probed quantitatively with three solid state NMR techniques that provide independent constraints on backbone ? and ? torsion angles in samples with sequential pairs of carbonyl 13C labels. Without GdnHCl, the combined data are well fit by ?-helical conformations. At [GdnHCl] = 4.5 M, corresponding to the approximate denaturation midpoint, the combined data are well fit by a combination of ?-helical and partially extended conformations at each site, but with a site-dependent population ratio. At [GdnHCl] = 7.0 M, corresponding to the fully denatured state, the combined data are well fit by a combination of partially extended and polyproline II conformations, again with a site-dependent population ratio. Two entirely different models for conformational distributions lead to nearly the same best-fit distributions, demonstrating the robustness of these conclusions. This work represents the first quantitative investigation of site-specific conformational distributions in partially folded and unfolded states of a protein by solid state NMR. PMID:19647001
Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins
Traaseth, Nathaniel J.; Chao, Fa-An; Masterson, Larry R.; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi
NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R1? and Carr¢Purcell¢Meiboom¢Gill (CPMG) R2 experiments are commonly used to characterize ?s to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R1? and transverse R2?) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (kex ~ 104¢105 s?1). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R1? and R2? relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R1? and R2? that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R1? experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent. PMID:22621977
Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins
NASA Astrophysics Data System (ADS)
Traaseth, Nathaniel J.; Chao, Fa-An; Masterson, Larry R.; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi
NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R1? and Carr-Purcell-Meiboom-Gill (CPMG) R2 experiments are commonly used to characterize ?s to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R1? and transverse R2?) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (kex ś 104-105 s-1). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R1? and R2? relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R1? and R2? that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R1? experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent.
Investigation of endogenous soybean food allergens by using a 2-dimensional gel electrophoresis approach.
Rouquiķ, David; Capt, Annabelle; Eby, William H; Sekar, Vaithilingam; Hķrouet-Guicheney, Corinne
As part of the safety assessment of genetically modified (GM) soybean, 2-dimensional gel electrophoresis analyses were performed with the isoxaflutole and glyphosate tolerant soybean FG72, its non-GM near-isogenic counterpart (Jack) and three commercial non-GM soybean lines. The objective was to compare the known endogenous human food allergens in seeds in the five different soybean lines in order to evaluate any potential unintended effect(s) of the genetic modification. In total, 37 protein spots representing five well known soybean food allergen groups were quantified in each genotype. Qualitatively, all the allergenic proteins were detected in the different genetic backgrounds. Quantitatively, among 37 protein spots, the levels of accumulation of three allergens were slightly lower in the GM soybean than in the non-GM counterparts. Specifically, while the levels of two of these three allergens fell within the normal range of variation observed in the four non-GM varieties, the level of the third allergen was slightly below the normal range. Overall, there was no significant increase in the level of allergens in FG72 soybean seeds. Therefore, the FG72 soybean can be considered as safe as its non-GM counterpart with regards to endogenous allergenicity. Additional research is needed to evaluate the biological variability in the levels of endogenous soybean allergens and the correlation between level of allergens and allergenic potential in order to improve the interpretation of these data in the safety assessment of GM soybean context. PMID:20932868
Determination of Three-Bond 1H3?¢ 31P Couplings in Nucleic Acids and Protein¢Nucleic Acid Complexes by Quantitative JCorrelation Spectroscopy
G. Marius Clore; Elizabeth C. Murphy; Angela M. Gronenborn; Ad Bax
A new sensitive two-dimensional quantitativeJcorrelation experiment is described for measuring3JH3?¢Pcouplings in nucleic acids and protein¢nucleic acid complexes. The method is based on measuring the change in intensity of the1H¢1H cross peaks in a constant-time1H¢1H COSY experiment which occurs in the presence and absence of3JH3?¢Pdephasing during the constant-time evolution period. For protein¢nucleic acid complexes where the protein is13C-labeled but the nucleic
Enhancing Centrifugal Separation With Electrophoresis
NASA Technical Reports Server (NTRS)
Herrmann, F. T.
Separation of biological cells by coil-planet centrifuge enhanced by electrophoresis. By itself, coil-planet centrifuge offers relatively gentle method of separating cells under low centrifugal force in physiological medium that keeps cells alive. With addition of voltage gradient to separation column of centrifuge, separation still gentle but faster and more complete. Since separation apparatus contains no rotary seal, probability of leakage, contamination, corrosion, and short circuits reduced.
Separation of biogenic materials by electrophoresis under zero gravity (L-3)
NASA Technical Reports Server (NTRS)
Kuroda, Masao
Electrophoresis separates electrically charged materials by imposing a voltage between electrodes. Though free-flow electrophoresis is used without carriers such as colloids to separate and purify biogenic materials including biogenic cells and proteins in blood, its resolving power and separation efficiency is very low on Earth due to sedimentation, flotation, and thermal convection caused by the specific gravity differences between separated materials and buffer solutions. The objective of this experiment is to make a comparative study of various electrophoresis conditions on the ground and in zero-gravity in order to ultimately develop a method for separating various important 'vial' components which are difficult to separate on the ground.
A quantitative protocol for dynamic measurements of protein interactions by F÷rster resonance energy transfer-sensitized fluorescence emission
Elder, A.D.; Domin, A.; Kaminski Schierle, G.S.; Lindon, C.; Pines, J.; Esposito, A.; Kaminski, C.F.
Fluorescence detection of acceptor molecules sensitized by F÷rster resonance energy transfer (FRET) is a powerful method to study protein interactions in living cells. The method requires correction for donor spectral bleed-through and acceptor cross-excitation as well as the correct normalization of signals to account for varying fluorophore concentrations and imaging parameters. In this paper, we review different methods for FRET signal normalization and then present a rigorous model for sensitized emission measurements, which is both intuitive to understand and practical to apply. The method is validated by comparison with the acceptor photobleaching and donor lifetime-imaging techniques in live cell samples containing EYFP and ECFP tandem constructs exhibiting known amounts of FRET. By varying the stoichiometry of interaction in a controlled fashion, we show that information on the fractions of interacting donors and acceptors can be recovered. Furthermore, the method is tested by performing measurements on different microscopy platforms in both widefield and confocal imaging modes to show that signals recovered under different imaging conditions are in quantitative agreement. Finally, the method is applied in the study of dynamic interactions in the cyclin¢cdk family of proteins in live cells. By normalizing the obtained signals for both acceptor and donor concentrations and using a FRET exhibiting control construct for calibration, stoichiometric changes in these interactions could be visualized in real time. The paper is written to be of practical use to researchers interested in performing sensitized emission measurements. The correct interpretation of the retrieved signals in a biological context is emphasized, and guidelines are given for the practical application of the developed algorithms.
Quantitation of amyloid beta-protein (A beta) in the cortex during aging and in Alzheimer's disease.
Funato, H.; Yoshimura, M.; Kusui, K.; Tamaoka, A.; Ishikawa, K.; Ohkoshi, N.; Namekata, K.; Okeda, R.; Ihara, Y.
In this study we sought to learn about when and how amyloid beta-protein (A beta) accumulates in the cortex of normal individuals and about the difference in the A beta accumulation between normal aged and Alzheimer's disease (AD) brains. From consecutive autopsy cases and AD cases, hippocampus CA1 and occipitotemporal cortex T4 were sampled for A beta quantitation by the well characterized two-site enzyme immunoassays (EIAs). There was a strong tendency toward A beta 42 accumulation between the ages of 50 and 70 years in T4 and a little later in CA1. The A beta 42 levels were consistently higher in T4 than those in CA1 in any given case. The levels of A beta 42 in AD brains were significantly higher than those in control brains, and the extent of A beta 42 amino-terminal modification was also much greater in AD brains than that in control brains. Even in cases in which no senile plaques were immunocytochemically detected, EIAs clearly showed that significant amounts of A beta 42 already had accumulated. In contrast to A beta 42, A beta 40 showed no apparent age-dependent accumulation, and its high levels were found to be associated with AD. PMID:9626067
Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli
Kumar, Ashwani; Stewart, Geordie; Samanfar, Bahram; Aoki, Hiroyuki; Wagih, Omar; Vlasblom, James; Phanse, Sadhna; Lad, Krunal; Yeou Hsiung Yu, Angela; Graham, Christopher; Jin, Ke; Brown, Eric; Golshani, Ashkan; Kim, Philip; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack; Houry, Walid A.; Parkinson, John; Emili, Andrew
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among ?-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems. PMID:24586182
Serum protein identification and quantification of the corona of 5, 15 and 80 nm gold nanoparticles
NASA Astrophysics Data System (ADS)
Schõffler, Martin; Semmler-Behnke, Manuela; Sarioglu, Hakan; Takenaka, Shinji; Wenk, Alexander; Schleh, Carsten; Hauck, Stefanie M.; Johnston, Blair D.; Kreyling, Wolfgang G.
When nanoparticles (NP) enter the body they come into contact with body fluids containing proteins which can adsorb to their surface. These proteins may influence the NP interactions with the biological vicinity, eventually determining their biological fate inside the body. Adsorption of the most abundantly binding proteins was studied after an in vitro 24 hr incubation of monodisperse, negatively charged 5, 15 and 80 nm gold spheres (AuNP) in mouse serum by a two-step analysis: proteomic protein identification and quantitative protein biochemistry. The adsorbed proteins were separated from non-adsorbed proteins by centrifugation and gel electrophoresis and identified using a MALDI-TOF-MS-Proteomics-Analyzer. Quantitative analysis of proteins in gel bands by protein densitometry, required the focus on predominantly binding serum proteins. Numerous proteins adsorbed to the AuNP depending on their size, e.g. apolipoproteins or complement C3. The qualitative and quantitative amount of adsorbed proteins differed between 5, 15 and 80 nm AuNP. Band intensities of adsorbed proteins decreased with increasing AuNP sizes based not only on their mass but also on their surface area. Summarizing, the AuNP surface is covered with serum proteins containing transport and immune related proteins among others. Hence, protein binding depends on the size, surface area and curvature of the AuNP.
Making DNA Hybridization Assays in Capillary Electrophoresis Quantitative
Krylov, Sergey
on P* for detection. The most well-known examples of hybridization assays are Southern and Northern blotting analyses in which the separation step is achieved on a surface.4,5 The target is photolinked. Southern and Northern analyses are time-consuming procedures (take no less than 24 h) with a relatively
Electromigration dispersion in Capillary Electrophoresis
Chen, Zhen; Ghosal, Sandip
In a previous paper (S. Ghosal and Z. Chen Bull. Math. Biol. 2010 72, pg. 2047) it was shown that the evolution of the solute concentration in capillary electrophoresis is described by a nonlinear wave equation that reduced to BurgerÆs equation if the nonlinearity was weak. It was assumed that only strong electrolytes (fully dissociated) were present. In the present paper it is shown that the same governing equation also describes the situation where the electrolytic buffer consists of a single weak acid (or base). A simple approximate formula is derived for the dimensionless peak variance which is shown to agree well with published experimental data. PMID:22147104
Electromigration dispersion in Capillary Electrophoresis
Chen, Zhen; 10.1007/s11538-011-9708-7
In a previous paper (S. Ghosal and Z. Chen Bull. Math. Biol. 2010, vol. 72, pg. 2047) it was shown that the evolution of the solute concentration in capillary electrophoresis is described by a nonlinear wave equation that reduced to Burger's equation if the nonlinearity was weak. It was assumed that only strong electrolytes (fully dissociated) were present. In the present paper it is shown that the same governing equation also describes the situation where the electrolytic buffer consists of a single weak acid (or base). A simple approximate formula is derived for the dimensionless peak variance which is shown to agree well with published experimental data.