text:
Ефремов Роман Гербертович
Доктор физико-математических наук, Профессор
Руководитель подразделения (Лаборатория моделирования биомолекулярных систем), Заместитель директора по науке (Дирекция), Заведующий лабораторией (Центр коллективного пользования "Биоорганика"), Руководитель подразделения (Группа спектрального анализа)
Эл. почта: email@example.com
Личная информация
Работа по профессии
1983: инженер, Отдел инструментальных методов анализа, Институт биоорганической химии им. М. М. Шемякина АН СССР;
1983—1986: аспирант, Факультет экспериментальной и теоретической физики МИФИ;
1986—2007: научный сотрудник, старший научный сотрудник, ведущий научный сотрудник ИБХ РАН;
2007-н. вр.: руководитель подразделения (зав. Лабораторией моделирования биомолекулярных систем), зам. директора ИБХ РАН по научной работе;
1992—1997: приглашенный профессор в Университете г. Реймс и Университете г. Лилль (Франция);
1998-н. вр.: старший научный сотрудник, ведущий научный сотрудник Межведомственного суперкомпьютерного центра РАН (МСЦ РАН);
2001-н. вр.: доцент кафедры биоинженерии Биологического ф-та МГУ им. М. В. Ломоносова.
Преподавательская деятельность
1987—1991: лабораторные занятия по оптическим методам и обработке спектральных данных для студентов МФТИ на базе УНЦ ИБХ АН СССР.
1993—1996: цикл лекций (50 часов) «Эмпирические методы в компьютерном моделировании молекул» для студентов Высшей Школы инженеров (Лилль, Франция), специализирующихся по молекулярной инженерии.
1997-н. вр.: курс лекций по молекулярному моделированию биополимеров для студентов 6 курса ф-та молекулярной и биологической физики МФТИ (на базе УНЦ ИБХ РАН).
1999-н. вр.: курс лекций по молекулярному моделированию биополимеров для студентов 5 курса ф-та молекулярной и биологической физики МФТИ (на базе МСЦ РАН).
2001-н. вр.: курс лекций по молекулярному моделированию для студентов 2 и 3 курсов кафедры биоинженерии Биологического ф-та МГУ.
Руководитель 6 кандидатских диссертаций.
|Период обучения
|Страна, город
|Учебное заведение
|Дополнительная информация
|Россия, Москва
|Московский инженерно-физический институт (МИФИ), Факультет экспериментальной и теоретической физики
|Диплом с отличием (тема: «Математические методы определения вторичной структуры белков и полипептидов на основании спектров КР и полуэмпирических расчетов»)
|Россия, Москва
|Московский государственный университет имени М.В. Ломоносова (МГУ), Биологический факультет
|Диплом кандидата физико-математических наук (тема диссертации: «Топография и микроокружение хромофоров в бактериальном и зрительном родопсинах (спектроскопия комбинационного рассеяния света и квантовохимические расчеты)»)
|Россия, Москва
|Московский государственный университет имени М.В. Ломоносова (МГУ), Биологический факультет
|Диплом доктора физико-математических наук (тема диссертации: «Молекулярное моделирование мембрано-связанных участков белков и пептидов»)
|Россия, Москва
|Московский государственный университет имени М.В. Ломоносова (МГУ), Биологический факультет
|Присвоено ученое звание профессора по специальности «биофизика».
Премии и заслуги
1993: Премия Европейской Академии (Academiae Europaeae) для молодых ученых РФ;
2001—2002, 2005: Стипендия Фонда содействия российской науке для молодых докторов наук.
Основные научные результаты
Основные труды посвящены разработке и применению новых подходов в исследовании пространственной структуры белков и пептидов с помощью оптической спектроскопии и молекулярного моделирования. Результаты исследований опубликованы в более чем 100 статьях в реферируемых журналах.
1985—1992. Серия исследований, посвященных разработке методов спектроскопии резонансного (РКР) и гигантского (ГКР) комбинационного рассеяния пептидов и белков. Впервые получены спектры ГКР мембранных белков — бактериального и зрительного родопсинов. На основании спектральных данных и результатов квантовохимических расчетов исследована топология их хромофор-связывающих центров. Для ряда мембранных белков зарегистрированы первые спектры РКР с возбуждением в УФ-области, предложены высокоэффективные методы цифровой обработки сигналов в спектрах РКР белков.
1992—1997. Выполнена серия работ по молекулярному моделированию структуры трансмембранного (ТМ) домена Na,K-АТФазы. Для этого впервые применен метод детального картирования гидрофобных/гидрофильных свойств ТМ спиралей с помощью метода молекулярного гидрофобного потенциала (МГП). МГП-подход также был успешно использован для изучения гидрофобной организации целого ряда водорастворимых и мембранных белков и пептидов.
1997—2001. Разработана оригинальная теоретическая модель неявно заданной мембраны, предназначенная для исследования поведения пептидов и белков в мембрано-подобном окружении. Результаты вычислений, выполненных для большого набора трансмембранных и периферических пептидов, продемонстрировали хорошее согласие с данными экспериментов.
2002-н. вр. Разработка новейших многоуровневых подходов в компьютерном моделировании пептидов и белков в мембранах различного состава и в водном растворе, в исследовании межмолекулярных взаимодействий белок-белок, белок-мембрана и белок-лиганд. Применение созданных методов в исследовании периферических и интегральных мембранных белков, мембрано-активных пептидов, в рациональном молекулярном конструировании новых биологически активных соединений с заданными свойствами, действующих в т. ч. и на мишени в мембранах клеток. Создание единого информационно-вычислительного комплекса для высокопроизводительного молекулярного моделирования белков и пептидов.
Членство в научных обществах
Член редколлегии журналов «Биоорганическая химия», Москва; «The Open Structural Biology Journal», «The Open Bioinformatics Journal».
Член Ученого Совета ИБХ РАН.
Член специализированных диссертационных советов (МГУ, ГУ НИИ БМХ РАМН).
Избранные публикации
- (2017). Cardiotoxins: Functional Role of Local Conformational Changes. Journal of chemical information and modeling 57 (11), 2799–2810 [+]
Локальная конформационная подвижность жестко структурированных и стабильных молекул цитотоксинов (ЦТ) оказывает влияние на их мембрано-активные свойства. На основании данных молекулярной динамики (МД) трех ЦТ (ЦТ 1, 2 из Naja oxiana и ЦТ А3 из Naja atra) в воде и анализа распределений значений двугранных углов аминокислотных остатков основной цепи выявили общие для исследуемых белков конформационные состояния, характеризующиеся высокоамплитудными изменениями двугранных углов φ и ψ в паре остатков (K5/L6). Указанные локальные конформационные изменения ЦТ являются специфическими «горячими точками», меняющими организацию функционально-активного гидрофобного паттерна (т.н. «гидрофобной подошвы») этих белков. Именно этот мотив отвечает за связывание ЦТ с клеточными мембранами. В ходе МД «подошва» может обратимо разделяться на два участка меньших размеров (Рисунок). Таким образом молекулы ЦТ осуществляют «тонкую подстройку» своей пространственной структуры при связывании с поверхностью клеточной мембраны в зависимости от размеров гидрофобных/гидрофильных кластеров на поверхности липидного бислоя.ID:2011
- (2017). Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin. J. Biomol. Struct. Dyn. , 1–16 [+]
Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from N.oxiana venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by (1)H-NMR spectroscopy. Then, via CG- and FA MD-computations, we evaluated partitioning of CT1 molecule into palmitoyloleoylphosphatidylcholine (POPC) membrane, using the toxin spatial models, obtained either in aqueous solution, or detergent micelle. The latter model exhibits minimal structural changes upon partitioning into the membrane, while the former deviates from the starting conformation, loosing the tightly bound water molecule in the loop-2. These data show that the structural changes elicited by CT1 molecule upon incorporation into DPC micelle take place likely in the lipid membrane, although the mode of the interaction of this toxin with DPC micelle (with the tips of the all three loops) is different from its mode in POPC membrane (primarily with the tip of the loop-1 and both the tips of the loop-1 and loop-2).ID:1943
- (2017). Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They? Biochemistry 56 (34), 4468–4477 [+]
Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly (13)C- and (15)N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.ID:1923
- (2016). High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Protein Surface Topography Method. Sci Rep 6, 36848 [+]
Despite some success for small molecules, elucidating structure-function relationships for biologically active peptides - the ligands for various targets in the organism - remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules' surface as projection maps, which enables the exposure of the structure-function dependencies. Here, we use PST to uncover the "activity pattern" in α-conotoxins - neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by "standard" structure-based drug design. The proposed combination of PST with a set of experiments proved very efficient for the rational construction of new bioactive molecules.ID:1604
- (2016). Структурно-динамическая модель комплекса лантибиотика низин с липидом-II в биомембране. Актуальные вопросы биологической физики и химии 1, 263–267 ID:1680
- (2016). Central loop of non-conventional toxin WTX from Naja kaouthia is important for interaction with nicotinic acetylcholine receptors. Toxicon 119, 274–9 [+]
'Three-finger' toxin WTX from Naja kaouthia interacts with nicotinic and muscarinic acetylcholine receptors (nAChRs and mAChRs). Mutagenesis and competition experiments with (125)I-α-bungarotoxin revealed that Arg31 and Arg32 residues from the WTX loop II are important for binding to Torpedo californica and human α7 nAChRs. Computer modeling suggested that loop II occupies the orthosteric binding site at α7 nAChR. The similar toxin interface was previously described as a major determinant of allosteric interactions with mAChRs.ID:1598
- (2016). Secreted Isoform of Human Lynx1 (SLURP-2): Spatial Structure and Pharmacology of Interactions with Different Types of Acetylcholine Receptors. Sci Rep 6, 30698 [+]
Human-secreted Ly-6/uPAR-related protein-2 (SLURP-2) regulates the growth and differentiation of epithelial cells. Previously, the auto/paracrine activity of SLURP-2 was considered to be mediated via its interaction with the α3β2 subtype of the nicotinic acetylcholine receptors (nAChRs). Here, we describe the structure and pharmacology of a recombinant analogue of SLURP-2. Nuclear magnetic resonance spectroscopy revealed a 'three-finger' fold of SLURP-2 with a conserved β-structural core and three protruding loops. Affinity purification using cortical extracts revealed that SLURP-2 could interact with the α3, α4, α5, α7, β2, and β4 nAChR subunits, revealing its broader pharmacological profile. SLURP-2 inhibits acetylcholine-evoked currents at α4β2 and α3β2-nAChRs (IC50 ~0.17 and >3 μM, respectively) expressed in Xenopus oocytes. In contrast, at α7-nAChRs, SLURP-2 significantly enhances acetylcholine-evoked currents at concentrations <1 μM but induces inhibition at higher concentrations. SLURP-2 allosterically interacts with human M1 and M3 muscarinic acetylcholine receptors (mAChRs) that are overexpressed in CHO cells. SLURP-2 was found to promote the proliferation of human oral keratinocytes via interactions with α3β2-nAChRs, while it inhibited cell growth via α7-nAChRs. SLURP-2/mAChRs interactions are also probably involved in the control of keratinocyte growth. Computer modeling revealed possible SLURP-2 binding to the 'classical' orthosteric agonist/antagonist binding sites at α7 and α3β2-nAChRs.ID:1597
- (2016). Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 6, 33112 [+]
Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed "iris-like" symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.ID:1558
- (2015). Latarcins: versatile spider venom peptides. Cell. Mol. Life Sci. 72 (23), 4501–22 [+]
Arthropod venoms feature the presence of cytolytic peptides believed to act synergetically with neurotoxins to paralyze prey or deter aggressors. Many of them are linear, i.e., lack disulfide bonds. When isolated from the venom, or obtained by other means, these peptides exhibit common properties. They are cationic; being mostly disordered in aqueous solution, assume amphiphilic α-helical structure in contact with lipid membranes; and exhibit general cytotoxicity, including antifungal, antimicrobial, hemolytic, and anticancer activities. To suit the pharmacological needs, the activity spectrum of these peptides should be modified by rational engineering. As an example, we provide a detailed review on latarcins (Ltc), linear cytolytic peptides from Lachesana tarabaevi spider venom. Diverse experimental and computational techniques were used to investigate the spatial structure of Ltc in membrane-mimicking environments and their effects on model lipid bilayers. The antibacterial activity of Ltc was studied against a panel of Gram-negative and Gram-positive bacteria. In addition, the action of Ltc on erythrocytes and cancer cells was investigated in detail with confocal laser scanning microscopy. In the present review, we give a critical account of the progress in the research of Ltc. We explore the relationship between Ltc structure and their biological activity and derive molecular characteristics, which can be used for optimization of other linear peptides. Current applications of Ltc and prospective use of similar membrane-active peptides are outlined.ID:1395
- (2015). Structural Insight into Specificity of Interactions between Nonconventional Three-finger Weak Toxin from Naja kaouthia (WTX) and Muscarinic Acetylcholine Receptors. J. Biol. Chem. 290 (39), 23616–30 [+]
Weak toxin from Naja kaouthia (WTX) belongs to the group of nonconventional "three-finger" snake neurotoxins. It irreversibly inhibits nicotinic acetylcholine receptors and allosterically interacts with muscarinic acetylcholine receptors (mAChRs). Using site-directed mutagenesis, NMR spectroscopy, and computer modeling, we investigated the recombinant mutant WTX analogue (rWTX) which, compared with the native toxin, has an additional N-terminal methionine residue. In comparison with the wild-type toxin, rWTX demonstrated an altered pharmacological profile, decreased binding of orthosteric antagonist N-methylscopolamine to human M1- and M2-mAChRs, and increased antagonist binding to M3-mAChR. Positively charged arginine residues located in the flexible loop II were found to be crucial for rWTX interactions with all types of mAChR. Computer modeling suggested that the rWTX loop II protrudes to the M1-mAChR allosteric ligand-binding site blocking the entrance to the orthosteric site. In contrast, toxin interacts with M3-mAChR by loop II without penetration into the allosteric site. Data obtained provide new structural insight into the target-specific allosteric regulation of mAChRs by "three-finger" snake neurotoxins.ID:1394
- (2015). Role of the Lipid Environment in the Dimerization of Transmembrane Domains of Glycophorin A. Acta Naturae 7 (4), 122–7 [+]
An efficient computational approach is developed to quantify the free energy of a spontaneous association of the α-helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested for the TM segments of human glycophorin A (GpA) and two mutant forms, Gly83Ala and Thr87Val. It was shown that lipids make a significant negative contribution to the free energy of dimerization, while amino acid residues forming the interface of the helix-helix contact may be unfavorable in terms of free energy. The detailed balance between different energy contributions is highly dependent on the amino acid sequence of the TM protein segment. The results show the dominant role of the environment in the interaction of membrane proteins that is changing our notion of the driving force behind the spontaneous association of TM α-helices. Adequate estimation of the contribution of the water-lipid environment thus becomes an extremely urgent task for a rational design of new molecules targeting bitopic membrane proteins, including receptor tyrosine kinases.ID:1396
- (2015). Rational design of new ligands for nicotinic receptors on the basis of α-conotoxin PnIA. Dokl. Biochem. Biophys. 461, 106–9 [+]
A variety of different subtypes of nicotinic acetylcholine receptors (nAChRs) and their involvement in a number of diseases and pathologies (Parkinson's and Alzheimer's diseases, schizophrenia, myasthenia, nicotine addiction) dictates the needs in potent and selective ligands for each subtype. These ligands can be used as a tool for detection and characterization of the distinct nAChR subtypes, as well as be the basis for drug design. Novel cholinergic ligands can emerge in the result of search among natural sources or design (with the use of modern computer modeling) on the basis of known molecules. The significance of the first way was confirmed in our hands by the detection of affinities of a set of marine alkaloids from sponges and ascidians towards some receptor subtypes. The most active of them — makaluvamines — showed micromolar affinity for muscle and neuronal α7 nAChRs. Application of the recently presented Protein Surface Topography method to known natural antagonist of some neuronal nAChRs — α-conotoxin PnIA — resulted in design of new potent analogs with nanomolar affinities for α7 nAChR. Radioactive derivatives of these analogs were successfully applied in radioligand tests for characterization of novel compounds and could be perspective as well for detection of α7 nAChR in the various preparations. Combining these two ways (search and design) was demonstrated in the synthesis of small peptide compounds on the basis of discovered by us in venom of Burmese Viper linear peptide azemiopsin — powerful blocker of muscle-type nAChRs. Some designed peptides have retained a certain affinity to receptor and showed high practical potential: in the absence of toxicity they contributed to the reduction of facial wrinkles (patent application for cosmetic use RU2013102410; PCT/RU2014/000032).ID:1393
- (2014). End-group differentiating ozonolysis of furocoumarins. RSC Advances 4 (106), 61277–61280 [+]
Ozonolysis of furocoumarins followed by reductive work-up yields not only common symmetrical dialdehydes, but also o-formylumbelliferones with moderate-to-high yields. Simultaneous formation of both products accounts for the transformation of carbonyl oxides – products of primary ozonide ring opening.ID:1097
- (2014). Поверхность молекулы -- источник биологической информации. Природа (10), 3–10 [+]
Компьютерное моделирование биологических молекул зачастую основано не на квантовой механике, описывающей строение вещества максимально корректно, а на наборе приближений, уводящих нас от физических «истоков», но позволяющих решать практически важные задачи с использованием ЭВМ. Одним из таких упрощений является концепция молекулярных поверхностей, представляющая молекулу в виде твердого тела, на поверхности которого распределены какие-либо физические свойства. Несмотря на кажущийся примитивизм, этот подход является довольно плодотворным, внося свою лепту в решение актуальных проблем молекулярной биологии, — например, дизайна новых антибиотиков и изучения молекулярных механизмов заболеваний.ID:1092
- (2014). Взаимодействие линейных катионных пептидов с фосфолипидными мембранами и полимерами сиаловой кислоты. Биохимия 79 (5), 583–594583–594 ID:1123
- (2014). Deciphering Fine Molecular Details of Proteins' Structure and Function with a Protein Surface Topography (PST) Method. Journal of chemical information and modeling 54 (4), 1189–99 [+]
Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them-protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.ID:1030
- (2014). PREDDIMER: a web server for prediction of transmembrane helical dimers. Bioinformatics 30 (6), 889–90 [+]
Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps.ID:975
- (2014). Cobra Cardiotoxins: Membrane Interactions and Pharmacological Potential. Curr. Med. Chem. 21 (3), 270–287 [+]
Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, СTs) from cobra venom. They are fully -structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to lipid bilayer was shown to depend on amino acid sequence in the tips of the three loops. In the present review, CT-membrane interactions are analyzed through the prism of data on binding of the toxins to phospholipid liposomes and detergent micelles, as well as their structural and computational studies in membrane mimicking environments. We assess different hydrophobicity scales to compare membrane partitioning of various CTs and their membrane effects. A comparison of hydrophobic/hydrophilic properties of CTs and linear polycationic peptides provides a key to their biological activity and creates a fundamental basis for rational design of new membrane-interacting compounds, including new promising drugs. For instance, since the viewpoint of the data obtained on model lipid membranes, cytotoxic activity of CTs against cancer cells is discussed.ID:974
- (2014). Liquid but Durable: Molecular Dynamics Simulations Explain the Unique Properties of Archaeal-Like Membranes. Sci Rep 4, 7462 [+]
Археи, прежде известные как архебактерии, в основном являются экстремофилами: их среда обитания — это высокие температура, давление, соленость и кислотность. Возможно, «особый путь» архей был определен необычными свойствами их мембран, существенно отличающихся по составу от «обычных» фосфолипидов у бактерий и эукариот. В Лаборатории моделирования биомолекулярных систем ИБХ РАН провели компьютерное исследование архейных мембран, объяснив взаимосвязь между химической структурой липидов и физическими свойствами мембран. Статья опубликована в журнале Scientific Reports. По ее материалам написан пресс-релиз: «Прочные, но гибкие: молекулярная динамика объясняет уникальность биомембран архей».ID:1110
- (2013). Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations. ACS Nano 7 (10), 9428–42 [+]
The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.ID:973
- (2013). Modular Organization of α-Toxins from Scorpion Venom Mirrors Domain Structure of Their Targets, Sodium Channels. J. Biol. Chem. 288 (26), 19014–27 [+]
To gain success in the evolutionary "arms race," venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Navs) and thereby modify the excitability of muscle and nerve cells. Although more than 100 α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Navs is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that despite the small size and relatively rigid structure, these toxins possess modular organization from structural, functional, and evolutionary perspectives. The more conserved and rigid "core module" is supplemented with the "specificity module" (SM) that is comparatively flexible and variable and determines the taxon (mammal versus insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of the extracellular loops of Navs suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain IV, whereas the more versatile SM interacts with the pore domain in repeat I of Navs. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Navs.ID:858
- (2013). Role of Dimerization Efficiency of Transmembrane Domains in Activation of Fibroblast Growth Factor Receptor 3. J. Am. Chem. Soc. , [+]
Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G380R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative "non-active") symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric ("intermediate") and alternative symmetric (putative "active") models. Results of our simulations provide novel atomistic prospective of the role of G380 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.ID:972
- (2013). Lipid-II forms potential "landing terrain" for lantibiotics in simulated bacterial membrane. Sci Rep 3, 1678 [+]
Bacterial cell wall is targeted by many antibiotics. Among them are lantibiotics, which realize their function via interaction with plasma membrane lipid-II molecule - a chemically conserved part of the cell wall synthesis pathway. To investigate structural and dynamic properties of this molecule, we have performed a series of nearly microsecond-long molecular dynamics simulations of lipid-II and some of its analogs in zwitterionic single component and charged mixed simulated phospholipid bilayers (the reference and the mimic of the bacterial plasma membrane, respectively). Extensive analysis revealed that lipid-II forms a unique "amphiphilic pattern" exclusively on the surface of the simulated bacterial membrane (and not in the reference one). We hypothesize that many lantibiotics exploit the conserved features of lipid-II along with characteristic modulation of the bacterial membrane as the "landing site". This putative recognition mechanism opens new opportunities for studies on lantibiotics action and design of novel armament against resistant bacterial strains.ID:839
- (2013). Interaction between the elastin peptide VGVAPG and human elastin binding protein. J. Biol. Chem. 288 (2), 1317–28 [+]
The elastin binding protein (EBP), a spliced variant of lysosomal β-galactosidase, is the primary receptor of elastin peptides that have been linked to emphysema, aneurysm and cancer progression. The sequences recognized by EBP share the XGXXPG consensus pattern found in numerous matrix proteins, notably in elastin where the VGVAPG motif is repeated. To delineate the elastin binding site of human EBP, we built a homology model of this protein and docked VGVAPG on its surface. Analysis of this model suggested that Gln-97 and Asp-98 were required for interaction with VGVAPG because they contribute to the definition of a pocket thought to represent the elastin binding site of EBP. Additionally, we proposed that Leu-103, Arg-107, and Glu-137 were essential residues because they could interact with VGVAPG itself. Site-directed mutagenesis experiments at these key positions validated our model. This work therefore provides the first structural data concerning the interaction of the VGVAPG with its cognate receptor. The present structural data should now allow the development of EBP-specific antagonists.ID:814
- (2013). A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1. J. Bacteriol. 195 (1), 95–104 [+]
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.ID:812
- (2013). На пути к новым антибиотикам. Суперкомпьютеры 12, 34–36 [+]
Проблема резистентности бактерий к действию антибиотиков серьезна как никогда, и медицина всеми силами ищет пути к новым бактерицидным веществам, способным сохранять эффективность в течение долгих лет. Современная биофизика поможет ей в этом — наблюдение за молекулой антибиотика, которая «атакует» бактериальную клетку, подскажет ученым, как создать новые вещества, убивающие бактерий и безвредные для человеческого организма. Возможность для такого наблюдения дают суперкомпьютерные расчеты, а также современные физические модели и математические алгоритмы, предназначенные для изучения в вычислительном эксперименте структуры, динамики и функций сложнейших биологических супрамолекулярных систем. Исследователи из Института биоорганической химии РАН, используя ресурсы нового суперкомпьютера, установленного в лаборатории iScalare МФТИ, изучили на атомном уровне особенности организации мембраны бактерий, используя которые антибиотики преодолевают защитные системы клетки и оказывают антимикробное действие. Полученный результат указывает на возможность разработки нового поколения антибиотиков, избавленных от бремени резистентности.ID:816
- (2013). Физическая водобоязнь. Природа 1, 24–34 [+]
Лист лотоса, по которому вода бегает, собравшись в шарики, водоотталкивающие поверхности и защитные составы для обуви, плавающие в бульоне кружки масла — всё это примеры свойства молекул, называемого гидрофобностью. Помимо этого, гидрофобный эффект играет важную биологическую роль: сворачивание и правильная работа белковых молекул, формирование биомембран, распознавание молекулами друг друга также «запрограммированы» с использованием гидрофобных свойств. Интересно, что гидрофобный эффект не сводится к «обычным» физическим взаимодействиям: за ним стоит Второй закон термодинамики и величина, именуемая энтропией.ID:817
- (2013). Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact. J. Biomol. Struct. Dyn. 31 (1), 87–95 [+]
Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules - this issue still resists easy characterization with modern experimental techniques. In this work, we propose a computational method to detect and analyze parts of membrane with different packing densities and hydrogen bonding patterns. A series of one- and two-component fluid systems containing lipids with the same polar heads and different acyl chains, dioleoylphosphatidylcholine (18:1) and dipalmitoylphosphatidylcholine (16:0), or with same acyl chains and different polar heads, dioleoylphosphatidylserine (18:1) and dioleoylphosphatidylcholine (18:1), were studied via molecular dynamics simulations. Four criteria of clustering were considered. It was shown that the water-lipid interface of biomembranes represents a highly dynamic and "mosaic" picture, whose parameters depend on the bilayer composition. Some systems (e.g. with 20-30% of the anionic lipid) demonstrate unusual clustering properties and demand further investigation at molecular level. Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell.ID:808
- (2012). How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case. Cell. Mol. Life Sci. 69 (24), 4205–13 [+]
The molecular features that dominate the binding mode of agonists by a broadly tuned olfactory receptor are analyzed through a joint approach combining cell biology, calcium imaging, and molecular modeling. The odorant/receptor affinities, estimated through statistics accrued during molecular dynamics simulations, are in accordance with the experimental ranking. Although in many systems receptors recognize their target through a network of oriented interactions, such as H-bonding, the binding by broadly tuned olfactory receptors is dominated by non-polar terms. We show how such a feature allows chemicals belonging to different chemical families to similarly activate the receptors through compensations of interactions within the binding site.ID:811
- (2012). Recent Advances in Computational Modeling of α-Helical Membrane- Active Peptides. Curr. Protein Pept. Sci. 13 (7), 644–57 [+]
Membrane-active peptides (MAPs) represent a broad variety of molecules, and biological functions of most are directly associated with their ability to interact with membranes. Taking into account the effect of MAPs on living cells they can be nominally divided into three major groups - fusion (FPs), antimicrobial/cytolytic (AMPs/CPs) and cellpenetrating (CPPs) peptides. Although spatial structure of different MAPs varies to a great extent, linear α-helical peptides represent the most studied class. These peptides possess relatively simple structural organization and share a set of similar molecular features, which make them very attractive to both experimental and computational studies. Here, we review different molecular modeling methods in prospective of their applications to study of α-helical MAPs. The most sophisticated of them, such as molecular dynamics simulations, give atomistic information about molecular interactions driving peptide binding to the water-lipid interface, cooperative mechanisms of membrane destabilization and thermodynamics of these processes. Significant progress has been achieved in this field during the last few years, resulting in a possibility to observe computationally MAPs action in realistic peptide-to-lipid ratios and over the microsecond timescale. Other relatively simple but powerful approaches allow assessment of important characteristics of MAPs such as α-helical propensity, amphiphilicity, total hydrophobicity, and spatial distribution of charge and hydrophobic/hydrophilic properties, etc. Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities.ID:813
- (2012). Multistate organization of transmembrane helical protein dimers governed by the host membrane. J. Am. Chem. Soc. 134 (35), 14390–400 [+]
Association of transmembrane (TM) helices taking place in the cell membrane has an important contribution to the biological function of bitopic proteins, among which receptor tyrosine kinases represent a typical example and a potent target for medical applications. Since this process depends on a complex interplay of different factors (primary structures of TM domains and juxtamembrane regions, composition and phase of the local membrane environment, etc.), it is still far from being fully understood. Here, we present a computational modeling framework, which we have applied to systematically analyze dimerization of 18 TM helical homo- and heterodimers of different bitopic proteins, including the family of epidermal growth factor receptors (ErbBs). For this purpose, we have developed a novel surface-based modeling approach, which not only is able to predict particular conformations of TM dimers in good agreement with experiment but also provides screening of their conformational heterogeneity. Using all-atom molecular dynamics simulations of several of the predicted dimers in different model membranes, we have elucidated a putative role of the environment in selection of particular conformations. Simulation results clearly show that each particular bilayer preferentially stabilizes one of possible dimer conformations, and that the energy gain depends on the interplay between structural properties of the protein and the membrane. Moreover, the character of protein-driven perturbations of the bilayer is reflected in the contribution of a particular membrane to the free energy gain. We have found that the approximated dimerization strength for ErbBs family can be related to their oncogenic ability.ID:810
- (2012). Structure and dynamics of cardiotoxins. Curr. Protein Pept. Sci. 13 (6), 570–84 [+]
Cytotoxins (or cardiotoxins; CTs) are toxins from cobra venom characterized by the three-finger (TF) fold. CTs are on average 60-residue-long peptides, possessing as many as 4 disulfide bonds. The elements of antiparallel β-structure take origin from the hydrophobic core formed by the disulfides. The β-strands adopt the shape of the three loops, giving the name of the fold. While neurotoxins (NTs) - also TF proteins from snake venom - exert their effect through specific interactions with protein receptors, no specific protein target has been found for CTs. Unlike NTs, CTs are amphiphilic and cytotoxic against a variety of cells, including cancer ones. Thus, the hypothesis that the activity of CTs is caused by their interactions with lipid membranes is currently central. To understand molecular basis behind variations in toxicities of CTs highly homologous in their sequences, detailed knowledge of their structure and dynamics is required. The present review summarizes experimental and computational data on the spatial organization of CTs and their dynamics in various environments (aqueous solution, membranous milieus).ID:772
- (2012). Липидный фундамент жизни. Природа (3), 3–12 [+]
Жизнь в том виде, в каком мы ее знаем, невозможно представить без биомембраны, разделяющей «внутренний мир» клетки и всё остальное пространство. Мембрана обеспечивает взаимодействие клетки с внешней средой, избирательно пропуская многие вещества, а также является средой протекания множества биохимических процессов. И хотя большую часть полезной работы выполняют белки, которыми мембрана буквально «нашпигована», роль липидного матрикса не стоит недооценивать. Липиды — это не просто «океан», в котором плавают белки. Это «умный» океан, чьи физико-химические свойства были тщательно подобраны в ходе эволюции так, чтобы создать эффективную платформу для функционирования и взаимодействия мембранных белков.ID:747
- (2012). Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit. J. Biomol. Struct. Dyn. 30 (1), 62–73 [+]
Enteropeptidase is a key enzyme in the digestion system of higher animals. It initiates enzymatic cascade cleaving trypsinogen activation peptide after a unique sequence DDDDK. Recently, we have found specific activity of human enteropeptidase catalytic subunit (L-HEP) being significantly higher than that of its bovine ortholog (L-BEP). Moreover, we have discovered that L-HEP hydrolyzed several nonspecific peptidic substrates. In this work, we aimed to further characterize species-specific enteropeptidase activities and to reveal their structural basis. First, we compared hydrolysis of peptides and proteins lacking DDDDK sequence by L-HEP and L-BEP. In each case human enzyme was more efficient, with the highest hydrolysis rate observed for substrates with a large hydrophobic residue in P2-position. Computer modeling suggested enzyme exosite residues 96 (Arg in L-HEP, Lys in L-BEP) and 219 (Lys in L-HEP, Gln in L-BEP) to be responsible for these differences in enteropeptidase catalytic activity. Indeed, human-to-bovine mutations Arg96Lys, Lys219Gln shifted catalytic properties of L-HEP toward those of L-BEP. This effect was amplified in case of the double mutation Arg96Lys/Lys219Gln, but still did not cover the full difference in catalytic activities of human and bovine enzymes. To find a missing link, we studied monopeptide benzyl-arginine-β-naphthylamide hydrolysis. L-HEP catalyzed it with an order lower K (m) than L-BEP, suggesting the monopeptide-binding S1 site input into catalytic distinction between two enteropeptidase species. Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles.ID:809
- (2010). Компьютерные игры в молекулярную биофизику. Природа (12), 36–43 [+]
Кконцу XX в. грань между «классическими» науками практически стерлась, исследования стали междисциплинарными. В текущем столетии тенденция усиливается — слияние «обычной» (хотя тоже междисциплинарной!) молекулярной биофизики и того, что называют theoretical computer science, породило необыкновенную область исследований — компьютерный, или in silico, эксперимент. Но прежде чем рассказать о методической подоплеке подхода in silico и о его конкретном использовании для имитационного изучения «жизни» биологических мембран и населяющих их белковых молекул, напомним предысторию.ID:746
- (2010). Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases. Biophys. J. 98 (5), 881–9 [+]
The Eph receptor tyrosine kinases and their membrane-bound ephrin ligands control a diverse array of cell-cell interactions in the developing and adult organisms. During signal transduction across plasma membrane, Eph receptors, like other receptor tyrosine kinases, are involved in lateral dimerization and subsequent oligomerization presumably with proper assembly of their single-span transmembrane domains. Spatial structure of dimeric transmembrane domain of EphA2 receptor embedded into lipid bicelle was obtained by solution NMR, showing a left-handed parallel packing of the transmembrane helices (535-559)(2). The helices interact through the extended heptad repeat motif L(535)X(3)G(539)X(2)A(542)X(3)V(546)X(2)L(549) assisted by intermolecular stacking interactions of aromatic rings of (FF(557))(2), whereas the characteristic tandem GG4-like motif A(536)X(3)G(540)X(3)G(544) is not used, enabling another mode of helix-helix association. Importantly, a similar motif AX(3)GX(3)G as was found is responsible for right-handed dimerization of transmembrane domain of the EphA1 receptor. These findings serve as an instructive example of the diversity of transmembrane domain formation within the same family of protein kinases and seem to favor the assumption that the so-called rotation-coupled activation mechanism may take place during the Eph receptor signaling. A possible role of membrane lipid rafts in relation to Eph transmembrane domain oligomerization and Eph signal transduction was also discussed.ID:320
- (2010). Computer simulations and modeling-assisted ToxR screening in deciphering 3D structures of transmembrane alpha-helical dimers: ephrin receptor A1. Phys Biol 7, 16014 [+]
Membrane-spanning segments of numerous proteins (e.g. receptor tyrosine kinases) represent a novel class of pharmacologically important targets, whose activity can be modulated by specially designed artificial peptides, the so-called interceptors. Rational construction of such peptides requires understanding of the main factors driving peptide-peptide association in lipid membranes. Here we present a new method for rapid prediction of the spatial structure of transmembrane (TM) helix-helix complexes. It is based on computer simulations in membrane-like media and subsequent refinement/validation of the results using experimental studies of TM helix dimerization in a bacterial membrane by means of the ToxR system. The approach was applied to TM fragments of the ephrin receptor A1 (EphA1). A set of spatial structures of the dimer was proposed based on Monte Carlo simulations in an implicit membrane followed by molecular dynamics relaxation in an explicit lipid bilayer. The resulting models were employed for rational design of wild-type and mutant genetic constructions for ToxR assays. The computational and the experimental data are self-consistent and provide an unambiguous spatial model of the TM dimer of EphA1. The results of this work can be further used to develop new biologically active 'peptide interceptors' specifically targeting membrane domains of proteins.ID:312
- (2010). The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution. Acta Crystallogr. D Biol. Crystallogr. 66 (Pt 1), 51–60 [+]
Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure of Salmonella typhimurium uridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2'-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 A resolution (R(cryst) = 17.6%, R(free) = 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2'-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2'-anhydrouridine that might improve the interaction of future inhibitors with StUPh and HUPhI.ID:321
- (2010). Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor. SAR QSAR Environ Res 21 (1), 37–55 [+]
The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists ('beta-blockers') thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor-ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular fragments in ligands and the analysis of their interactions with receptors separately. A series of beta-blockers, based on phenylethanolamines and phenoxypropanolamines, were docked to the beta2-adrenoceptor binding site in the crystal structure. Hydrophobic complementarity between the ligand and the receptor was calculated using the PLATINUM web-server (http://model.nmr.ru/platinum). Based on the analysis of the hydrophobic match for molecular fragments of beta-blockers, we have developed a new scoring function which efficiently predicts dissociation constant (pKd) with strong correlations (r(2) approximately 0.8) with experimental data.ID:323
- (2009). Specific membrane binding of neurotoxin II can facilitate its delivery to acetylcholine receptor. Biophys. J. 97 (7), 2089–97 [+]
The action of three-finger snake alpha-neurotoxins at their targets, nicotinic acetylcholine receptors (nAChR), is widely studied because of its biological and pharmacological relevance. Most such studies deal only with ligands and receptor models; however, for many ligand/receptor systems the membrane environment may affect ligand binding. In this work we focused on binding of short-chain alpha-neurotoxin II (NTII) from Naja oxiana to the native-like lipid bilayer, and the possible role played by the membrane in delivering the toxin to nAChR. Experimental (NMR and mutagenesis) and molecular modeling (molecular-dynamics simulation) studies revealed a specific interaction of the toxin molecule with the phosphatidylserine headgroup of lipids, resulting in the proper topology of NTII on lipid bilayers favoring the attack of nAChR. Analysis of short-chain alpha-neurotoxins showed that most of them possess a high positive charge and sequence homology in the lipid-binding motif of NTII, implying that interaction with the membrane surrounding nAChR may be common for the toxin family.ID:319
- (2009). N-terminal amphipathic helix as a trigger of hemolytic activity in antimicrobial peptides: a case study in latarcins. FEBS Lett. 583 (14), 2425–8 [+]
In silico structural analyses of sets of alpha-helical antimicrobial peptides (AMPs) are performed. Differences between hemolytic and non-hemolytic AMPs are revealed in organization of their N-terminal region. A parameter related to hydrophobicity of the N-terminal part is proposed as a measure of the peptide propensity to exhibit hemolytic and other unwanted cytotoxic activities. Based on the information acquired, a rational approach for selective removal of these properties in AMPs is suggested. A proof of concept is gained through engineering specific mutations that resulted in elimination of the hemolytic activity of AMPs (latarcins) while leaving the beneficial antimicrobial effect intact.ID:318
- (2009). PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 25 (9), 1201–2 [+]
The PLATINUM (Protein-Ligand ATtractions Investigation NUMerically) web service is designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical Molecular Hydrophobicity Potential (MHP). AVAILABILITY: The PLATINUM web tool as well as detailed documentation and tutorial are available free of charge for academic users at http://model.nmr.ru/platinum/. PLATINUM requires Java 5 or higher and Adobe Flash Player 9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.ID:184
- (2009). Adaptation of a membrane-active peptide to heterogeneous environment. I. Structural plasticity of the peptide. The journal of physical chemistry. B 113 (4), 1107–19 [+]
В статье приводится детальное описание различных факторов, определяющих процесс взаимодействия мембрано-активного пептида (неспецифический переносчик—пенетратин) с липидными бислоями разного состава. К ключевым факторам следует отнести: конформационную подвижность пептида, способность аминокислотных остатков образовывать специфические контакты с другими остатками пептида, а также полярными головками липидов.ID:125
- (2009). Adaptation of a membrane-active peptide to heterogeneous environment. II. The role of mosaic nature of the membrane surface. The journal of physical chemistry. B 113 (4), 1120–6 [+]
В статье постулируется мозаичная гидрофобно-гдрофильная организация поверхности липидной мембраны. Рассматривается влияние гетерогенности полярных свойств границы раздела вода-липиды на процесс связывания мембрано-активных агентов (на примере неспецифического пептидного переносчика — пенетратина).ID:126
- (2009). Ligand-specific scoring functions: improved ranking of docking solutions. SAR QSAR Environ Res 19 (1-2), 91–9 [+]
Molecular docking is a powerful computational method that has been widely used in many biomolecular studies to predict geometry of a protein-ligand complex. However, while its conformational search algorithms are usually able to generate correct conformation of a ligand in the binding site, the scoring methods often fail to discriminate it among many false variants. We propose to treat this problem by applying more precise ligand-specific scoring filters to re-rank docking solutions. In this way specific features of interactions between protein and different types of compounds can be implicitly taken into account. New scoring functions were constructed including hydrogen bonds, hydrophobic and hydrophilic complementarity terms. These scoring functions also discriminate ligands by the size of the molecule, the total hydrophobicity, and the number of peptide bonds for peptide ligands. Weighting coefficients of the scoring functions were adjusted using a training set of 60 protein-ligand complexes. The proposed method was then tested on the results of docking obtained for an additional 70 complexes. In both cases the success rate was 5-8% better compared to the standard functions implemented in popular docking software.ID:316
- (2009). [Prediction of the spatial structure of proteins: emphasis on membrane targets]. Bioorg. Khim. 35 (6), 744–60 [+]
Knowledge of the spatial structure of proteins is a prerequisite for both awareness of their functional mechanisms and the framework for rational drug discovery and design. Meanwhile, direct structural determination is often hampered or impractical due to the complexity, expensiveness, and limited capabilities of experimental techniques. These issues are especially pronounced for integral membrane proteins. On numerous occasions, the theoretical prediction of protein structures may facilitate the process by exploiting physical or empirical principles. This paper surveys modern techniques for the prediction of the spatial structure of proteins using computer algorithms, and the main emphasis is placed on the most "complex" targets - membrane proteins (MPs). The first part of the review describes de novo methods based on empirical physical principles; in the second part, a comparative modeling philosophy, which accounts for the structure of related proteins, is described. Special focus is made regarding pharmacologically relevant classes of G-coupled receptors, receptor tyrosine ki-nases, and other MPs. Algorithms for the assessment of the models quality and potential fields of application of computer models are discussed.ID:322
- (2009). Structure elucidation of dimeric transmembrane domains of bitopic proteins. Cell Adh Migr 4 (2), 284–98 [+]
The interaction between transmembrane helices is of great interest because it directly determines biological activity of a membrane protein. Either destroying or enhancing such interactions can result in many diseases related to dysfunction of different tissues in human body. One much studied form of membrane proteins known as bitopic protein is a dimer containing two membrane-spanning helices associating laterally. Establishing structure-function relationship as well as rational design of new types of drugs targeting membrane proteins requires precise structural information about this class of objects. At present time, to investigate spatial structure and internal dynamics of such transmembrane helical dimers, several strategies were developed based mainly on a combination of NMR spectroscopy, optical spectroscopy, protein engineering and molecular modeling. These approaches were successfully applied to homo- and heterodimeric transmembrane fragments of several bitopic proteins, which play important roles in normal and in pathological conditions of human organism.ID:1047
- (2008). Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1. J. Biol. Chem. 283 (43), 29385–95 [+]
Eph receptors are found in a wide variety of cells in developing and mature tissues and represent the largest family of receptor tyrosine kinases, regulating cell shape, movements, and attachment. The receptor tyrosine kinases conduct biochemical signals across plasma membrane via lateral dimerization in which their transmembrane domains play an important role. Structural-dynamic properties of the homodimeric transmembrane domain of the EphA1 receptor were investigated with the aid of solution NMR in lipid bicelles and molecular dynamics in explicit lipid bilayer. EphA1 transmembrane segments associate in a right-handed parallel alpha-helical bundle, region (544-569)(2), through the N-terminal glycine zipper motif A(550)X(3)G(554)X(3)G(558). Under acidic conditions, the N terminus of the transmembrane helix is stabilized by an N-capping box formed by the uncharged carboxyl group of Glu(547), whereas its deprotonation results in a rearrangement of hydrogen bonds, fractional unfolding of the helix, and a realignment of the helix-helix packing with appearance of additional minor dimer conformation utilizing seemingly the C-terminal GG4-like dimerization motif A(560)X(3)G(564). This can be interpreted as the ability of the EphA1 receptor to adjust its response to ligand binding according to extracellular pH. The dependence of the pK(a) value of Glu(547) and the dimer conformational equilibrium on the lipid head charge suggests that both local environment and membrane surface potential can modulate dimerization and activation of the receptor. This makes the EphA1 receptor unique among the Eph family, implying its possible physiological role as an "extracellular pH sensor," and can have relevant physiological implications.ID:317
- (2008). Homology modeling of MT1 and MT2 receptors. European journal of medicinal chemistry 43 (9), 1926–44 [+]
Melatonin is a neurohormone synthesized and secreted mainly during the dark period of the circadian cycle by the pineal gland. It has already been proved to be involved in a number of chronobiological processes, most of them being mediated by its membranar receptors MT1 and MT2. Both are members of the GPCR class and, despite the interest they elicit, their 3D structure is still to be described. Models for both human MT1 and MT2 receptors have been constructed by homology modeling, using the X-ray structure of bovine rhodopsin as template. These models have been evaluated in terms of hydrophobic properties of the helices and refined to take into account the rearrangement of GPCRs necessary for their activation, thus leading to a putative activated model for each subtype.ID:179
- (2008). Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity. Biochemistry 47 (11), 3525–33 [+]
Latarcins, linear peptides from the Lachesana tarabaevi spider venom, exhibit a broad-spectrum antimicrobial activity, likely acting on the bacterial cytoplasmic membrane. We study their spatial structures and interaction with model membranes by a combination of experimental and theoretical methods to reveal the structure-activity relationship. In this work, a 26 amino acid peptide, Ltc1, was investigated. Its spatial structure in detergent micelles was determined by (1)H nuclear magnetic resonance (NMR) and refined by Monte Carlo simulations in an implicit water-octanol slab. The Ltc1 molecule was found to form a straight uninterrupted amphiphilic helix comprising 8-23 residues. A dye-leakage fluorescent assay and (31)P NMR spectroscopy established that the peptide does not induce the release of fluorescent marker nor deteriorate the bilayer structure of the membranes. The voltage-clamp technique showed that Ltc1 induces the current fluctuations through planar membranes when the sign of the applied potential coincides with the one across the bacterial inner membrane. This implies that Ltc1 acts on the membranes via a specific mechanism, which is different from the carpet mode demonstrated by another latarcin, Ltc2a, featuring a helix-hinge-helix structure with a hydrophobicity gradient along the peptide chain. In contrast, the hydrophobic surface of the Ltc1 helix is narrow-shaped and extends with no gradient along the axis. We have also disclosed a number of peptides, structurally homologous to Ltc1 and exhibiting similar membrane activity. This indicates that the hydrophobic pattern of the Ltc1 helix and related antimicrobial peptides specifies their activity mechanism. The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane.ID:315
- (2008). Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state. J. Biol. Chem. 283 (11), 6950–6 [+]
Proper lateral dimerization of the transmembrane domains of receptor tyrosine kinases is required for biochemical signal transduction across the plasma membrane. The spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 embedded into lipid bicelles was obtained by solution NMR, followed by molecular dynamics relaxation in an explicit lipid bilayer. ErbB2 transmembrane segments associate in a right-handed alpha-helical bundle through the N-terminal tandem GG4-like motif Thr652-X3-Ser656-X3-Gly660, providing an explanation for the pathogenic power of some oncogenic mutations.ID:314
- (2007). Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 69 (2), 309–25 [+]
Предложен вычислительный метод предсказания пространственной структуры димеров трансмембранных альфа-спиралей. Подход основан на применении модели неявно заданной мембраны и конформационного поиска методом Монте-Карло в пространстве двугранных углов пептидов. Эффективность метода продемонстрирована на примере трансмембранного домена проапоптотического митохондриального белка BNIP3.ID:124
- (2007). The membrane-proximal fusion domain of HIV-1 GP41 reveals sequence-specific and fine-tuning mechanism of membrane binding. J. Biomol. Struct. Dyn. 25 (2), 195–205 [+]
The membrane interface-partitioning region preceding the transmembrane anchor of the human immunodeficiency virus type 1 (HIV-1) gp41 envelope protein is one of the sites responsible for virus binding to its host cell membrane and subsequent fusion events. Here, we used molecular modeling techniques to assess membrane interactions, structure, and hydrophobic properties of the fusion-active peptide representing this region, several of its homologs from different HIV-1 strains, as well as a peptide - defective gp41 phenotype - unable to mediate cell-cell fusion and virus entry. It is shown that the wild-type peptides bind to the water-membrane interface in alpha-helical conformation, while the mutant adopts partly destabilized helix-break-helix structure on the membrane surface. The wild-type peptides reveal specific "tilted oblique-oriented" pattern of hydrophobicity on their surfaces - the property specific for fusion regions of other viruses. Fusion peptides penetrate into the membrane with their N-termini and reveal "fine-tuning" interactions with membrane and water environments: the shift of this balance (e.g., due to point mutations) may dramatically change the mode of membrane binding, and therefore, may cause loss of fusion activity. The modeling results agree well with experimental data and provide a strategy to delineate fusogenic regions in amino acid sequences of viral proteins.ID:313
- (2007). Method to assess packing quality of transmembrane alpha-helices in proteins. 1. Parametrization using structural data. Journal of chemical information and modeling 47 (3), 1150–62 [+]
Integral membrane proteins (MPs) are pharmaceutical targets of exceptional importance. Modern methods of three-dimensional protein structure determination often fail to supply the fast growing field of structure-based drug design with the requested MPs' structures. That is why computational modeling techniques gain a special importance for these objects. Among the principal difficulties limiting application of these methods is the low quality of the MPs' models built in silico. In this series of two papers we present a computational approach to the assessment of the packing "quality" of transmembrane (TM) alpha-helical domains in proteins. The method is based on the concept of protein environment classes, whereby each amino acid residue is described in terms of its environment polarity and accessibility to the membrane. In the first paper we analyze a nonredundant set of 26 TM alpha-helical domains and compute the residues' propensities to five predefined classes of membrane-protein environments. Here we evaluate the proposed approach only by various test sets, cross-validation protocols and ability of the method to delimit the crystal structure of visual rhodopsin, and a number of its erroneous theoretical models. More advanced validation of the method is given in the second article of this series. We assume that the developed "membrane score" method will be helpful in optimizing computer models of TM domains of MPs, especially G-protein coupled receptors.ID:1
- (2007). Method to assess packing quality of transmembrane alpha-helices in proteins. 2. Validation by "correct vs misleading" test. Journal of chemical information and modeling 47 (3), 1163–70 [+]
We describe a set of tests designed to check the ability of the new "membrane score" method (see the first paper of this series) to assess the packing quality of transmembrane (TM) alpha-helical domains in proteins. The following issues were addressed: (1) Whether there is a relation between the score (S(mem)) of a model and its closeness to the "nativelike" conformation? (2) Is it possible to recognize a correct model among misfolded and erroneous ones? (3) To what extent the score of a homology-built model is sensitive to errors in sequence alignment? To answer the first question, two test cases were considered: (i) Several models of bovine aquaporin-1 (target protein) were built on the structural templates provided by its homologs with known X-ray structure. (ii) Side chains in the spatial models of visual rhodopsin and cytochrome c oxidase were rebuilt based on the backbone scaffolds taken from their crystal structures, and the resulting models were iteratively fitted into the full-atom X-ray conformations. It was shown that the higher the S(mem) value of a model is, the lower its root-mean-square deviation is from the "correct" (crystal) structure of a target. Furthermore, the "membrane score" method successfully identifies the rhodopsin crystal structure in an ensemble of "rotamer-type" decoys, thus providing the way to optimize mutual orientations of alpha-helices in models of TM domains. Finally, being applied to a set of homology models of rhodopsin built on its crystal structure with systematically shifted alignment, the approach demonstrates a prominent ability to detect alignment errors. We therefore assume that the "membrane score" method will be helpful in optimization of in silico models of TM domains in proteins, especially those in GPCRs.ID:2
- (2007). A novel method for packing quality assessment of transmembrane alpha-helical domains in proteins. Biochemistry Mosc. 72 (3), 293–300 [+]
Here we present a novel method for assessment of packing quality for transmembrane (TM) domains of alpha-helical membrane proteins (MPs), based on analysis of available high-resolution experimental structures of MPs. The presented concept of protein-membrane environment classes permits quantitative description of packing characteristics in terms of membrane accessibility and polarity of the nearest protein groups. We demonstrate that the method allows identification of native-like conformations among the large set of theoretical MP models. The developed "membrane scoring function" will be of use for optimization of TM domain packing in theoretical models of MPs, first of all G-protein coupled receptors.ID:186
- (2007). Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions. Proteins 66 (2), 388–98 [+]
Анализ экспериментально установленных пространственных структур комплексов АТФ-белок был проведен с целью выявить основные закономерности, определяющие молекулярное узнавание аденин-белок. Было показано что основную роль играют гидрофобные котакты и стэкинг, и разработан эффективный метод учета этих взаимодействий в аденин-специфичной оценочной функции.ID:123
- (2007). Molecular lipophilicity in protein modeling and drug design. Curr. Med. Chem. 14 (4), 393–415 [+]
Hydrophobic interactions play a key role in the folding and maintenance of the 3-dimensional structure of proteins, as well as in the binding of ligands (e.g. drugs) to protein targets. Therefore, quantitative assessment of spatial hydrophobic (lipophilic) properties of these molecules is indispensable for the development of efficient computational methods in drug design. One possible solution to the problem lies in application of a concept of the 3-dimensional molecular hydrophobicity potential (MHP). The formalism of MHP utilizes a set of atomic physicochemical parameters evaluated from octanol-water partition coefficients (log P) of numerous chemical compounds. It permits detailed assessment of the hydrophobic and/or hydrophilic properties of various parts of molecules and may be useful in analysis of protein-protein and protein-ligand interactions. This review surveys recent applications of MHP-based techniques to a number of biologically relevant tasks. Among them are: (i) Detailed assessment of hydrophobic/hydrophilic organization of proteins; (ii) Application of this data to the modeling of structure, dynamics, and function of globular and membrane proteins, membrane-active peptides, etc. (iii) Employment of the MHP-based criteria in docking simulations for ligands binding to receptors. It is demonstrated that the application of the MHP-based techniques in combination with other molecular modeling tools (e.g. Monte Carlo and molecular dynamics simulations, docking, etc.) permits significant improvement to the standard computational approaches, provides additional important insights into the intimate molecular mechanisms driving protein assembling in water and in biological membranes, and helps in the computer-aided drug discovery process.ID:185
- (2006). Differences in binding sites of two melatonin receptors help to explain their selectivity to some melatonin analogs: a molecular modeling study. J. Biomol. Struct. Dyn. 24 (2), 91–107 [+]
Numerous diseases have been linked to the malfunction of G-protein coupled receptors (GPCRs). Their adequate treatment requires rational design of new high-affinity and high-selectivity drugs targeting these receptors. In this work, we report three-dimensional models of the human MT(1) and MT(2) melatonin receptors, members of the GPCR family. The models are based on the X-ray structure of bovine rhodopsin. The computational approach employs an original procedure for optimization of receptor-ligand structures. It includes rotation of one of the transmembrane alpha-helices around its axis with simultaneous assessment of quality of the resulting complexes according to a number of criteria we have developed for this purpose. The optimal geometry of the receptor-ligand binding is selected based on the analysis of complementarity of hydrophobic/hydrophilic properties between the ligand and its protein environment in the binding site. The elaborated "optimized" models are employed to explore the details of protein-ligand interactions for melatonin and a number of its analogs with known affinity to MT(1) and MT(2) receptors. The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed.ID:187
- (2006). Solution of the Spatial Structure of Dimeric Transmembrane Domains of Proteins by Heteronuclear NMR Spectroscopy and Molecular Modeling. Biophysics 51 (S1), S23–S27 [+]
Membrane proteins play an important role in various biological processes. An approach combiningID:347
NMR spectroscopy with molecular modeling was used to study the spatial structure and intramolecular dynamics of protein transmembrane domains consisting of two interacting α-helices. The approach was tested with model transmembrane domains and yielded detailed atomic-level data on the protein–protein and protein–lipid interactions.
- (2005). Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations. The journal of physical chemistry. B 109 (31), 15052–9 [+]
Anionic unsaturated lipid bilayers represent suitable model systems that mimic real cell membranes: they are fluid and possess a negative surface charge. Understanding of detailed molecular organization of water-lipid interfaces in such systems may provide an important insight into the mechanisms of proteins' binding to membranes. Molecular dynamics (MD) of full-atom hydrated lipid bilayers is one of the most powerful tools to address this problem in silico. Unfortunately, wide application of computational methods for such systems is limited by serious technical problems. They are mainly related to correct treatment of long-range electrostatic effects. In this study a physically reliable model of an anionic unsaturated bilayer of 1,2-dioleoyl-sn-glycero-3-phosphoserine (DOPS) was elaborated and subjected to long-term MD simulations. Electrostatic interactions were treated with two different algorithms: spherical cutoff function and particle-mesh Ewald summation (PME). To understand the role of lipid charge in the system behavior, similar calculations were also carried out for zwitterionic bilayer composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). It was shown that, for the charged DOPS bilayer, the PME protocol performs much better than the cutoff scheme. In the last case a number of artifacts in the structural organization of the bilayer were observed. All of them were attributed to inadequate treatment of electrostatic interactions of lipid headgroups with counterions. Electrostatic properties, along with structural and dynamic parameters, of both lipid bilayers were investigated. Comparative analysis of the MD data reveals that the water-lipid interface of the DOPC bilayer is looser than that for DOPS. This makes possible deeper penetration of water molecules inside the zwitterionic (DOPC) bilayer, where they strongly interact with carbonyls of lipids. This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers.ID:843
- (2003). Pyrenemethyl ara-uridine-2'-carbamate: a strong interstrand excimer in the major groove of a DNA duplex. Chembiochem 4 (9), 841–7 [+]
The synthesis of new nucleoside derivatives, ara-uridine-2'-carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA-DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a "reversed" absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence-dependent excimer formation in the major groove.ID:768
- (1999). A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. Biophys. J. 76 (5), 2448–59 [+]
В работе дается описание неявно заданной модели мембраны. Показана эффективность модели в предсказании доли альфа-спиральной конформации для нескольких гомопептидов (поли-Leu, поли-Val, поли-Ile, поли-Gly) методом Монте-Карло.ID:122
- (1995). The hydrophobic nature of membrane-spanning alpha-helices as revealed by Monte Carlo simulations and molecular hydrophobicity potential analysis. J. Phys. Chem. 99 (26), 10658–10666 [+]
С помощью двух независимых подходов – метода молекулярного гидрофобного потенциала (МГП) и расчета поведения пептида в явно заданных растворителях с различной степенью полярности методом Монте-Карло – исследована гидрофобная организация альфа-спиральных трансмембранных сегментов нескольких белков. Показана высокая эффективность МГП-подхода в количественной характеризации и картировании гидрофобных/гидрофильных характеристик трансмембранных сегментов белков.ID:121


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Related Content
In the latest Debt Advisory newsletter from Clearwater International, we look at asset based finance and its increasing presence in high-growth and private equity backed businesses.
Asset based finance comprises of invoice finance and asset based lending (ABL). It is an established form of financing that has existed for many years, but has more recently seen increased levels of activity in the mid-market and with sponsored businesses. This is primarily due to the funders having an appetite to lend against assets that were previously excluded and the increased competition from new entrants to the market.
Invoice finance is the most common form of asset based finance, where funding is generated against unpaid invoices and is available to businesses that sell products or services on credit. The funding can help bridge the cash flow cycle between work being done and it being paid for. Facilities can increase as the business debtor book increases, therefore is attractive to businesses experiencing growth.
ABL facilities can be provided against debtors, stock, plant & equipment or property assets. We have also seen financing provided against intangible assets and contractual income streams. Funding is provided as a % of the value of each asset class and can, in some circumstances, be topped up with a cashflow loan, subject to debt servicing and leverage covenants.
The advantages of ABL are typically cheaper interest costs than cash flow loans and funding is often provided on a revolving basis with no amortisation. Committed facilities are also available in the market. The disadvantage is the additional administrative burden with increased reporting, and if sales slow or decrease then funding available will reduce.
Private equity has historically been cautious of asset based finance as the industry was seen as a lender of last resort for distressed businesses. An improved reputation of the lenders has meant there is now a growing acceptance of asset based finance as a viable source of funding.
In summary, asset based finance is now a viable and deliverable funding type that can support a range of businesses and shareholder related transactions. The competitive pricing, committed aspect and revolving nature of the facilities can be structured to meet the growth strategies of many mid-market businesses.
Example ABL Private Equity Transactions
ARLINGTON INDUSTRIES – Cartesian Capital Group
Clearwater International's Debt Advisory team advised Arlington Industries on the £45m (€50m) debt raise from Wells Fargo and Shawbrook Bank for the acquisition of automotive mechanical engineering firm Magal Engineering Group and a refinance of current debt. This will support both the acquisition of Magal Engineering Group and future growth of the enlarged group.
Arlington Industries, backed by US Cartesian Capital Group, provides supply chain integration to global OEMs in the aerospace and automotive sectors. The company's focus is to deliver greater efficiency, shorter supply chains, and consolidation of product and services to its clients. By acquiring various businesses across the aerospace and automotive industries, Arlington is able to better enhance its supply chain offering and utilise the diverse spectrum of talent across the board. The business provides a vast range of services across the markets, from design to manufacture, as well as welding, pressings, coatings, maintenance and logistics.
Magal Engineering Group is an automotive component and system supplier across Europe, Asia and the US. Magal delivers complex design solutions with a depth of engineering capability and competitive pricing. Recognised as a Tier 1 global strategic supplier to the major OEMs, the business is a preferred supplier to brands such as Ford, Jaguar Land Rover and Renault Nissan amongst others.
Clearwater International has advised private equity firm LDC on the management buyout of TXM Plant, including raising a bespoke ABL debt package from PNC Business Credit. TXM Plant is the UK's largest supplier of road rail vehicles and associated attachments to Network Rail and its major contractors involved in maintenance, track renewal and infrastructure projects.
TXM Plant has more than doubled its turnover in the last three years to €57m, securing several major contracts. During this period, it has secured Principal Contractor status and recently secured a four year framework contract to undertake track renewal on the Tyne & Wear Metro, which is operated by Nexus.
The management buyout was backed by leading mid-market private equity firm LDC for an undisclosed sum. The investment comes amidst the UK's biggest ever period of investment in rail infrastructure, which includes major electrification schemes such as; Great Western, Thameslink, and Crossrail, Europe's biggest construction project. Construction of the £56bn (€64bn) HS2 project is expected to start next year and Crossrail 2 recently received Government support.

subset: commoncrawl


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the Biriwa Kona Ebiradze Ebusua and Acting Ebusuapanyin, Joseph Kweku Mensah (Saltpond); Ebusuapanyin Nana Acquaah Harrison (Anomabo); Ebusuapanyin Nana Sam (Cape Coast); Oheneba Kweku Agyepong (Breman Asikuma); Mr. and Mrs J. D. Dadson (Accra); Opanyin J. K. Eshun, (Biriwa); Nana Akyɛr I, (Nyamebɛkyerɛ, near Beposo); Okyeame Kweku Awotwe (Biriwa); Obaapanyin Ama Anooba (Kumasi); Ebusuahemaa Esi Otua (Accra); Ebusuabaatan Adjoa Gyeamisa (Kumasi); Kobina Gyan (Biriwa); Kofi Atta (Accra); Mrs. Rose Amissah (Accra); Arthur Family (Yamoransa); Management and Staff of Capital O2; the General Overseer and the entire membership of International Central Gospel Church (ICGC), Christ Temple, Abossey Okai, Accra; General Overseer and the entire membership of International Charismatic Church, (ICC) Fadama, Accra, regretfully announce the sudden painful death of:
Dr. John Daniel Otoo
(aka Capital O2)
Aged 67
At the Korle-Bu Teaching Hospital on 2nd December 2016
There will be NO wake keeping.
Burial service: FRIDAY 3rd March 2017, at 7:00 a.m. at Christ Temple, International Central Gospel Church (ICGC), Abossey Okai, Accra.
Interment: FRIDAY 3rd March 2017 at Emmanuel Methodist Church Cemetery, Biriwa (Central Region).
Funeral Rites: FRIDAY 3rd March 2017 at St. Martin de Porres School compound, near Dansoman Roundabout.
Thanksgiving Service: SUNDAY 5th March 2017, at 10:00 a.m. at Christ Temple, International Central Gospel Church (ICGC), Abossey Okai, Accra.
Final Funeral rites: SUNDAY 5th March 2017, at St. Martin de Porres School, near Dansoman Roundabout.
Widows: Ms. Josephine Ashun-Sarpy, & Ms. Margaret Quartey-Papafio
Children: Daniel Kwesi Otoo, Rev. Benedict Kweku Otoo, Mrs. Benedicta Ekua Quayson, Linda Patricia Nyaaku (all of Accra); Mrs. Elsie Esi Yeboah (USA); Mrs. Rebecca Baah (UK); Mrs. Eunice Abrokwah, Mrs. Comfort Ekua Yankson, Gloria and Gifty Mensah-Otoo, Kojo Nyamekyɛ Otoo, Mrs. Kate Sonne McJakes (all of Accra).
Grandchildren: Danielle, Faith, Jethro, Benedicta, Emmanuella, Isaac, K.O., Baafour, Ohene Konadu, Leah, Javan, Nikita, Ewura Adjoa, Glen, Janelle, Kwesi George, Nana Aba, Nhyira, Maame Ama.
In-laws: Mrs. Afua Otoo; Mrs. Iris Otoo; Isaac Quayson; Anthony Yeboah; Michael Abrokwah, Moses Baah and Francis Yankson.
Brothers and sisters: Esi Otua(Accra), Kwesi Budu,(Biriwa) J.K. Eshun (Biriwa); Sarah Quashie (USA); Agatha Dadson (Accra); Juliana Obuam-Sekyi (Nyanyano); Janet Obuam (Takoradi); Alex Egyin-Nyenku (Accra); Jane Arthur (Yamoransa); Ama Anooba (Kumasi), Mrs . Elizabeth Aidoo (UK)
Cousins: Isaac and Jacob Eshun (all of Accra) Emmanuel Eshun, Marian Quashie, Emmanuel Kwame Piedu (all of Obuasi); Susanna Eshun (Biriwa); Stephen Quashie (Konongo); Elizabeth Quashie (New Tafo); Agatha Akonor-Mills (Accra); Angelina Kwarteng (Jacobu) John Cassar Fry (Kumasi); Valentine Obuam-Sekyi (Nyanyano); Gilbert Obuam-Sekyi (Takoradi); Dadson siblings—Lily (Rev.) & Bertha (Accra) Gifty & Matilda(USA), Maud & Joseph (UK); Victoria Obuam (Mim); Joseph &Michael Obuam (all of Agona Swedru); Isaac Kwaku Boadu & Mary Boadu (all of Accra; Very Rev. Samuel Esiako (Good Shepherd Methodist Church (Barekese); Adjoa Esuon (Kumasi) Godwin Thompson Baidoo (Biriwa).
Nephews and Nieces: (42) Ama, Kweku and Kofi Baffoe; Monica Baffoe; Josephine Mensah, Kwesi Akyen Annan and siblings, Mrs Henrietta Afful Mensah and siblings, Eric Arthur (Abi Joe) AND OTHERS.
Chief mourners: Biriwa Kona Ebiradze Ebusua; Ag. Ebusuapanyin, Joseph Kweku Mensah; Ebusuapanyin Nana Acquaah Harrison; Ebusuapanyin Nana Sam; Oheneba Kweku Agyepong; Mr. and Mrs. J. D. Dadson; Opanyin J. K. Eshun, Nana Akyɛr I; Okyeame Kweku Awotwe; Obaapanyin Ama Anooba; Ebusuahemaa Esi Otua; Ebusuabaatan Adjoa Gyeamisa; Kobina Gyan; Kofi Atta; Mrs. Rose Amissah; Jane, Agnes and Kwaa Tawia Arthur; Ms. Josephine Ashun-Sarpy, Ms. Margaret Quartey-Papafio; Management and Staff of Capital O2; the General Overseer (ICGC) and the General Overseer (ICC).
All sympathisers are cordially invited
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By Elton on November 09,2006
Hello and welcome to affiliate-tips.co.uk.
This site was launched in November, 2006, as a means to share some of my experiences of affiliate programmes over the years and, hopefully, to exchange information with other webmasters who use affiliate schemes to earn money from their websites.
The site was created as a direct result of me being appointed the Affiliate Manager of TackleBargains, a UK based mail order fishing tackle company. Rather than just email the TackleBargains affiliates, it makes sense to me to publish the ideas on a website so that they can be accessed 365 days a year, by existing and new affiliates.
Also, many of the ideas that I hope to publish over the coming months will apply to any number of affiliate schemes. Some have been learnt by me the hard way, others I've found on the internet in use by people far cleverer than me!
I'll admit that, like many other website owners, I haven't paid enough attention to affiliate schemes over the years. They've always been one of those "when I've got some spare time" jobs that never seem to get done. How stupid have I been? The earlier you do some positive work in relation to affiliate schemes, the more money it can make you over time! All the time that the bright idea you've had (or seen elsewhere) appears in your pending tray and not on your website, it's earning you NOTHING! Get it done today and it could earn you money every day of the week!!
I got a wake up call recently, when I got a cheque from http://www.spex-4-less.com/ and took a look at my stats. I had done no work whatsoever the previous month, yet my earnings for that affiliate alone were over over £100 from a couple of old links on old pages deep within my website. How much could that have been with some effort? I'll never know....but I intend to not let that happen again.
Anyway, enough waffle. This was supposed to be a brief introduction! Hopefully, it's given some idea of what I want this website to be and encouraged you to bookmark it. It may have even encouraged you to click the two links above and sign up to their schemes. Why not? It's free to sign up and takes about a minute to do. You know it makes sense.....
Elton Murphy - Webmaster