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The Prediction of Membrane Protein Structure and Genome Structural Annotation

New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β-barrel and all-α membrane proteins with high accuracy and a low rate of false positives and false negatives. These methods have been integrated in a suite of programs to filter proteomes of Gram-negative bacteria, searching for new membrane proteins.


Introduction
Presently less than 1% of the PDB structures are membrane proteins solved with atomic resolution. Considering also that membrane proteins, even when they belong to the same functional family, share little sequence identity, it is still problematic to develop low-resolution models, with very few exceptions. For this reason, efforts have been directed towards the high accuracy prediction of the location of transmembrane segments along protein sequences (topography) as well as the positions of the N-and C-termini of proteins, with respect to the membrane plane [3]. These predictors take advantage of the fact that membrane proteins are constrained by lipid bilayers of different composition to just two known types of architecture: the so-called all-α helical proteins of the inner membrane, and the β-barrel proteins of the outer membrane of Gram-negative bacteria.
Among all the possible methods described to predict the topology of all-α membrane proteins [3], two are particularly interesting, and consider two different approaches.
Transmembrane propensity scales indicate, on the basis of physicochemical properties, the membrane interacting segments along a protein chain. Experiment-based scales (MPXe) make it possible to account, for example, for the effect of buried salt bridges on hydropathy plot results, which is extremely important when considering proteins involved in ion transport (contributed by Stephen White [9,10]), and, used in combination with other scales (MPtopo) can also predict membrane protein topology.
Alternatively, prediction methods such as TMHMM and HMMTOP [11,16], based on automatic learning, can identify the helix bundle membrane proteins encoded in fully sequenced genomes with very high precision (sensitivity and specificity both around 95%). Topology prediction is also quite good (correct predictions 65-70% of the time). Recently, new topologies have been determined by a combination of topology predictions and standard experimental approaches such as PhoA-or GFP-fusions [5] (contributed by Gunnar von Heijne).
We developed different predictors for the all-β and one for the all-α membrane proteins, Membrane protein structure and genome structural annotation 407 respectively [8,13]. Considering that these predictors are presently among the best performing of their type [3], we propose to integrate them into a suite of predictors (Hunter) capable of filtering the whole proteome for finding new membrane proteins [1]. By this, it is proposed that structural genomics tools can help in classifying ORFs into structural classes.

Prediction of all-β membrane proteins
The outer membrane of Gram-negative bacteria contains unique membrane proteins folded into βbarrel-like structures, comprising an even number of antiparallel β-strands. This type of architecture is well conserved among prokaryotes [15].
Recently, it has also been proposed that in the outer membrane of chloroplasts and mitochondria, proteins containing a similar membrane interacting portion can perform different functions, including voltage-dependent anion channel (VDAC) [2] and unfolded protein transport (TOM40) [7]. To date, the development of methods suited to locating the membrane-spanning regions of these proteins, starting from the sequence, has been scarce [18].
We have implemented two different methods, both based on machine learning, to predict the topography of this type of membrane protein. The first (IRENE, http://www.biocomp.unibo.it, [8]) is based on neural networks, and the second is based on HMMs (CINZIA [13]). The two methods, trained and tested with a jackknife procedure on sequence profiles, and endowed with a dynamic programming-based filter [6], perform similarly on a set of 15 non-redundant all-β membrane proteins taken from the PDB. The HMM-based method is superior to NN only when both are trained with sequence profiles [13].
However, when tested on a much larger set of well-annotated sequences from the SWISS PROT database, the rate of false positives is lower in the case of the HMM-based predictor. This is due to the intrinsic capability of HMMs to act as more stringent filters than NN, especially when, as in this case, patterns are rather difficult to discriminate based only on the local context. Indeed, transmembrane β-strands are rather similar to the β-strands of globular proteins in both composition and pattern [8].  Starting from the sequence of any outer membrane protein of mitochondria and chloroplasts, it is possible to locate the transmembrane strands along the chain (Figure 1). If the number of strands is equal to that of a known β-barrel in the database, then threading is possible. The alignment can be made with the constraint that the positions of the β-strands are conserved. This procedure made possible the evaluation of the first model of a voltagedependent anion channel capable of fitting most of the experimental data published so far [2].

Prediction of all-α membrane proteins
Membrane proteins in the inner membrane fold as α-helix bundles [17]. Several predictors are available through the web [3,4]. However, none of them have been specifically trained on the structures available with atomic resolution. Prompted by the finding that most predictors fail in correctly locating the positions of the membrane spanning regions of recently crystallized proteins, we implemented a tool integrating one neural network and two HMMs, suited to predicting more and less hydrophobic helices (ENSEMBLE) [12]. The predictor trained and tested with the sequence profiles of 59 chains of well-resolved membrane proteins with a jackknife procedure, correctly predicts the topography of 53 proteins ( Figure 2).

Proteome filtering
A requisite of any predictor used to screen a whole proteome is that the rate of false predictions is known. An estimate of this measure can be obtained by filtering some 1000 non-redundant chains including different structural classes of globular proteins, and a large set of well-annotated chains of membrane proteins from the SWISS PROT database. The reported rate of false predictions for both CINZIA [13] and ENSEMBLE [12] is rather low (10% of false positives and 15% of false negatives for CINZIA, 3% of false positives and 3% of false negatives for ENSEMBLE, respectively). A possible application of these predictors is therefore genome screening, with the specific aim of fishing out new membrane proteins. This issue has so far been addressed separately in the literature for either type of membrane proteins. In our case, we implemented a suite of predictors (HUNTER, [1]) that also includes a signal peptide predictor of the SignalP type [14], and is capable of screening a proteome of some 5000 proteins in about 2 days, on a 1GHz PC.
The results of this analysis, as performed on a selection of freely available genomes of Gramnegative bacteria, suggests that the approximate content of alpha helical membrane proteins is in the range of 20%, confirming the results of other similar screenings with different predictors.
However, the novelty is that the amount of beta barrel membrane proteins in the proteome is in the range of 1-2% of the whole protein content and that this is quite independent of the type of bacterium, and of its pathogenicity. In this way, complete lists of proteins in a given structural class (membrane all-α, or all-β, and globular, as a complement of the first two types) can be produced and can then be aligned to the SWISS PROT database. Using this procedure, those ORFs that have not yet been assigned an annotation, that are classified in either class of membrane proteins, can be highlighted. The non-annotated protein list is then available for experimental determination. We suggest that this tool can help in focusing on those proteins of the proteome that still lack annotation.