Detecting pore-lining regions in transmembrane protein sequences - PubMed (original) (raw)

Detecting pore-lining regions in transmembrane protein sequences

Timothy Nugent et al. BMC Bioinformatics. 2012.

Abstract

Background: Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer. However, the experimental difficulties associated with obtaining high quality crystals has led to their significant under-representation in structural databases. Computational methods that can identify structural features from sequence alone are therefore of high importance.

Results: We present a method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. By labelling pore-lining residues in crystal structures using geometric criteria, we have trained a support vector machine classifier to predict the likelihood of a transmembrane helix being involved in pore formation. Results from testing this approach under stringent cross-validation indicate that prediction accuracy of 72% is possible, while a support vector regression model is able to predict the number of subunits participating in the pore with 62% accuracy.

Conclusion: To our knowledge, this is the first tool capable of identifying pore-lining regions in proteins and we present the results of applying it to a data set of sequences with available crystal structures. Our method provides a way to characterise pores in transmembrane proteins and may even provide a starting point for discovering novel routes of therapeutic intervention in a number of important diseases. This software is freely available as source code from: http://bioinf.cs.ucl.ac.uk/downloads/memsat-svm/.

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Figures

Figure 1

Figure 1

Prediction of pore-lining residues from sequence mapped onto native crystal structures. Homotetrameric calcium-gated potassium channel MthK (left, 1LNQ) bottom-up view; no false positives were predicted. Homodimeric molybdate transporter ModB2C2 (centre, 2ONK) top-down view. Homotetrameric AMPA-subtype glutamate receptor (3KG2, right) bottom-up view. The pore identified by Pore-Walker is shown by yellow spheres, while residues correctly predicted as pore-lining are shown in green (true positives), incorrectly predicted as pore-lining are shown in orange (false positives), correctly predicted as non-pore-lining are shown in grey (true negatives) and incorrectly predicted as non-pore-lining are shown in magenta (false negatives).

Figure 2

Figure 2

Prediction of pore-lining helices from sequence, mapped onto native crystal structures. Homotetrameric potassium channel Kir3.1 (left, 2QKS); both helices in each subunit are correctly classified. Monomeric 12 transmembrane helix multiple-drug resistance transporter NorM (right, 3MKT); 10 out of 12 helices are correctly classified–one false positive and one false negative are predicted. The pore identified by Pore-Walker is shown in yellow spheres, while helices correctly predicted as pore-lining are shown in green (true positives), incorrectly predicted as pore-lining are shown in orange (false positives), correctly predicted as non-pore-lining are shown in grey (true negatives) and incorrectly predicted as non-pore-lining are shown in magenta (false negatives). In both cases, all transmembrane helices were correctly predicted by MEMSAT-SVM.

Figure 3

Figure 3

Correctly predicted stoichiometries of three multimeric pore complexes. Bottom-up view of the heterodimeric maltose transporter malFG (left, 2R6G chain F), homotetrameric inward rectifier potassium channel KirBac1.1 (centre, 1P7B) and heterohexameric formate dehydrogenase (right, 1KQG chain B). Stoichiometry relates to the pore-lining membrane region only–extramembranous chains or those that do not line the pore are excluded. Complexes are coloured by chain, with the Pore-Walker predicted location of the pore shown by yellow spheres.

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