transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels

Abstract

Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of beta-barrel outer membrane proteins makes them an important protein class. At the present time, very few non-homologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane (TM) proteins. The transFold web server uses pairwise inter-strand residue statistical potentials derived from globular (non-outer-membrane) proteins to predict the supersecondary structure of TMB. Unlike all previous approaches, transFold does not use machine learning methods such as hidden Markov models or neural networks; instead, transFold employs multi-tape S-attribute grammars to describe all potential conformations, and then applies dynamic programming to determine the global minimum energy supersecondary structure. The transFold web server not only predicts secondary structure and TMB topology, but is the only method which additionally predicts the side-chain orientation of transmembrane beta-strand residues, inter-strand residue contacts and TM beta-strand inclination with respect to the membrane. The program transFold currently outperforms all other methods for accuracy of beta-barrel structure prediction. Available at http://bioinformatics.bc.edu/clotelab/transFold.

Figure 1

(a) Linear representation of three consecutive and paired TM β-strands (standard output). Inter-strand residue contacts are indicated by arrows. (b) Sketch of a four-column tab-delimited text file summarizing the transFold prediction.

Figure 2

Input form for advanced users. The user can set bounds on the number of TM strands, bounds on strand length, shear number (inclination to plane), bounds on lengths of periplasmic and extra-cellular loops. In addition to choosing from a pull-down menu of a variety of hydrophobicity scales, the user can upload customized contact energies.