Professor Bonnie Berger

transFold: a Web Server for Predicting Transmembrane β-barrels and Inter-strand Residue Interactions from Sequence

J. Waldispühl, B. Berger, P. Clote, and J.-M. Steyaert


Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of β-barrel outer membrane proteins (omps) 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 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 β-strand residues, inter-strand residue contacts and transmembrane β-strand inclination with respect to the membrane. The program transFold currently outperforms all other methods for accuracy of β-barrel structure prediction.

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