Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 50, Issue 4, Pages 537-545Publisher
WILEY
DOI: 10.1002/prot.10304
Keywords
fold recognition; knowledge based; simulated annealing; transmembrane helix; membrane propensity
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We present the results of applying a novel knowledge-based method (FILM) to the prediction of small membrane protein structures. The basis of the method is the addition of a membrane potential to the energy terms (pairwise, solvation, steric, and hydrogen bonding) of a previously developed ab initio technique for the prediction of tertiary structure of globular proteins (FRAG-FOLD). The method is based on the assembly of supersecondary structural fragments taken from a library of highly resolved protein structures using a standard simulated annealing algorithm. The membrane potential has been derived by the statistical analysis of a data set made of 640 transmembrane helices with experimentally defined topology and belonging to 133 proteins extracted from the SWISS-PROT database. Results obtained by applying the method to small membrane proteins of known 3D structure show that the method is able to predict, at a reasonable accuracy level, both the helix topology and the conformations of these proteins. (C) 2003 Wiley-Liss, Inc.
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