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Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures

Pellegrini-Calace, M; Carotti, A; Jones, DT; (2003) Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures. PROTEINS , 50 (4) 537 - 545. 10.1002/prot.10304.

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Abstract

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.

Type:Article
Title:Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3D structures
DOI:10.1002/prot.10304
Keywords:fold recognition, knowledge based, simulated annealing, transmembrane helix, membrane propensity, MOLECULAR-DYNAMICS, RECOGNITION, HELIX, MODEL, ENVIRONMENT, TRYPTOPHAN, INTERFACES, INSERTION, PEPTIDES, BILAYERS
UCL classification:UCL > School of BEAMS > Faculty of Engineering Science > Computer Science

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