Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures.
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 (FRAGFOLD). 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.
Pellegrini-Calace
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Dipartimento Farmaco-Chimico, Università degli Studi, Bari, Italy.
Carotti
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Jones
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DT
D000596:Amino Acids / Q000032:analysis; D016229:Amyloid beta-Peptides / Q000737:chemistry; D002135:Calcium-Binding Proteins / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry; D016000:Cluster Analysis; D006021:Glycophorins / Q000737:chemistry; D006801:Humans; D008563:Membrane Lipids / Q000737:chemistry / Q000502:physiology; D008564:Membrane Potentials; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D006180:Proton-Translocating ATPases / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*; D000099211:Phospholamban
D000596:Amino Acids; D016229:Amyloid beta-Peptides; D002135:Calcium-Binding Proteins; D036022:Capsid Proteins; D006021:Glycophorins; D008563:Membrane Lipids; D008565:Membrane Proteins; D006180:Proton-Translocating ATPases; D000099211:Phospholamban