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Optimal potentials for predicting inter‐helical packing in transmembrane proteins
Author(s) -
Dobbs H.,
Orlandini E.,
Bonaccini R.,
Seno F.
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10229
Subject(s) - bacteriorhodopsin , glycophorin , transmembrane protein , decoy , protein structure prediction , transmembrane domain , folding (dsp implementation) , chemistry , protein folding , dimer , globular protein , membrane protein , plastocyanin , crystallography , protein structure , biological system , amino acid , membrane , biology , biochemistry , photosystem i , receptor , organic chemistry , chloroplast , electrical engineering , gene , engineering
A set of pairwise contact potentials between amino acid residues in transmembrane helices was determined from the known native structure of the transmembrane protein (TMP) bacteriorhodopsin by the method of perceptron learning, using Monte Carlo dynamics to generate suitable “decoy” structures. The procedure of finding these decoys is simpler than for globular proteins, since it is reasonable to assume that helices behave as independent, stable objects and, therefore, the search in the conformational space is greatly reduced. With the learnt potentials, the association of the helices in bacteriorhodopsin was successfully simulated. The folding of a second TMP (the helix‐dimer glycophorin A) was then accomplished with only a refinement of the potentials from a small number of decoys. Proteins 2002;49:342–349. © 2002 Wiley‐Liss, Inc.