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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
Author(s) -
Favrin Giorgio,
Irbäck Anders,
Wallin Stefan
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.10072
Subject(s) - protein folding , hydrogen bond , protein structure prediction , amino acid , chemistry , folding (dsp implementation) , crystallography , statistical potential , pairwise comparison , protein structure , energy minimization , lattice protein , sequence (biology) , protein design , protein secondary structure , topology (electrical circuits) , biological system , computational chemistry , mathematics , biology , biochemistry , combinatorics , molecule , statistics , organic chemistry , electrical engineering , engineering
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three‐helix‐bundle protein, a 46‐amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Gō approximation, which ignores non‐native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root‐mean‐square deviation of 1.8 Å from the native structure. The sequence‐dependent part of our potential is pairwise additive. Our calculations suggest that fine‐tuning this potential by parameter optimization is of limited use. Proteins 2002;47:99–105. © 2002 Wiley‐Liss, Inc.