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Ranking the factors that contribute to protein β‐sheet folding
Author(s) -
Parisien Marc,
Major François
Publication year - 2007
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.21475
Subject(s) - beta sheet , folding (dsp implementation) , lattice protein , protein folding , function (biology) , hydrogen bond , hydrophobic effect , ranking (information retrieval) , chemistry , energy (signal processing) , biological system , protein structure , chemical physics , computer science , topology (electrical circuits) , mathematics , combinatorics , artificial intelligence , biology , molecule , engineering , biochemistry , statistics , organic chemistry , evolutionary biology , electrical engineering
The formation of β‐sheet domains in proteins involves five energetically important factors: the formation of networks of hydrogen bonds and hydrophobic faces, and the residue propensities, or preferences, to be found at the edges of the β‐sheet, to adopt the extended conformation, and to make contact with other residues. These relative energy contributions define a potential energy function. Here, we show how optimizing this potential energy function reveals the formation of hydrophobic faces as the utmost factor. The potential energy function was optimized to minimize the Z ‐scores of the native topologies among the exhaustive sets of over 400 different β‐sheets. These results corroborate with experimental data that showed the environment of a protein is an important modulator of β‐sheet folding. The contact propensities were found to be the least important, which could explain the poor predictive power of β‐strand alignment methods based on pair‐wise contact matrices. Proteins 2007. © 2007 Wiley‐Liss, Inc.