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Secondary structure length as a determinant of folding rate of proteins with two‐ and three‐state kinetics
Author(s) -
Huang JiTao,
Cheng JinPei,
Chen Hui
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.21282
Subject(s) - folding funnel , folding (dsp implementation) , metastability , lattice protein , protein secondary structure , contact order , chemistry , protein folding , phi value analysis , kinetics , crystallography , downhill folding , native state , unobservable , protein structure , limiting , intermediate state , biophysics , chemical physics , biology , physics , biochemistry , mathematics , organic chemistry , quantum mechanics , electrical engineering , engineering , mechanical engineering , atomic physics , econometrics
We present a simple method for determining the folding rates of two‐ and three‐state proteins from the number of residues in their secondary structures (secondary structure length). The method is based on the hypothesis that two‐ and three‐state foldings share a common pattern. Three‐state proteins first condense into metastable intermediates, subsequent forming of α‐helices, turns, and β‐sheets at slow rate‐limiting step. The folding rate of such proteins anticorrelate with the length of these β‐secondary structures. It is also assumed that in two‐state folding, rapidly folded α‐helices and turns may facilitate formation of fleeting unobservable “intermediates” and thus show two‐state behavior. There is an inverse relationship between the folding rate and the length of β‐sheets and loops. Our study achieves 94.0 and 88.1% correlations with folding rates determined experimentally for 21 three‐ and 38 two‐state proteins, respectively, suggesting that protein‐folding rates are determined by the secondary structure length. The kinetic kinds are selected on the basis of a competitive formation of hydrophobic collapse and α‐structure in early intermediates. Proteins 2007. © 2007 Wiley‐Liss, Inc.