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Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
Author(s) -
Kaya Hüseyin,
Chan Hue Sun
Publication year - 2003
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.10478
Subject(s) - cooperativity , contact order , chemistry , protein folding , folding (dsp implementation) , chemical physics , crystallography , lattice protein , logarithm , thermodynamics , statistical physics , physics , native state , mathematics , mathematical analysis , biochemistry , electrical engineering , engineering
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally occurring small single‐domain proteins are investigated by evaluating postulated interaction schemes for a set of three‐dimensional 27mer lattice protein models with 97 different CO values. Many‐body interactions are constructed such that contact energies become more favorable when short chain segments sequentially adjacent to the contacting residues adopt native‐like conformations. At a given interaction strength, this scheme leads to folding rates that are logarithmically well correlated with CO (correlation coefficient r = 0.914) and span more than 2.5 orders of magnitude, whereas folding rates of the corresponding Gō models with additive contact energies have much less logarithmic correlation with CO and span only approximately one order of magnitude. The present protein chain models also exhibit calorimetric cooperativity and linear chevron plots similar to that observed experimentally for proteins with apparent simple two‐state folding/unfolding kinetics. Thus, our findings suggest that CO‐dependent folding rates of real proteins may arise partly from a significant positive coupling between nonlocal contact favorabilities and local conformational preferences. Proteins 2003;52:524–533. © 2003 Wiley‐Liss, Inc.