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Kinetic consequences of native state optimization of surface‐exposed electrostatic interactions in the Fyn SH3 domain
Author(s) -
ZarrineAfsar Arash,
Zhang Zhuqing,
Schweiker Katrina L.,
Makhatadze George I.,
Davidson Alan R.,
Chan Hue Sun
Publication year - 2012
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.23243
Subject(s) - folding (dsp implementation) , contact order , chemical physics , protein folding , chemistry , fyn , sh3 domain , charge density , kinetics , electrostatics , native state , crystallography , physics , biochemistry , proto oncogene tyrosine protein kinase src , kinase , quantum mechanics , electrical engineering , engineering
Abstract Optimization of surface exposed charge–charge interactions in the native state has emerged as an effective means to enhance protein stability; but the effect of electrostatic interactions on the kinetics of protein folding is not well understood. To investigate the kinetic consequences of surface charge optimization, we characterized the folding kinetics of a Fyn SH3 domain variant containing five amino acid substitutions that was computationally designed to optimize surface charge–charge interactions. Our results demonstrate that this optimized Fyn SH3 domain is stabilized primarily through an eight‐fold acceleration in the folding rate. Analyses of the constituent single amino acid substitutions indicate that the effects of optimization of charge–charge interactions on folding rate are additive. This is in contrast to the trend seen in folded state stability, and suggests that electrostatic interactions are less specific in the transition state compared to the folded state. Simulations of the transition state using a coarse‐grained chain model show that native electrostatic contacts are weakly formed, thereby making the transition state conducive to nonspecific, or even nonnative, electrostatic interactions. Because folding from the unfolded state to the folding transition state for small proteins is accompanied by an increase in charge density, nonspecific electrostatic interactions, that is, generic charge density effects can have a significant contribution to the kinetics of protein folding. Thus, the interpretation of the effects of amino acid substitutions at surface charged positions may be complicated and consideration of only native‐state interactions may fail to provide an adequate picture. Proteins 2011. © 2012 Wiley Periodicals, Inc.