Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain†‡§
Arash Zarrine-Afsar
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Arash Zarrine-Afsar and Zhuqing Zhang contributed equally to this work.
Search for more papers by this authorZhuqing Zhang
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7 Canada
Arash Zarrine-Afsar and Zhuqing Zhang contributed equally to this work.
Search for more papers by this authorKatrina L. Schweiker
Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
Search for more papers by this authorGeorge I. Makhatadze
Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
Search for more papers by this authorCorresponding Author
Alan R. Davidson
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada===Search for more papers by this authorCorresponding Author
Hue Sun Chan
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7 Canada
Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada===Search for more papers by this authorArash Zarrine-Afsar
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Arash Zarrine-Afsar and Zhuqing Zhang contributed equally to this work.
Search for more papers by this authorZhuqing Zhang
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7 Canada
Arash Zarrine-Afsar and Zhuqing Zhang contributed equally to this work.
Search for more papers by this authorKatrina L. Schweiker
Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
Search for more papers by this authorGeorge I. Makhatadze
Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
Search for more papers by this authorCorresponding Author
Alan R. Davidson
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada===Search for more papers by this authorCorresponding Author
Hue Sun Chan
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7 Canada
Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada===Search for more papers by this authorArash Zarrine-Afsar's current address is Lash Miller Chemical Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
Katrina L. Schweiker's current address is Air Force Research Laboratory, 3550 Aberdeen Ave SE, Kirtland AFB, NM 87117 USA
Zhuqing Zhang's current address is College of Life Science, Graduate University of the Chinese Academy of Sciences, 19A Yuquanlu, Shijingshan District, Beijing 100049, China
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.
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