Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle

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Contents Vol 63(3)

doi:10.1071/CH09509

Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle

Qiao Sun ^A ^E, Sufan Wang ^B ^E, Hong Zhang ^A, Zhen Li ^A, Christoph Pifisterer ^C, Stefan Fischer ^C, Shinko Nanbu ^D, Sean C. Smith ^A ^F

^A Centre for Computational Molecular Science, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia.
^B College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
^C Computational Biochemistry Group, IWR, University of Heidelberg, D-69120 Heidelberg, Germany.
^D Department of Materials and Life Sciences, Faculty of Science & Technology, Sophia University, Kioi-Cho 7-1, Chiyoda-ku, Tokyo 102-8554, Japan.
^E Q. Sun and S. Wang contributed equally to this work.
^F Corresponding author. Email: s.smith@uq.edu.au





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Australian Journal of Chemistry 63(3) 363–370 http://dx.doi.org/10.1071/CH09509
Submitted: 21 September 2009 Accepted: 30 November 2009 Published online: 26 March 2010

Abstract

We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.