TCB Publications - Abstract

Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Photochemical reaction dynamics of the primary event of vision studied by a hybrid molecular simulation. Biophysical Journal, 96:403-416, 2009. (PMC: 19167292)

HAYA2009 Photoisomerization reaction dynamics of a retinal chromophore in a visual receptor rhodopsin (Rh) is investigated by hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. The photoisomerization reaction of retinal constitutes the primary step of vision, and is known as one of the fastest reactions in nature. In order to elucidate the molecular mechanism of the high efficiency of the reaction, we carried out hybrid ab initio QM/MM MD simulations of the complete reaction process from the vertically excited state to the photoproduct via electronic transition in the entire chromophore-protein complex. An ensemble of the reaction trajectories unveil that the excited state dynamics is dynamically homogeneous and coherent even in the presence of thermal fluctuation of the protein, giving rise to the very fast formation of the photoproduct. The coherent nature of the reaction dynamics is found to originate from weak perturbation of the protein surroundings and dynamic regulation of volume conserving motions of the chromophore. The simulations also provide a detailed view of time-dependent modulations of hydrogen-out-of-plane (HOOP) vibrations during the reaction process, identifying molecular motions underlying dynamic spectral modulations observed experimentally.

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