Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation

Shigehiko Hayashi, Emad Tajkhorshid, Klaus Schulten

Research output: Contribution to journalArticlepeer-review


The photoisomerization reaction dynamics of a retinal chromophore in the visual receptor rhodopsin was investi gated by means of 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. 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 reaction trajectories reveal that the excited-state dynamics is dynamically homogeneous and synchronous even in the presence of thermal fluctuation of the protein, giving rise to the very fast formation of the photo- product. The synchronous nature of the reaction dynamics in rhodopsin is found to originate from weak perturbation of the protein surroundings and from 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 vibrations during the reaction process, and identify molecular motions underlying the experimentally observed dynamic spectral modulations.

Original languageEnglish (US)
Pages (from-to)403-416
Number of pages14
JournalBiophysical journal
Issue number2
StatePublished - Jan 21 2009

ASJC Scopus subject areas

  • Biophysics


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