ArticleBiophysical journal2009
Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Critical Assessment of Curvature-Driven Surface Hopping Algorithms.Journal of chemical theory and computation · 2025Article
- Investigation of the Nonradiative Photoprocesses of Unnatural DNA Base: 7-(2-Thienyl)-imidazo[4,5-The journal of physical chemistry. A · 2024Article
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- Multifaceted aspects of charge transfer.Physical chemistry chemical physics : PCCP · 2020Article
- Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies.Biomolecules · 2020Review
- An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin.Biophysical journal · 2018Article
- COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.Journal of molecular modeling · 2018Article
- Local vibrational coherences drive the primary photochemistry of vision.Nature chemistry · 2015Article
- Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures.Biochemistry · 2014Article
- Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.Chemical reviews · 2014Review
- Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment.The journal of physical chemistry. A · 2013Article
- Re-evaluation of rhodopsin's relaxation kinetics determined from femtosecond stimulated Raman lineshapes.The journal of physical chemistry. B · 2011Article
- Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy.Biophysical journal · 2011Article
- Article
- Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy.Biochimica et biophysica acta · 2010Review
- Understanding functional residues of the cannabinoid CB1.Current topics in medicinal chemistry · 2010Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The photoisomerization reaction dynamics of a retinal chromophore in the visual receptor rhodopsin was investigated 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 photoproduct. 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.
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