Molecular Dynamics Simulation of the Excited‐State Dynamics of Bacteriorhodopsin

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Abstract
Abstract— The excited‐state dynamics of bacteriorhodopsin was studied by molecular dynamics simulation. For the purpose of suppressing large displacement of amino acid residues on the surface of bacteriorhodopsin, positional restraints were imposed on these residues. A new method was developed to investigate the movement of amino acid residues upon photoexcitation and their role on the ultrafast photoisomerization of the chromophore. The structural change of bacteriorhodopsin was then traced up to 200 fs, i.e. until the formation of the intermediate I. We found that when all the conjugated bonds of the chromophore were allowed to twist freely in the excited state, many bonds including the C13=C14 bond twist in large scale within 100 fs. When only the C13=C14 bond and the single bonds were allowed to twist freely, the twisting took place at most 20° within 200 fs. From these results, it is claimed that a special potential surface is provided for the C13=C14 bond twisting by the protein environment in the course of the isomerization reaction, giving rise to the specific, ultrafast photoisomerization of bacteriorhodopsin. As a trace of such a mechanism, we observed that several functionally important residues incuding Asp85, Asp212 and Tyr185 responded quickly to the photoexcitation of the chromophore.