MOLECULAR-DYNAMICS SIMULATION OF THE EXCITED-STATE DYNAMICS OF BACTERIORHODOPSIN

The excited-state dynamics of bacteriorhodopsin was studied by molecul ar dynamics simulation. For the purpose of suppressing large displacem ent of amino acid residues on the surface of bacteriorhodopsin, positi onal restraints were imposed on these residues. A new method was devel oped to investigate the movement of amino acid residues upon photoexci tation and their role on the ultrafast photoisomerization of the chrom ophore. The structural change of bacteriorhodopsin was then traced up to 200 fs, i.e. until the formation of the intermediate I. We found th at when all the conjugated bonds of the chromophore were allowed to tw ist 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 th e single bonds were allowed to twist freely, the twisting took place a t most 20 degrees within 200 fs. From these results, it is claimed tha t a special potential surface is provided for the C13=C14 bond twistin g by the protein environment in the course of the isomerization reacti on, giving rise to the specific, ultrafast photoisomerization of bacte riorhodopsin. As a trace of such a mechanism, we observed that several functionally important residues incuding Asp85, Asp212 and Tyr185 res ponded quickly to the photoexcitation of the chromophore.