Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol soln., and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/mol. mechanics (QM/MM) descriptions). Finite temp. effects are taken into account by mol. dynamics simulations. The different components that det. the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in soln. the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in soln. and in the protein, while it differs greatly with respect to min.-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation. [on SciFinder (R)]