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Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore
Author(s) -
Röhrig Ute F.,
Guidoni Leonardo,
Rothlisberger Ursula
Publication year - 2005
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200500066
Subject(s) - chromophore , rhodopsin , chemical physics , molecular dynamics , chemistry , dipole , photochemistry , bacteriorhodopsin , computational chemistry , retinal , organic chemistry , biochemistry , membrane
The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine 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 solution 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 solution and in the protein, while it differs greatly with respect to minimum‐energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond‐length alternation.