Ab initio molecular dynamics of rhodopsin

Abstract

We present a Car-Parrinello ab initio molecular dynamics study of the retinylidene chromophore of rhodopsin, the protein responsible for the first step in vision. The primary photochemical event involves an 11-cis to all-trans photoisomerization of a protonated Schiff base of retinal. The ground-state structures of the two conformations of the chromophore, before and after the photon absorption, have been determined by a simulated annealing procedure. We compute the electrostatic and the torsional contributions to the energy storage in the primary photoproduct and study the role played by a counterion located in the vicinity of the chromophore. We also analyse localization and dynamics of a positively charged soliton on the chromophore backbone. The non-planarity of the chromophore results in a strong coupling of the soliton dynamics to the out-of-plane hydrogen oscillations, which may be relevant for the photoinduced isomerization process.