Ab initio molecular dynamics of rhodopsin

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Abstract
We present a Car-Paninello 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 114s to all-trans photo- isomerization 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.

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