Visual pigment rhodopsin: a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre

Based on a computer molecular simulation, we have investigated the conformational dynamics of rhodopsin and its free opsin. A special emphasis was made on the behaviour of the chromophore group — 11-cis-retinal within the rhodopsin molecule in its dark-adapted state. The molecular dynamics trajectories were traced in the time range of 3000 ps. We have generated 3×10⁶ discrete states of free opsin and rhodopsin in order to compare the rhodopsin and opsin structural conformation changes. Analysis of the 11-cis-retinal adjustment process in the chromophore site of opsin in correlation with the behaviour of the nearest surrounding amino acid residues has been carried out. The possible molecular mechanisms of the conformational adaptation of 11-cis-retinal in the protein binding pocket, which occur during the physiological regeneration of the visual pigment rhodopsin, are discussed.