Molecular dynamics simulation of dark-adapted rhodopsin and free opsin

Molecular dynamics simulation was carried out for the rhodopsin protein to investigate its conformational changes in respect to inclusion of 11-cis retinal chromophore. Molecular dynamics calculations were performed within the time frame 3000 ps. Totally, 3 X 10(6) configurations ofrhodopsin and free opsin were analyzed and compared. It has been shown that the 11-cis retinal rearrangement (adaptation) in opsin strongly affects the surrounding amino acid residues of protein binding pocket and the protein cytoplasmic region. The extracellular part, however, shows comparatively little changes. On basis of the simulation results obtained we propose a molecular mechanism for the rhodopsin protein function as a G-protein-coupled receptor in the state of darkness. We discuss the role of the retinal chromophore as a ligand-antagonist stabilizing the inactive conformation of rhodopsin.