Molecular dynamics study of the M412 intermediate of bacteriorhodopsin

Molecular dynamics simulations have been carried out to study the M₄₁₂ intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L₅₅₀ intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M₄₁₂ intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR₅₆₈ obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L₅₅₀ intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M₄₁₂ intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (3) adds two water molecules to the three water molecules existing in the cytoplasmic channel at the bR₅₆₈ stage and forms a proton conduction pathway. The conformational change (2) of the protein involves a 60° bent of the cytoplasmic side of helix F and is induced through a break of a hydrogen bond between Tyr-185 and a water-side group complex in the counterion region.