Molecular dynamics study of the M(412) intermediate of bacteriorhodopsin

Molecular dynamics simulations have been carried out to study the M(412) intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L(550)intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M(412) intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR(568) obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein, The structures of the L(550) intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M(412) 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 bR(568) stage and forms a proton conduction pathway, The conformational change (2) of the protein involves a 60 degrees 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.