TCB Publications - Abstract

Dong Xu, Mordechai Sheves, and Klaus Schulten. Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophysical Journal, 69:2745-2760, 1995. (PMC: 1236512)

XU95C 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 sixteen waters inside the protein (Humphrey et al., Biochemistry, 33:3668, 1994). The structures of the $L_{550}$ intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics and simulated annealing (Humphrey et al., submitted for publication). Our simulations reveal that the $M_{412}$ intermediate actually comprises a series of conformations involving (i) a motion of retinal, (ii) protein conformational changes, and (iii) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group: (i) turns the retinal Schiff base nitrogen from an early orientation towards Asp-85 to a late orientation towards Asp-96; (ii) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (iii) 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 observed conformational change (ii) of the protein involves a 60 degree bent of the cytoplasmic side of helix F and is induced through a break of hydrogen bond between Tyr-185 and a water-side group complex in the counterion region.

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