Dynamics Of Water Molecules In Bacteriorhodopsin Mutants

Abstract

Water molecules are essential for the functioning of proton-pumping proteins. Bacteriorhodopsin is a light-driven proton pump whose reaction cycle is accompanied by changes in the interactions between the protein and the retinal chromophore with water molecules. Of particular importance is the formation of a chain of water molecules that mediate the reprotonation of the retinal Schiff base from the Asp96 residue. Asp96 is replaced by histidine in channelrhodopsin-1 (G. Nagel et al, Science 296, 2395-2398, 2002), and by glutamate in Neurospora rhodopsin (Y. Fan, L. Shi & L. S. Brown, FEBS 581, 2557-2561, 2007). Significant effects of mutating Asp96 on the proton-pumping kinetics of bacteriorhodopsin, and effects of mutating the corresponding residues in other retinal proteins, have been documented. To understand how replacement of Asp96 affects the dynamics of water molecules in bacteriorhodopsin, we perform molecular dynamics simulations of bacteriorhodopsin wild type and Asp96 mutants.