THERMODYNAMIC STABILITY OF WATER-MOLECULES IN THE BACTERIORHODOPSIN PROTON CHANNEL - A MOLECULAR-DYNAMICS FREE-ENERGY PERTURBATION STUDY

The proton transfer activity of the light-driven proton pump, bacterio rhodopsin (bR) in the photochemical cycle might imply internal water m olecules. The free energy of inserting water molecules in specific sit es along the bR transmembrane channel has been calculated using molecu lar dynamics simulations based on a microscopic model, The existence o f internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site, Th ermodynamic integration and perturbation methods were used to calculat e free energies of hydration for each hydrated model from molecular dy namics simulations of the creation of water molecules into specific pr otein-binding sites, A rigorous statistical mechanical formulation all owing the calculation of the free energy of transfer of water molecule s from the bulk to a protein cavity is used to estimate the probabilit ies of occupancy in the putative bR proton channel. The channel contai ns a region lined primarily by nonpolar side-chains, Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permi tted, The column forms a continuous hydrogen-bonded chain over 12 Angs trom between a proton donor, Asp 96, and the retinal Schiff base accep tor, The presence of two water molecules in direct hydrogen-bonding as sociation with the Schiff base is found to be strongly favorable therm odynamically, The implications of these results for the mechanism of p roton transfer in bR are discussed.