Molecular simulation of hydrogen bonding interaction and proton transfer mechanism in bacteriorhodopsin

The bacteriorhodopsin crystal structure from PDB (1R84) was taken as the model system to study the possible mechanism of the proton transfer by molecular simulations. The change of the system in I ps was simulated by using CHARMM package, under the conditions of constant temperature and volume. The proton transfers among Asp85, Asp212, water and retinal were analyzed through the change of separation distance. Two structures, EC and CP, which indicate different distance between the proton of Schiff base and the acid residues, were paid particular attention to. Simulations suggest a possible sequential mechanism for the proton transfer: the proton on Schiff base is transferred to oxygen of water molecule at first, and the proton transfer from water molecule to oxygen of Asp85 residue follows. During the simulation, Asp212 was found to retain the EC pattern, thus the sequential proton transfer was predicted favorably.