Mechanism of Proton Transfer in Bacteriorhodopsin

Photoinduced proton pumping in bateriorhodopsin (bR) was extensively studied using multiple experimental methods and utilizing various theoretical modeling approaches. These studies usually refer to well-resolved structural data of bacteriorhodopsin. However, despite obtained results, the origin of the proton pumping force initiated by the electronic excitation of retinal remains questionable. Here we discuss the challenges and approaches to modeling the proton transfer in bR and demonstrate that the process, which starts from the electronic excitation of the retinal molecule, is mainly due to the detailed arrangement of the protein environment. Using quantum chemical calculations, we have revealed that the retinal molecule after its excitation is fixed in the ground state of 13-cis,15-syn configuration, as a result of interaction with specific protein residuals. Thus, reaching this fixed configuration, the proton is first transferred to the Asp-85 residue from the water molecule, which is subsequently restored by the proton initially located in the Schiff base.