Mechanism of proton transfer in bacteriorhodopsin
Photoinduced proton pumping in bateriorhodopsin (bR) was extensively studied using multiple experimental methods and utilizing various theoretical modelling approaches. These studies usually refer to the well-resolved structural data of bacteriorhodopsin. However, despite the obtained results, the origin of the proton pumping force initiated by the electronic excitation of retinal remains questionable. 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. Reaching this fixed configuration, the proton is first transferred to the aspartic acid No. 85 (Asp-85) residue from the water molecule, which is subsequently restored by the proton initially located in the Schiff base. We discuss the challenges and approaches to modelling 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.