Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pKa and Infrared Spectra

Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of plc shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.