The creation and utilization of transmembrane pH gradients by membrane-spanning proteins is central to bioenergetics. These processes involve the coupling of proton motion to other changes in the protein such as conformational change or redox state. The objective of this project is to develop a general kinetic model of proton transfer through conformational coupling in with particular application to bacteriorhodopsin. This research will move beyond the equilibrium assumptions implied in pKa calculations while using the energetics of protonation states calculated by the electrostatic model, together with other computational techniques to create a kinetic model in which a system of differential equations represents events such as the transfer of a proton from one sidechain to another, or the switching of protein conformations. This methodology will be applied to the light-driven proton pump, bacteriorhodopsin, for which there is a wealth of structural, spectroscopic and kinetic data, and many mutational studies. This system presents opportunities to challenge the model by comparison of detailed predictions with experimental results.
The model and software will be used in computer science education through a collaboration with Professor Vinhthuy Phan, a professor of computer science at the University of Memphis. The PI will provide versions of the software that implement a stripped-down, rapidly-executable version of the model, and Professor Phan will use them for student projects in his Advanced Algorithms Class. The PI will interact with Professor Phan's students, either one-on-one or in a presentation to the class, explaining the biophysics behind the model and its relationship to biology more broadly. The PI has an adjunct appointment in the Chemistry Department of U. Memphis and currently serves on the advisory committee of a graduate student there working on a computational study of an enzyme mechanism. The University of Memphis has ~22% minority enrollment. The software developed for both research and education will be distributed on an open-source basis. This project is jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Theoretical and Computational Chemistry Program in the Division of Chemistry in the Mathematical and Physical Sciences Directorate.
