| Abstract
| - A modeling method is presented for protein systems in which proton transport is coupled toconformational change, as in proton pumps and in motors driven by the proton-motive force. Previouslydeveloped methods for calculating pKa values in proteins using a macroscopic dielectric model are extendedbeyond the equilibrium case to a master-equation model for the time evolution of the system through statesdefined by ionization microstate and a discrete set of conformers. The macroscopic dielectric model suppliesfree energy changes for changes of protonation microstate, while the method for obtaining the energeticsof conformational change and the relaxation rates, the other ingredients needed for the master equation,are system dependent. The method is applied to the photoactivated proton pump, bacteriorhodopsin, usingconformational free energy differences from experiment and treating relaxation rates through three adjustableparameters. The model is found to pump protons with an efficiency relatively insensitive to parameter choiceover a wide range of parameter values, and most of the main features of the known photocycle from veryearly M to the return to the resting state are reproduced. The boundaries of these parameter ranges aresuch that short-range proton transfers are faster than longer-range ones, which in turn are faster thanconformational changes. No relaxation rates depend on conformation. The results suggest that an“accessibility switch”, while not ruled out, is not required and that vectorial proton transport can be achievedthrough the coupling of the energetics of ionization and conformational states.
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