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PROTON-PUMPING MECHANISM

Energy diagram

Four lowest protonation states of wild-type bacteriorhodopsin at pH=7. Filled and empty circles represent protonated and de-protonated sites respectively. The calculations are based on a structure representing the BR (resting) state of the photocycle. In the ground protonation state, Asp96 is protonated, Schiff Base (216) is protonated, Asp85 is deprotonated, and Arg82 is protonated. The release group is protonated, sharing a proton between residues Glu194 and Glu204. A large, ~ 3kT, gap between the ground and the first excited protonation states ensures that the ground state is realized at room temperature and in a wide range of pH. This gap is the basis of experimentally observed extreme robustness of the BR molecular machine which, in Nature, functions efficiently under very broad range of ambient conditions.