MOLECULAR MECHANISMS CONTROLLING BACTERIORHODOPSIN

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The light driven proton pump bacteriorhodopsin is one of the simplest energy conversion devices and ion pumps in nature. The convergence of information on the structure, photochemistry, and proton pumping properties of bacteriorhodopsin make it an ideal protein in which to try to understand the molecular mechanisms controlling a proton pump. Thus, the focus of this application is on the individual amino acids near the Schiff base, the active site of bacteriorhodopsin, from bR's initial state through the transformations that it undergoes after absorbing a photon and as it returns to the initial state. In particular, the following four questions will be probed: 1) What controls the pKa(s) of the Schiff base and of D85, the initial proton acceptor and part of the counter ion to the Schiff base? 2) what controls the rate of dark adaptation, and a related process, the rate of thermal reisomerization of the chromophore at the end of the photocycle? 3). What controls (or causes) the proton movements during the photocycle. For example, does the pK of the Schiff base change during the photocycle? What controls the rate of Schiff base deprotonation, the L to M transition? and 4) what is the proton release group and how is proton release controlled? The following ionizable amino acids near the active site will be studied: tyrosine 57 and 185, arginine 82 and lysine 129, as well as the Schiff base and the aspartic acids 85 and 212. We will manipulate not only the protein part of the pigment but also the light-absorbing chromophore using chemically modified retinals.