Biophys. J.

The dynamics of proton transfer between the surface of purple membrane and the aqueous bulk have recently been investigated by the Laser Induced Proton Pulse Method. Following a Delta- function release of protons to the bulk, the system was seen to regain its state of equilibrium within a few hundreds of microseconds. These measurements set the time frame for the relaxation of any state of acid-base disequilibrium between the bacteriorhodopsin's surface and the bulk. It was also deduced that the released protons react with the various proton binding within less than 10 mus. In the present study, we monitored the photocycle and the proton-cycle of photo-excited bacteriorhodopsin, in the absence of added buffer, and calculated the proton balance between the Schiff base and the bulk phase in a time-resolved mode. It was noticed that the late phase of the M decay (beyond 1 ms) is characterized by a slow (subsecond) relaxation of disequilibrium, where the Schiff base is already reprotonated but the pyranine still retains protons. Thus, it appears that the protonation of D96 is a slow rate-limiting process that generates a "proton hole" in the cytoplasmic section of the protein. The velocity of the hole propagation is modulated by the ionic strength of the solution and by selective replacements of charged residues on the interhelical loops of the protein, at domains that seems to be remote from the intraprotein proton conduction trajectory