The dynamic feature of the proton collecting antenna of a protein surface

AbstractThe surface of a protein is a condense matrix of proton binding sites having wide range of pK values. In domains where proton uptake is a part of the catalytic cycle, the surface sites endow the region with special kinetic features which represents the ensemble properties of the proton binding sites. Low pK carboxylate can merge their Coulomb cages to form an extended proton trap, where the binding of a proton to one is rapidly followed by shuttling to another. Neutral pK moieties can act as a temporary proton reservoir which delay the proton at the site, enhancing the probability that upon dissociation it will be taken up by the other elements of the active site. These features had been experimentally identified in small model molecules, where detailed kinetic analysis was carried out. On the base of these measurements the dynamics of protonation of the proton entry sites of bacteriorhodopsin and cytochrome oxidase were investigated

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

pH-Jump overshooting

Acid – base systems are commonly expected to equilibrate on a timescale much faster than any other chemical reaction, so their composition can be deduced from the corresponding pKa or pKb values. In a pH-jump experiment done on a multi acid/base pair system, it was found that it takes tens of microseconds before an equilibrium is established. Within that time, the system is kinetically driven reaching surprising states far different from its final equilibrium, for example carboxylate groups were protonated in the presence of hydroxyl ions