Proton transfer, hydrogen bonds bacteriorhodopsin

Wolf and co-workers presented a combined experimental and theoretical study employing molecular-dynamics simulations, in which they investigated the proton transfer from a water cluster to bulk water in the same membrane protein bacteriorhodopsin. Their efforts were directed towards the detailed mechanism. They found that the breaking of a hydrogen bond is activating a gate-opening, so that a proton can be released from a water cluster to extracellular water. This is a directed proton transfer and, thus, very different from random proton transfer as observed in liquids (as discussed in Section 2). 

See, N.A. Dencher, G. Boldt, J. Heberle, H.-D. Hdltje and M. Hditje, in T. Bounds (Ed.), Proton-Transfer in Hydrogen-Bonded Systems, NATO ASI, Ser. B, Vol. 291, Plenum Press, 1992, pp. 171-186. On p. 180 of this paper there is a diagram of a computer-graphics model of the pathways for protons across bacteriorhodopsin. 

The structural information on such a short distance between the Schiff base and the counterion has led to confusion among researchers. This is because many researchers believed that a water molecule should be present between the Schiff base and the coimterion, as in the case of bacteriorhodopsin. In general, pKa of a Schiff base is higher than that of a glutamate, so that a proton on the Schiff base should be transferred to the glutamate if these two molecules interact directly with each other. Moreover, there is ample evidence that a water molecule is present and forms a hydrogen-bonding network near the Schiff base and the counterion. - Therefore, a water molecule was speculated to be located between the Schiff... 

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