Proton transfer in water wires in proteins: modulation by local constraint and polarity in gramicidin a channels

The transfer of protons in membrane proteins is an essential phenomenon in biology. However, the basic rules by which H(+) transfer occurs in water wires inside proteins are not well characterized. In particular, the effects of specific atoms and small groups of atoms on the rate of H(+) transfer in water wires are not known. In this study, new covalently linked gramicidin-A (gA) peptides were synthesized, and the effects of specific atoms and peptide constraints on the rate of H(+) transfer were measured in single molecules. The N-termini of two gA peptides were linked to various molecules: S,S-cyclopentane diacid, R,R-cyclopentane diacid, and succinic acid. Single-channel proton conductances (g(H)) were measured at various proton concentrations ([H(+)]) and compared to previous measurements obtained in the S,S- and R,R-dioxolane-linked as well as in native gA channels. Replacing the S,S-dioxolane by an S,S-cyclopentane had no effects on the g(H)-[H(+)] relationships, suggesting that the constrained and continuous transition between the two gA peptides via these S,S linkers is ultimately responsible for the two- to fourfold increase in g(H) relative to native gA channels. It is likely that constraining a continuous transition between the two gA peptides enhances the rate of H(+) transfer in water wires by decreasing the number of water wire configurations that do not transfer H(+) at higher rates as in native gA channels (a decrease in the activation entropy of the system). On the other hand, g(H) values in the R,R-cyclopentane are considerably larger than those in R,R-dioxolane-linked gA channels. One explanation would be that the electrostatic interactions between the oxygens in the dioxolane and adjacent carbonyls in the R,R-dioxolane-linked gA channel attenuate the rate of H(+) transfer in the middle of the pore. Interestingly, g(H)-[H(+)] relationships in the R,R-cyclopentane-linked gA channel are quite similar to those in native gA channels. g(H) values in succinyl-linked gA channels display a wide distribution of values that is well represented by a bigaussian. The larger peaks of these distributions are similar to g(H) values measured in native gA channel. This observation is also consistent with the notion that constraining the transition between the two beta-helical gA peptides enhances the rate of H(+) transfer in water wires by decreasing the activation entropy of the system.