Application of classical molecular dynamics for evaluation of proton transfer mechanism on a protein.

Proton transfer reactions on surfaces are prevalent in biology, chemistry and physics. In the present study, we employed classical Molecular Dynamics simulations to search for the presence of transient configurations that enable proton transfer, or proton sharing, between adjacent carboxylate groups on the protein surface. The results demonstrate that, during random fluctuations of the residues on the surface, there are repeated situations in which nearby carboxylates either share a common proton through a hydrogen bond, or are connected by a few water molecules that form conducting networks. These networks do not extend out of the common Coulomb cage of the participating residues and the lifetimes of the bridged structures are sufficiently long to allow passage of a proton between the carboxylates. The detection of domains capable of supporting a rapid proton transfer on a protein supports the notion that clusters of carboxylates are the operative elements of proton collecting antennae, as in bacteriorhodopsin, cytochrome c oxidase or the photosynthetic reaction center.