The dynamics of proton transfer between adjacent sites

Abstract

The mechanism of proton transfer at the interface is the most prevalent reaction in the biosphere, yet its modeling at atomic level is still technically impossible. The difficulties emerge from the quantum mechanical nature of the proton, the modulation of the local electrostatic potential by the protein–water dielectric boundary and the formation of covalent bonds with proton binding sites whenever encounters take place. To circumvent some of these difficulties, and to identify the effect of the local electrostatic field, we present molecular dynamics simulations, where Na⁺ and Cl⁻ ions diffuse at the surface of a small model protein, the S6 of the bacterial ribosome. The analysis reveals the presence of a detained state, where an ion is located for a relatively long period within the immediate environment of certain attractor residues. In the detained state the ion retains its ability to diffuse, yet the local field deters it from leaving to the bulk. When an ion is detained inside a Coulomb cage, it has a high probability to be transferred between nearby attractors, thus forming a mechanism similar to that responsible for the proton collecting antenna present on proton proteins.