Water-mediated long-range interactions between the internal vibrations of remote proteins

Abstract

It is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations. The analyzed atoms were located at the two distant protein surfaces that were facing each other. We demonstrated that the low-frequency (ca. 2 THz and less) collective movements of these two separate sets of atoms are to some extent interdependent. Based on this finding, it can be inferred that the low frequency large-scale internal motions of these proteins are also partially interdependent. The water-mediated protein–protein interactions, which are responsible for this interdependence, have a relatively long range of at least 2 nm at room temperature.