Water residence times around copper plastocyanin: a molecular dynamics simulation approach

Abstract

In order to study the dynamical properties of the solvent-protein interface, a detailed analysis of the time-relaxation behaviour of the hydration shells around each atom of copper plastocyanin has been performed by means of a time correlation function technique. In computing the function, which allowed us to extract average water residence times and coordination numbers within atomic shells of a given radius, we focused on the short and long time limits of the function itself, also in connection with a detailed analysis of the statistical uncertainty. Water residence times distribution around plastocyanin has been calculated for the first coordination shell. Water residence times near charged and polar atoms were found to be longer than those of non-polar ones; moreover side-chain oxygens and nitrogens, which form hydrogen bonds with solvent molecules, show larger water residence times than other atom types and, for negatively and positively charged residues, these times correlate to the hydrogen bond average duration. The accessibility of the solvent to protein atoms, investigated in terms of coordination numbers, has been compared to the more standard Solvent Accessible Surface. The active site, including the copper atom and its ligands, has been studied in greater detail to better understand the connections between the water molecule dynamical properties and the protein biological functionality. In particular for copper site, which was believed to be inaccessible to the solvent, it has been found that at least one water molecule which does not exchange with bulk has permanent contact with the metal.