Deducing hydration sites of a protein from molecular dynamics simulations

Invariant water molecules that are of structural or functional importance t o proteins are detected from their presence in the same location in differe nt crystal structures of the same protein or closely related proteins. In t his study we have investigated the location of invariant water molecules fr om MD simulations of ribonuclease A. HIV l-protease and Hen egg white lysoz yme. Snapshots of MD trajectories represent the structure of a dynamic prot ein molecule in a solvated environment as opposed to the static picture pro vided by crystallography. The MD results are compared to an analysis on cry stal structures. A good correlation is observed between the two methods wit h more than half the hydration sites identified as invariant from crystal s tructures featuring as invariant in the MD simulations which include most o f the functionally or structurally important residues. It is also seen that the propensities of occupying the various hydration sites on a protein for structures obtained from MD and crystallographic studies are different. In general MD simulations can be used to predict invariant hydration sites wh en there is a paucity of crystallographic data or to complement crystallogr aphic results.