Because of difficulties associated with experimental measurement techniques, the distribution of water density around many proteins is not well-resolved. We present, in this paper, a molecular dynamics approach to the general problem of comparing the instantaneous vs average view of protein hydration via a 150-ps simulation of metmyoglobin in an explicit aqueous environment. Densities as a function of position for both water and myoglobin were computed by time-averaging the volume fraction occupied at different positions in space. The picture so obtained challenges the view of hydration taken from accessible surface features related to the average structure. A detailed picture of protein hydration is given that includes significant surface penetration and transient channels, in conjunction with the accepted concepts of a tightly bound partial layer of water on the surface near charged groups.
ASJC Scopus subject areas
- General Engineering
- Physical and Theoretical Chemistry