Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces.
Motivated by a quasi-chemical view of protein hydration, we define specific hydration sites on the surface of globular proteins in terms of the local water density at each site relative to bulk water density. The corresponding kinetic definition invokes the average residence time for a water molecule at each site and the average time that site remains unoccupied. Bound waters are identified by high site occupancies using either definition. In agreement with previous molecular dynamics simulation studies, we find only a weak correlation between local water densities and water residence times for hydration sites on the surface of two globular proteins, lysozyme and staphylococcal nuclease. However, a strong correlation is obtained when both the average residence and vacancy times are appropriately taken into account. In addition, two distinct kinetic regimes are observed for hydration sites with high occupancies: long residence times relative to vacancy times for a single water molecule, and short residence times with high turnover involving multiple water molecules. We also correlate water dynamics, characterized by average occupancy and vacancy times, with local heterogeneities in surface charge and surface roughness, and show that both features are necessary to obtain sites corresponding to kinetically bound waters.
Priya
M Hamsa
MH
Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, USA.
Shah
J K
JK
Asthagiri
D
D
Paulaitis
M E
ME
D001665:Binding Sites; D003198:Computer Simulation; D007700:Kinetics; D008836:Micrococcal Nuclease / Q000737:chemistry*; D008956:Models, Chemical; D009113:Muramidase / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D011506:Proteins; D014867:Water; D008836:Micrococcal Nuclease; D009113:Muramidase