Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation.
The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.
Dastidar
Shubhra Ghosh
SG
Department of Chemistry, University of Calcutta, 92. A.P.C. Road, Kolkata, 700 009, India.
Mukhopadhyay
Chaitali
C
D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004058:Diffusion; D006801:Humans; D046911:Macromolecular Substances; D008968:Molecular Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013997:Time Factors; D025801:Ubiquitin / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D046911:Macromolecular Substances; D011506:Proteins; D025801:Ubiquitin; D014867:Water