Molecular dynamics simulation of interfacial water structure and dynamics in a parvalbumin solution

Abstract

A 106-ps molecular dynamics simulation of the calcium-binding protein parvalbumin in water has been used as a basis for studying interfacial water. A general conclusion is that structure and dynamics of the interfacial water are only marginally affected by the presence of the protein. A few water molecules, which reside close to charge groups, are immobilized throughout the simulation. In the analysis the water molecules have been classified according to the distance to the nearest protein atom. Close to the protein the authors find a decrease in radial diffusion, while lateral diffusion is enhanced. In the inner water layers the dipole moment vector is preferentially oriented perpendicular to the radius vector of the protein. The reorientational correlation times have a minimum 4-5 /Angstrom/ from the protein, with values similar to those obtained from simulations of pure water.