Paper Citing NAMD - Abstract
Pal, Somedatta; Bandyopadhyay, Sanjoy
Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water
CHEMICAL PHYSICS, 420:35-43, JUL 11 2013
Protein-water interactions and their influence on surrounding water is a long-standing problem. Despite its importance, the origin of differential water behavior at the protein surface is still elusive. We have performed molecular simulations of the protein barstar in aqueous medium. Efforts have been made to explore how the conformational motions of the protein segments in the native form and the heterogeneous electrostatic interactions with the polar and charged groups of the protein affect the interfacial water properties. The calculations reveal that reduced dimension of the hydration layer on freezing the protein's degrees of freedom does not modify the heterogeneous water distributions around the protein. However, turning off the protein-water electrostatic contribution leads to non-preferential near-uniform water arrangements at the surface. It is further shown that with protein-water electrostatic interactions turned on, the local structuring of water molecules around the segments are correlated with their degree of exposure to the solvent. (C ) 2013 Elsevier B. V. All rights reserved.
