Paper Citing NAMD - Abstract
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Polar solvation dynamics of lysozyme from molecular dynamics studies
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 185102, MAY 14 2012
The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the alpha-helices and beta-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4712036]
