Paper Citing NAMD - Abstract
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 115101, MAR 21 2011
We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two alpha-helical segments in domain-1 and the other connecting a 3(10) helix and a beta-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies. (C) 2011 American Institute of Physics. [doi:10.1063/1.3560442]
