title: Polar solvation dynamics of lysozyme from molecular dynamics studies.
abstract: 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 α-helices and β-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.
authors.affiliation: Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.
authors.forename: Sudipta Kumar
authors.initials: SK
authors.lastname: Sinha
authors.forename: Sanjoy
authors.initials: S
authors.lastname: Bandyopadhyay
mesh_terms: D000818:Animals; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry*; D013997:Time Factors
chemical_list: D012997:Solvents; D009113:Muramidase