Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36.
Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.
Chakraborty
Sudip
S
Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India.
Bandyopadhyay
Sanjoy
S
D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D014867:Water / Q000737:chemistry*
D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide; D014867:Water