Coupling between hydration layer dynamics and unfolding kinetics of HP-36.
We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings.
Bandyopadhyay
Sanjoy
S
Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India. sanjoy@iitkgp.ac.in
Chakraborty
Sudip
S
Bagchi
Biman
B
D000595:Amino Acid Sequence; D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D007700:Kinetics; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013696:Temperature; D014867:Water / Q000737:chemistry*
D016900:Neurofilament Proteins; D010446:Peptide Fragments; D011506:Proteins; D012997:Solvents; C115223:villin headpiece subdomain peptide; D014867:Water