Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study.
An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.
Chakraborty
Sudip
S
Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India.
Sinha
Sudipta Kumar
SK
Bandyopadhyay
Sanjoy
S
D006860:Hydrogen Bonding; D011506:Proteins / Q000737:chemistry*; D014732:Vibration; D014867:Water / Q000737:chemistry*
D011506:Proteins; D014867:Water