Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study

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• 作者：Sudip Chakraborty ; Sudipta Kumar Sinha ; Sanjoy Bandyopadhyay
• 刊名：Journal of Physical Chemistry B
• 出版年：2007
• 出版时间：December 6, 2007
• 年：2007
• 卷：111
• 期：48
• 页码：13626 - 13631
• 全文大小：87K
• 年卷期：v.111,no.48(December 6, 2007)
• ISSN：1520-5207

文摘

An atomistic molecular dynamics simulation has been carried out to understand the low-frequencyintermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiecesubdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layersof different segments (three helices) of the protein, strength of the protein-water hydrogen bonds, andtheir differential relaxation behavior influence the distribution of the intermolecular vibrational density ofstates of water in the hydration layers. The calculations revealed that compared to bulk water these bands arenonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for watermolecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed forthe water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structuralrelaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.