Polar solvation dynamics of lysozyme from molecular dynamics studies

The Journal of Chemical Physics
Sudipta Kumar Sinha, Sanjoy Bandyopadhyay

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.

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Citations

Mar 10, 2017·Physical Chemistry Chemical Physics : PCCP·Yulian GavrilovYaakov Levy
Oct 5, 2019·The Analyst·Subham Adak, Laxmi Narayan Tripathi
Jan 8, 2013·Langmuir : the ACS Journal of Surfaces and Colloids·Somedatta Pal, Sanjoy Bandyopadhyay
Dec 11, 2013·The Journal of Physical Chemistry. B·Oleksandr SushkoRobert S Donnan

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Methods Mentioned

BETA
fluorescence spectroscopy
nuclear magnetic relaxation
fluorescence studies
neutron scattering

Software Mentioned

CHARMM22

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