Entropy connects water structure and dynamics in protein hydration layer

Physical Chemistry Chemical Physics : PCCP
Jayangika N Dahanayake, Katie R Mitchell-Koch

Abstract

The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics. In particular, it was seen that regions of higher density exhibit faster water dynamics. This is analogous to the behavior of bulk water, where dynamics (diffusion coefficients) are connected to water structure (density and tetrahedrality) by excess (or pair) entropy, detailed in the Rosenfeld scaling relationship. Additionally, effects of protein surface topology and hydrophobicity on water structure and dynamics were evaluated using multiregression analysis, showing that topology has a somewhat larger effect on hydration layer structure-dynamics. Concave and hydrophobic protein surfaces favor a les...Continue Reading

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Citations

Mar 15, 2020·Annual Review of Chemical and Biomolecular Engineering·Jacob MonroeM Scott Shell
Sep 19, 2019·Nature Chemistry·Michael C ThompsonJames S Fraser
Jul 31, 2018·Frontiers in Molecular Biosciences·Jayangika N Dahanayake, Katie R Mitchell-Koch
Dec 12, 2018·The Journal of Chemical Physics·Jeppe C Dyre
Jun 11, 2019·Frontiers in Chemistry·Alexandra SchindlAnna K Croft
Sep 15, 2020·Physical Chemistry Chemical Physics : PCCP·Abhinav SrivastavaAnanya Debnath
Feb 6, 2021·Biophysical Journal·Kevin PounotGiorgio Schirò
Jul 17, 2021·Physical Chemistry Chemical Physics : PCCP·Maddalena BinFivos Perakis
Mar 14, 2019·Journal of Chemical Information and Modeling·Jayangika N DahanayakeKatie R Mitchell-Koch
Jun 28, 2019·ACS Chemical Biology·Brian FuglestadA Joshua Wand
May 30, 2019·Journal of Chemical Information and Modeling·Mohan R PradhanChandra S Verma

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Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

Amber03
CALB
GROMACS
Fortran

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