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How Does Solvation Layer Mobility Affect Protein Structural Dynamics?

Jayangika N Dahanayake1, Katie R Mitchell-Koch1

  • 1Department of Chemistry, Wichita State University, Wichita, KS, United States.

Frontiers in Molecular Biosciences
|July 31, 2018
PubMed
Summary
This summary is machine-generated.

Local solvent mobility, not bulk viscosity, dictates protein flexibility across various solvents. This study reveals how solvation layer dynamics influence enzyme structural dynamics in both aqueous and organic environments.

Keywords:
CALBKramers' theoryMarkov state modelhydration dynamicsnon-aqueous enzymesprotein dynamicssolvation shellviscosity

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Area of Science:

  • Biochemistry
  • Physical Chemistry
  • Computational Biology

Background:

  • Solvation significantly impacts protein structural dynamics and function.
  • Previous studies linked protein and solvent dynamics, with gas binding rates inversely related to solution viscosity.
  • Understanding enzyme behavior in diverse solvents is crucial for biocatalysis.

Purpose of the Study:

  • To investigate the relationship between protein structural dynamics and solvation shell dynamics.
  • To determine if local viscosity explains correlations between protein flexibility and solvent mobility.
  • To characterize regional protein and solvent dynamics in various aqueous and organic solvents.

Main Methods:

  • Molecular dynamics simulations of *Candida antarctica* lipase B.
  • Modeling the enzyme in water, acetonitrile, cyclohexane, *n*-butanol, and *tert*-butanol.
  • Regional characterization of protein (α-helix, β-sheet, loop) and solvation shell dynamics.

Main Results:

  • Correlations observed between solvent mobility and protein flexibility across different regions.
  • Local solvent shell dynamics showed a stronger correlation with protein flexibility than bulk viscosity.
  • Protein flexibility best correlated with local interfacial viscosity or relative solvent mobility ratios.

Conclusions:

  • Local solvation layer dynamics, rather than bulk viscosity, are key drivers of protein structural dynamics.
  • Findings offer a framework for predicting enzyme behavior in non-aqueous solvents based on solvation shell mobility.
  • Suggests future application of Kramers' theory incorporating local viscosity for modeling protein transitions.