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High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
Published on: April 28, 2022
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The geometry of protein hydration
Filip Persson1, Pär Söderhjelm1, Bertil Halle1
1Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
The Journal of Chemical Physics
|June 10, 2018
Summary
Molecular dynamics simulations reveal a universal protein-water interface area of 11.1 Ų, with denser water packing in hydration shells. Protein-induced water perturbations are short-ranged.
Area of Science:
- Biophysics
- Computational Chemistry
- Physical Chemistry
Background:
- The protein-water interface is crucial for biological processes.
- Geometrical aspects of hydration shells remain incompletely understood.
Purpose of the Study:
- To investigate controversial geometrical aspects of the protein-water interface.
- To compare hydration shell definitions and analyze water molecule coordination and packing density.
Main Methods:
- Molecular dynamics simulations of four globular proteins using three water models.
- Analysis of spatial and topological proximity criteria for hydration shell definition.
- Additively weighted Voronoi tessellation for local packing density determination.
Main Results:
- A 5 Å water-carbon and 4 Å water-water cutoff optimally defines hydration shells.
- A universal mean interfacial water area of 11.1 Ų was determined.
- Water in the first hydration shell is 6% denser than bulk water, with short-ranged perturbations.
Conclusions:
- The defined hydration shell method provides a robust approach to studying the protein-water interface.
- Observed water density excess differs from previous studies due to realistic interface definitions.
- Protein-induced water perturbations decay rapidly with distance.
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