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Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution
T Rudas1, C Schröder, S Boresch
1Department of Biomolecular Structural Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.
The Journal of Chemical Physics
|July 11, 2006
Summary
Molecular dynamics simulations reveal how proteins affect water
Area of Science:
- Computational Biophysics
- Physical Chemistry
Background:
- Understanding protein-water interactions is crucial for biological processes.
- Dielectric properties offer insights into molecular behavior in solution.
Purpose of the Study:
- To compute dielectric properties of protein-water systems using molecular dynamics simulations.
- To analyze the contributions of protein and water to dielectric properties at mesoscopic resolution.
Main Methods:
- Molecular dynamics (MD) simulations of ubiquitin, apo-calbindin D(9K), and a protein SH2 domain.
- Development of theory for charged species in simulations.
- Dielectric component analysis of frequency-dependent dielectric susceptibility.
- Decomposition into protein, solvation shells, and bulk water.
Main Results:
- Proteins influence water's dielectric properties beyond the second solvation shell.
- Dielectric contributions from the second shell and bulk water are similar across systems.
- Protein and first solvation shell contributions are system-specific.
- Anticorrelation observed between protein and first water shell for ubiquitin and apo-calbindin; positive correlation for the SH2 domain.
Conclusions:
- Protein solvation affects dielectric properties even at a distance.
- System-specific interactions dominate close to the protein surface.
- Dielectric analysis provides mesoscopic insights into protein hydration.
