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Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study
V A Makarov1, M Feig, B K Andrews
1Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
Biophysical Journal
|July 2, 1998
Summary
Molecular dynamics simulations reveal how macromolecules like proteins and DNA affect water and ion movement. Solute surfaces slow diffusion, with distinct effects parallel and perpendicular to the surface.
Area of Science:
- Biophysics
- Computational Chemistry
- Molecular Dynamics
Background:
- Macromolecular solutes influence the dynamic behavior of surrounding solvent molecules and ions.
- Understanding these interactions is crucial for various biological and chemical processes.
Purpose of the Study:
- To investigate the effects of macromolecular solutes on the translational mobility of water, Na+, and Cl- ions.
- To analyze solvent diffusion patterns relative to solute surfaces and atom types.
Main Methods:
- Utilized high-quality, long molecular dynamics (MD) simulation trajectories.
- Analyzed myoglobin and a DNA decamer as model solutes.
- Calculated diffusion coefficients as a function of distance from solute atoms.
Main Results:
- Solvent diffusion is generally reduced near macromolecular surfaces compared to bulk.
- Diffusion is enhanced parallel to the solute surface and reduced perpendicular to it within 15 Å.
- Characteristic depressions in diffusion coefficients were observed in solvation shells, correlating with radial distribution functions.
- Similar diffusion patterns were found for water, sodium, and chloride ions.
Conclusions:
- The effects of protein and DNA solutes on water diffusion are comparable.
- Solute-solvent interactions significantly alter translational mobility, with directional dependencies.
- MD simulations provide detailed insights into ion and water dynamics around macromolecules.