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Water rotational relaxation and diffusion in hydrated lysozyme
Massimo Marchi1, Fabio Sterpone, Matteo Ceccarelli
1Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France. marchi@villon.saclay.cea.fr
Journal of the American Chemical Society
|June 6, 2002
Summary
Water dynamics near proteins slow down significantly. Molecular dynamics simulations show surface water diffusion and relaxation are retarded compared to bulk water, impacting nuclear magnetic relaxation dispersion studies.
Area of Science:
- Biophysics
- Physical Chemistry
- Computational Biology
Background:
- Understanding protein- hydration shell interactions is crucial for biological processes.
- Water dynamics near protein surfaces differ from bulk water.
- Nuclear magnetic relaxation dispersion (NMRD) studies rely on assumptions about water dynamics.
Purpose of the Study:
- To investigate the dynamics of water molecules in the vicinity of a globular protein (lysozyme).
- To compute dipolar second-rank relaxation times and diffusion properties of surface water.
- To compare simulation results with NMRD estimates and evaluate different water models.
Main Methods:
- Extensive molecular dynamics (MD) simulations of lysozyme in water.
- Total simulation time of 28 nanoseconds.
- Calculation of rotational relaxation and translational diffusion properties of water molecules.
Main Results:
- Water rotational relaxation near lysozyme is 3-7 times slower than in bulk water.
- Translational diffusion of water near lysozyme shows similar retardations.
- Surface water exhibits dispersive diffusion or subdiffusion dynamics.
- Good agreement between computed relaxation times and NMRD estimates was achieved.
Conclusions:
- Protein surface water dynamics are significantly slower than bulk water.
- MD simulations provide valuable insights into water dynamics relevant for NMRD studies.
- The SPC/E water model offers a more realistic description of water dynamics around lysozyme compared to TIP3P.
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