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Monte Carlo studies on water in the dCpG/proflavin crystal hydrate
M Mezei1, D L Beveridge, H M Berman
1Chemistry Department, Hunter College of the City University of New York, N.Y. 10021.
Journal of Biomolecular Structure & Dynamics
|October 1, 1983
Summary
Computer simulations accurately predict water positions in DNA crystal hydrates, aiding diffraction data interpretation. This study validates theoretical calculations for nucleic acid-water systems.
Area of Science:
- Computational chemistry
- Structural biology
- Biophysics
Background:
- Crystallographic studies revealed an extensive water network in dCpG/Proflavin hydrate.
- Accurate modeling of nucleic acid-water interactions is crucial for understanding DNA hydration and crystal structures.
Purpose of the Study:
- To assess the accuracy of statistical thermodynamic computer simulations for nucleic acid-water systems.
- To explore the utility of computer simulations in predicting water positions within crystal hydrates for diffraction data refinement.
Main Methods:
- Monte Carlo simulations were performed on water molecules within the dCpG/Proflavin unit cell.
- The nucleic acid complex was held fixed, with periodic boundary conditions applied to the condensed phase environment.
- Intermolecular interactions were modeled using potential functions derived from quantum mechanical calculations and empirical potentials.
Main Results:
- Simulations accurately reproduced experimentally observed water positions and hydrogen bond characteristics.
- Analysis included hydrogen bond topology, distances, energies, mean water positions, and probability density maps.
- The sensitivity of simulation results to the choice of potential functions was evaluated.
Conclusions:
- Statistical thermodynamic computer simulations are accurate for modeling nucleic acid-water systems.
- Computer simulations can reliably predict water positions in crystal hydrates, aiding diffraction data interpretation and refinement.