The extensive water network identified in the crystallographic studies of the dCpG/Proflavin hydrate by Neidle, Berman and Shieh (Nature 288, 129, 1980) forms an ideal test case for a) assessing the accuracy of theoretical calculations on nucleic acid-water systems based on statistical thermodynamic computer simulation, and b) the possible use of computer simulation in predicting the water positions in crystal hydrates for use in the further refinement and interpretation of diffraction data. Monte Carlo studies have been carried out on water molecules in the unit cell of dCpG/ proflavin, with the nucleic acid complex fixed and the condensed phase environment of the system treated by means of periodic boundary conditions. Intermolecular interactions are described by potential functions representative of quantum mechanical calculations developed by Clementi and coworkers, and widely used in recent studies of the aqueous hydration of various forms of DNA fragments. The results are analyzed in terms of hydrogen bond topology, hydrogen bond distances and energies, mean water positions, and water crystal probability density maps. Detailed comparison of calculated and experimentally observed results are given, and the sensitivity of results to choice of potential is determined by comparison with simulation results based on a set of empirical potentials.
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology