Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.
The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.
Resat
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Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029-6574, USA.
Mezei
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D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D003460:Crystallization; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D007364:Intercalating Agents; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011370:Proflavine / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D015226:Dinucleoside Phosphates; D007364:Intercalating Agents; C059782:deoxy(cytidylyl-guanosine) dimer; D014867:Water; D011370:Proflavine