Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory.
Because proteins and DNA interact with each other and with various small molecules in the presence of water molecules, we cannot ignore their hydration when discussing their structural and energetic properties. Although high-resolution crystal structure analyses have given us a view of tightly bound water molecules on their surface, the structural data are still insufficient to capture the detailed configurations of water molecules around the surface of these biomolecules. Thanks to the invention of various computational algorithms, computer simulations can now provide an atomic view of hydration. Here, we describe the apparent patterns of DNA hydration calculated by using two different computational methods: Molecular dynamics (MD) simulation and three-dimensional reference interaction site model (3D-RISM) theory. Both methods are promising for obtaining hydration properties, but until now there have been no thorough comparisons of the calculated three-dimensional distributions of hydrating water. This rigorous comparison showed that MD and 3D-RISM provide essentially similar hydration patterns when there is sufficient sampling time for MD and a sufficient number of conformations to describe molecular flexibility for 3D-RISM. This suggests that these two computational methods can be used to complement one another when evaluating the reliability of the calculated hydration patterns.
Yonetani
Yoshiteru
Y
Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto, Japan.
Maruyama
Yutaka
Y
Hirata
Fumio
F
Kono
Hidetoshi
H
D000465:Algorithms; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D008954:Models, Biological; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D012997:Solvents; D014867:Water; D004247:DNA; D010100:Oxygen