Comparison of DNA hydration patterns obtained from MD simulation and 3D-RISM theory

Yonetani, Yoshiteru; Maruyama, Yutaka*; Hirata, Fumio*; Kono, Hidetoshi

Because biomolecules in cell such as proteins, DNA and various small molecules interact with each other 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. In this presentation, we describe the hydration patterns of DNA calculated using two distinct computational methods, MD simulation and 3D-RISM theory. The B-form of DNA is suitable for the evaluation of calculated hydrations because a well-defined hydration pattern known as water spine appears in the minor groove of particular sequences. Both methods are promising for obtaining hydration properties, but until now there have been no thorough comparisons of the 3D distributions of hydrating water. Our 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.