Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

分子動力学シミュレーション計算とRISM理論によって得られたDNAの水和パターンの比較

米谷 佳晃*; 丸山 豊*; 平田 文男*; 河野 秀俊

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

Although high-resolution, crystal structure analyses have given us a view of tightly bound water molecules on their surface, the structural data is 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 using two different computational methods, MD simulation and 3D-RISM theory. 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 calculated hydration patterns.