Theoretical study on the charge transfer through DNA induced by structural and solvent fluctuation

2015 Fiscal Year Final Research Report

• Project/Area Number: 25410021
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: Kyushu University
• Principal Investigator: YOSHIDA NORIO 九州大学, 高等研究院, 准教授 (10390650)
• Co-Investigator(Renkei-kenkyūsha): NAKANO HARUYUKI 九州大学, 大学院理学研究院, 教授 (90251363) ; WATANABE YOSHIHIRO 九州大学, 大学院理学研究院, 助教 (20315055) ; NISHIYAMA KATSURA 島根大学, 教育学部, 教授 (40283725)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Keywords: 電荷移動 / ＦＭＯ / ３Ｄ－ＲＩＳＭ / 理論化学 / 構造揺らぎ

Outline of Final Research Achievements

We developed a hybrid method of the fragment molecular orbital (FMO) method and the three-dimensional reference interaction site model (3D-RISM) theory, referred to as the FMO/3D-RISM method. We also derived its analytical free energy gradient formula, which allows us to evaluate the force on the solute biomolecule from the solvent distribution. We applied the method to a model system of DNA and demonstrated the validity of the method.
We investigated the mechanism of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase by the combinational use of the molecular dynamics simulation and the 3D-RISM method, and clarified the origin of the resistance. The methods used in this study can efficiently treat the structural fluctuation of biomolecule and the solvation thermodynamics.

Free Research Field

理論化学