Development of high-precision statistical thermodynamic model of ligand-receptor interactions

2016 Fiscal Year Final Research Report

• Project/Area Number: 26600154
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Computational science
• Research Institution: Keio University
• Principal Investigator: Mikami Masuhiro 慶應義塾大学, 理工学研究科(矢上), 特任教授 (50358074)
• Research Collaborator: Yamamoto Eiji ; Inoue Kento ; Takaiwa Daisuke ; Tsukumo Keishi
• Project Period (FY): 2014-04-01 – 2017-03-31
• Keywords: リガンド / 受容体 / 分子間相互作用 / 分子動力学法 / ハイブリッド法 / 粗視化モデル / 古典密度汎関数法 / 統計熱力学

Outline of Final Research Achievements

In order to realize high-precision and high-speed calculation of ligand-receptor interactions in aqueous solution, we examined the applicability of coarse-grained model force field function: MARTINI which can calculate a large scale system faster than atomic model. As a result, we obtained that MARTINI qualitatively reproduce experimental results of ligand-receptor interaction between hemagglutinin molecule on the surface of influenza virus and human type glycolipid molecules. In addition, we investigated the previous studies on hybrid method of molecular dynamics method and classical density functional theory method in colloidal suspension, we obtained the possibility to calculate the whole system at further high speed by handling the water molecules which are the majority of the system with the SAFT theory which is one kind of classical density functional theory.

Free Research Field

物理化学