Interactions among biological molecular assembly and among artificial molecular assembly and large-scale structural transformations

2017 Fiscal Year Final Research Report

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 25102009
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: Nagoya University
• Principal Investigator: OKAMOTO Yuko 名古屋大学, 理学研究科, 教授 (70185487)
• Project Period (FY): 2013-06-28 – 2018-03-31
• Keywords: 生体分子系 / 人工分子系 / 分子シミュレーション / 拡張アンサンブル法 / 自由エネルギー計算

Outline of Final Research Achievements

We have applied the generalized-ensemble algorithms that we developed by ourselves to various bimolecular and artificial molecular systems and showed their effectiveness. For instance, we applied the Replica-Exchange Molecular Dynamics Method to the development of the method for predicting membrane protein structures, analyses of three-dimensional structures of glycans attached to a protein, and the prediction of the three-dimensional structures of a supra molecule that consists of ligands and metals. We applied the Replica-Exchange Umbrella Sampling to the development of binding free energy calculation method for protein-ligand system and the calculation of isozyme selectivity of histon deacetylate. We applied the pressure simulated tempering to the chemical shift calculations of a protein under high pressure.

Free Research Field

生物物理学、計算化学、計算物理学