Development of Automated Reaction Path Search Methods for Systematic Elucidation of Enzymatic Reaction Mechanisms

2014 Fiscal Year Final Research Report

• Project/Area Number: 23685004
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Physical chemistry
• Research Institution: Hokkaido University (2012-2014); Kyoto University (2011)
• Principal Investigator: MAEDA Satoshi 北海道大学, 理学(系)研究科(研究院), 准教授 (60584836)
• Project Period (FY): 2011-04-01 – 2015-03-31
• Keywords: 量子化学計算 / 反応経路 / 遷移状態 / 酵素反応 / 反応経路自動探索

Outline of Final Research Achievements

Toward systematic elucidation of enzymatic reaction mechanisms, development of our own automated reaction path search methods has been conducted. At the beginning, the anharmonic downward distortion following method was employed. While, the other approach called artificial force induced reaction (AFIR) method was found to show higher applicability to large molecular systems. Thus, using the AFIR method, automated search of reaction pathways in the iso-penicillin N synthase (IPNS), which is an enzyme for penicillin synthesis, was performed. This application to the system consisting of ~5,000 atoms was achieved by combining the AFIR method with the QM/MM-OMIOM method and the geometrical microiteration approach. Furthermore, development of the AFIR method and its applications to organic reactions were also made actively.

Free Research Field

基礎化学・物理化学