Development of Periodic boundary FMO-MD via multipole expansion of environmental electrostatic potential

2021 Fiscal Year Final Research Report

• Project/Area Number: 19K12010
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 60100:Computational science-related
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: Komeiji Yuto 国立研究開発法人産業技術総合研究所, 生命工学領域, 主任研究員 (30357032)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Keywords: 第一原理分子動力学法 / フラグメント分子軌道法 / FMO / 周期境界 / 溶媒 / 新型コロナウィルス

Outline of Final Research Achievements

The fragment molecular orbital method (FMO) is an electronic structure calculation method applicable to macromolecular systems. FMO-MD is a type of ab initio molecular dynamics method in which FMO is extended to the molecular dynamics simulation (MD). In this study, we have successfully implemented the environmental electrostatic interactions with the Cholesky decomposition with a view to deploying the FMO-MD method to periodic boundary condition. In parallel with the development of FMO-MD, we performed electronic structure calculations of MPro and Spike proteins of SARS-CoV 2 using the MM-MD/FMO protocol (FMO applied to structures sampled by classical MD), which is a preliminary version of FMO-MD. We analyzed the interactions between these proteins and their substrates to elucidate the dynamic features of the interactions and to explain the enhanced affinity of the mutant proteins to their receptor.

Free Research Field

分子シミュレーション

Academic Significance and Societal Importance of the Research Achievements

FMO-MD法の速度や精度を上げて、今後適用範囲を広げるための準備を整える意義があった。特に、近い将来、酵素反応のリアルな第一原理シミュレーションに拡張することが期待できる。加えて、MM-MD/FMO法による新型コロナウィルスのタンパク質（MProとSpike)の電子状態計算は、富岳を使った、世界最大レベルのものであるが、そのタンパク質、さらにはウィルスの性質の解明の一助になり、製薬への示唆を与えることができた。