Theoretical investigation of reaction fields of biological macromolecular systems based on quantum sciences and mathematical informatics

2016 Fiscal Year Final Research Report

• Project/Area Number: 25287099
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Mathematical physics/Fundamental condensed matter physics
• Research Institution: University of Hyogo
• Principal Investigator: Tateno Masaru 兵庫県立大学, 生命理学研究科, 教授 (40291926)
• Co-Investigator(Kenkyū-buntansha): 山崎 和彦 国立研究開発法人産業技術総合研究所, その他部局等, 研究員 (00358243) ; 筒井 公子 岡山大学, 医歯(薬)学総合研究科, 名誉教授 (70144748)
• Co-Investigator(Renkei-kenkyūsha): KINO HIORI 独立行政法人物質・材料研究機構, 計算科学センター, 主任研究員 (70282605)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Keywords: 電子ダイナミクス / ハイブリッド触媒 / 電子状態理論 / パターン認識 / 情報微分幾何学 / ゲノムDNA / リボザイム / 転写制御

Outline of Final Research Achievements

By systematically combining quantum science and mathematical informatics, we obtained the following achievements: i) To precisely identify even weak and subtle signals that act as functional sequence motifs in genome DNA, novel algorithms were developed together with mathematical descriptions based on an information geometrical manifold, and applied to reveal the motifs recognized by DNA topoisomerase (topo) IIb. ii) Mechanisms to recognize the identified motifs were also analyzed in combination with structural modeling of the DNA-topoIIb complex and hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of the complex. The informatics and QM analyses showed that the catalysis acts in concert with the DNA recognition by topoIIb. iii) In some biological systems, the catalytic mechanisms that could uniquely be characteristic to organisms were revealed by using hybrid MD simulations, and dynamical processes of the electronic structure rearrangements were elucidated.

Free Research Field

生命物理学理論