Theoretical investigation of reaction fields of biological macromolecular systems based on quantum sciences and mathematical informatics
| Project/Area Number |
25287099
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Partial Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Mathematical physics/Fundamental condensed matter physics
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| Research Institution | University of Hyogo |
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Principal Investigator |
Tateno Masaru 兵庫県立大学, 生命理学研究科, 教授 (40291926)
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| 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)
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| 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)
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| Project Period (FY) |
2013-04-01 – 2017-03-31
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| Project Status |
Completed (Fiscal Year 2016)
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| Budget Amount *help |
¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2015: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2014: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2013: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
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| 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 / 電子構造理論 / 情報理論 / 機械学習 / 情報幾何学 / ゲノム情報学 / 多様体 / 計算科学 / 情報科学 / 量子科学 / 生命物理学 / 生体高分子 / DNA / タンパク質 / 核酸 / 生体触媒反応における電子構造のダイナミクス / ゲノムDNAの高次構造モデル / 転写制御配列の自動同定システム / 自動解析ウェブサービスシステム / 細胞内情報伝達の生体反応 / GTP加水分解反応メカニズム / 結晶構造のリファインメント解析技術 / 情報科学・計算科学の融合 |
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| 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.
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Report
(5 results)
Research Products
(146 results)
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[Journal Article] The CENP-O complex requirement varies among different cell types.2014
Author(s)
Kagawa, N., Hori, T., Hoki, Y., Hosoya, O., Tsutsui, K., Saga, Y., Sado, T., and *Fukagawa, T.
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Journal Title
Chrom. Research
Volume: in press
Issue: 3
Pages: 293-303
DOI
Related Report
Peer Reviewed / Open Access
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[Presentation] A novel domain of topoisomerase IIb regulates nuclear dynamics and catalytic activity of the enzyme by binding to RNA2014
Author(s)
Tsutsui, K.M., Hosoya, O., Onoda, A., Sano, K., Kimura, H., Miyaji, M., and Tsutsui, K.
Organizer
第37回日本分子生物学会年会
Place of Presentation
パシフィコ横浜（横浜）
Year and Date
2014-11-25 – 2014-11-27
Related Report
Invited
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[Presentation] RNA regulates nuclear dynamics and catalytic activity of topoisomerase IIbeta by binding to a novel domain of the enzyme2014
Author(s)
Tsutsui, K.M., Hosoya, O., Onoda, A., Sano, K., Kawano, S., Miyaji, M., and Tsutsui, K.
Organizer
Cell Symposia “Regulatory RNAs”
Place of Presentation
Berkeley (US)
Year and Date
2014-10-19 – 2014-10-21
Related Report
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