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Computational study for multistery of intrinsic disordered region of proteins with post-translational modification

Research Project

Project/Area Number 16K14711
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionOsaka University

Principal Investigator

Nakamura Haruki  大阪大学, たんぱく質研究所, 教授 (80134485)

Co-Investigator(Renkei-kenkyūsha) HIGO Junichi  大阪大学, 蛋白質研究所, 特任教授 (80265719)
Project Period (FY) 2016-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords理論生物学 / バイオインフォマティクス / 蛋白質間相互作用 / 分子シミュレーション / 天然変性 / 蛋白質相互作用
Outline of Final Research Achievements

The Intrinsic Disordered Regions (IDRs) of proteins with post-translational modification were examined using the IDR database, IDEAL, and their structural properties were analyzed by molecular simulations for the protein-protein interactions. Here, the interaction of Ser-rich region existing in the IDR of a transcription factor Ets1 and the DNA binding region in its core domain, and that of a peptide fragment having 8 amino acids in the IDR of human Myeloid leukemia factor 1(MLF1)and the 14-3-3εprotein were investigated respectively, with and without phosphorylated Ser residues.
In the both systems, the free energy landscapes were drawn after computations by enhanced structural sampling with our own molecular simulation algorithms.
Consequently, a few specific complex structures appeared in the systems with phosphorylated Ser residues. On the contrary, fuzzy properties were observed in the systems with non-modified Ser residues.

Report

(3 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • Research Products

    (23 results)

All 2018 2017 2016

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 6 results,  Acknowledgement Compliant: 3 results) Presentation (17 results) (of which Int'l Joint Research: 10 results,  Invited: 6 results)

  • [Journal Article] Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an out-inhibitory state.2018

    • Author(s)
      Kota Kasahara, Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura.
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: 5 Pages: 2243-2251

    • DOI

      10.1093/nar/gkx1297

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhancement of canonical sampling by virtual-state transitions2017

    • Author(s)
      Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura
    • Journal Title

      J. Chem. Phys.

      Volume: 146 Issue: 4 Pages: 44104-44104

    • DOI

      10.1063/1.4974087

    • Related Report
      2017 Annual Research Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer2017

    • Author(s)
      Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H
    • Journal Title

      PloS One

      Volume: 12 Issue: 2 Pages: e0172654-e0172654

    • DOI

      10.1371/journal.pone.0172654

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor2017

    • Author(s)
      G.-J. Bekker, N. Kamiya, M. Araki, I. Fukuda, Y. Okuno, H. Nakamura
    • Journal Title

      J. Chem. Theory Comput.

      Volume: 13 Issue: 6 Pages: 2389-2399

    • DOI

      10.1021/acs.jctc.6b01127

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multi-dimensional virtual system introduced to enhance canonical sampling.2017

    • Author(s)
      Junichi Higo, Kota Kasahara, Haruki Nakamura.
    • Journal Title

      J. Chem. Phys.

      Volume: 147 Issue: 13 Pages: 134102-134102

    • DOI

      10.1063/1.4986129

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Revisiting Antibody Modeling Assessment for CDR-H3 loop2016

    • Author(s)
      Hiroshi Nishigami, Narutoshi Kamiya, Haruki Nakamura
    • Journal Title

      Protein Engineering, Design and Selection

      Volume: 29 Issue: 11 Pages: 477-484

    • DOI

      10.1093/protein/gzw028

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Prediction of complex structure and affinity between cyclin-dependent kinase 2 and its inhibitor using multicanonical molecular dynamics and thermodynamic integration simulations2018

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
    • Organizer
      The 61st annual meeting of the Biophysical Society, New Orleans (USA)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and its Inhibitor2017

    • Author(s)
      Haruki Nakamura
    • Organizer
      Mini-Symposium, Astbury Centre, Leeds University (U. K.)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Oct4の2つのDNA結合サブドメインを結ぶLinker領域の構造多様性2017

    • Author(s)
      速水智教、高田彰二、笠原浩太、中村春木、肥後順一
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Flexible Docking between cyclin-dependent kinase 2 and its inhibitor CS3 using multicanonical MD and thermodynamic integration simulations.2017

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Complex structure and Affinity of CDK2 and its Inhibitor Using McMD and TI Simulations2017

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
    • Organizer
      19th IUPAB congress, Edinburgh (U.K.)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Non-Ewald method for accurately and efficiently calculating electrostatic interactions in molecular simulations2017

    • Author(s)
      Ikuo Fukuda, Narutoshi Kamiya, Kota Kasahara, Han Wang, Shun Sakuraba, Haruki Nakamura
    • Organizer
      “Conformational Ensembles from Experimental Data and Computer Simulations” meeting sponsored by the Biophysical Society
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and its Inhibitor2017

    • Author(s)
      Haruki Nakamura
    • Organizer
      The Trilateral Workshop for Frontier Protein Studies, Shanghai (China)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Flexible docking and affinity calculation between CDK2 and its inhibitor CS3 using multicanonical MD and thermodynamic integration.2017

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Oct4の2つのDNA結合サブドメインを結ぶLinker領域の構造多様性2017

    • Author(s)
      速水智教、高田彰二、笠原浩太、中村春木、肥後順一
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Enhanced Sampling for Analysis and Prediction of Protein-Ligand Interactions2017

    • Author(s)
      Haruki Nakamura
    • Organizer
      Seminar at Science for Life LaboratoryStockholm (Sweden)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In-Silico Drug Development Using Data Science and Computational Chemistry2017

    • Author(s)
      Haruki Nakamura
    • Organizer
      Kickoff Meeting (JSPS Symposium) for the ZIAM/GBB and ISIR/IPR Collaboration, Groningen (Netherlands)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Beyond Classical In-silico Drug Docking by Data Science and Molecular Simulation2017

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 15th Chinese Biophysics CongressShanghai (China)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Flexible docking between cyclin-dependent kinase 2 and its inhibitor using multicanonical MD2016

    • Author(s)
      Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Yasushi Okuno, Haruki Nakamura
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Oct4の2つのDNA結合サブドメインを結ぶ柔軟なlinker領域の自由エネルギー地形2016

    • Author(s)
      速水智教、高田彰二、中村春木、肥後順一
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] 分子シミュレーションにおける静電相互作用計算法:零多重極子法の理論と実際2016

    • Author(s)
      福田育夫, Wang Han, 神谷成敏, 笠原浩太, 寺田透, 櫻庭俊, 中村春木
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県、つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Computational Approaches to Coupled Folding and Binding in Protein-Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      The 11th International Symposium of the Protein Society of Thailand
    • Place of Presentation
      Bangkok (Thailand)
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational Approaches to Protein Interactions2016

    • Author(s)
      Haruki Nakamura
    • Organizer
      Japan-Slovenia JSPS Bilateral scientific exchange
    • Place of Presentation
      Koper (Slovenia)
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited

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Published: 2016-04-21   Modified: 2019-03-29  

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