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Oligomer formation of amyloid-beta studied by new constant pH simulations

Research Project

Project/Area Number 16K18531
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionInstitute for Molecular Science

Principal Investigator

Itoh Satoru  分子科学研究所, 理論・計算分子科学研究領域, 助教 (90595381)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2018: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2016: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywordsアミロイド線維 / 分子シミュレーション / アミロイド / 生物物理 / 生体分子
Outline of Final Research Achievements

The oligomer formation process of Abeta(29-42), which is a fragment of the amyloid beta (Abeta) peptide, was studied by Coulomb replica-permutation molecular dynamics simulations. It was found that an oligomer increased in size by addition of a monomer to the oligomer sequentially.
We also performed Coulomb replica-permutation molecular dynamics simulations to clarify the dimer formation process of the full-length Abeta peptides. As a result, it was found that the intramolecular beta-sheet structure accelerated the formation of an intermolecular beta-sheet structure.

Academic Significance and Societal Importance of the Research Achievements

アミロイドベータペプチド(Abeta)が形成するオリゴマーはアルツハイマー病との関連が指摘されており、アルツハイマー病を克服するためにはオリゴマー形成過程の解明は不可欠である。本研究によりAbetaのオリゴマー形成初期過程を原子レベルで明らかにした。本研究を発展させることでアルツハイマー病の治療薬開発に貢献できると考える。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (20 results)

All 2018 2017 2016

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 2 results,  Open Access: 1 results) Presentation (16 results) (of which Int'l Joint Research: 8 results,  Invited: 7 results)

  • [Journal Article] Effects of a Hydrophilic/Hydrophobic Interface on Amyloid-β Peptides Studied by Molecular Dynamics Simulations and NMR Experiments2018

    • Author(s)
      Itoh Satoru G.、Yagi-Utsumi Maho、Kato Koichi、Okumura Hisashi
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123 Issue: 1 Pages: 160-169

    • DOI

      10.1021/acs.jpcb.8b11609

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Oligomer formation of amyloid-β(29-42) from its monomers using the Hamiltonian replica-permutation molecular dynamics simulation2016

    • Author(s)
      Satoru G. Itoh and Hisashi Okumura
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 27 Pages: 6555-6561

    • DOI

      10.1021/acs.jpcb.6b03828

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences.2016

    • Author(s)
      Gupta R, Saito S, Mori Y, Itoh S, Okumura H, Tominaga M.
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 37460-37460

    • DOI

      10.1038/srep37460

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulation predicts only one end has open conformations2016

    • Author(s)
      Hisashi Okumura and Satoru G. Itoh
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 38422-38422

    • DOI

      10.1038/srep38422

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 水溶液表面及び水中でのAβ単量体に関する 分子動力学シミュレーション2018

    • Author(s)
      伊藤 暁、奥村 久士
    • Organizer
      第21回理論化学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Aβ40とAβ42の二量体形成における違いに関する理論的研究2018

    • Author(s)
      伊藤 暁、奥村 久士
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Molecular dynamics simulations of a full-length amyloid-β peptide at a hydrophobic/hydrophilic interface2018

    • Author(s)
      Satoru G. Itoh
    • Organizer
      The 22th International Annual Symposium on Computational Science and Engineering
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ハミルトニアンレプリカ置換分子動力学シミュレーションによるAβ40 とAβ42 の二量体形成2018

    • Author(s)
      伊藤 暁、奥村 久士
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Oligomer formation of Aβ(29-42) by Coulomb replica-permutation molecular dynamics simulations2018

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      Asian Biophysics Association Symposium 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] アミロイドβペプチドの全原子分子動力学シミュレーション2018

    • Author(s)
      伊藤暁
    • Organizer
      第1回松山道後・分子論セミナー
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] レプリカ置換法とそのアミロイドβペプチドへの応用2017

    • Author(s)
      伊藤暁
    • Organizer
      凝集系の理論化学
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Oligomerization pathway of Abeta fragments by the Hamiltonian replica-permutation method2017

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      11th European Biophysics Congress
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Replica-permutation method: efficient sampling for biomolecules2017

    • Author(s)
      Satoru G. Itoh
    • Organizer
      阪大ミニワークショップ
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Oligomerization pathway of amyloid-beta fragments studied by the Hamiltonian replica-permutation method2017

    • Author(s)
      Satoru G. Itoh
    • Organizer
      The 21th International Annual Symposium on Computational Science and Engineering
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ハミルトニアンレプリカ置換分子動力学シミュレーションによるAβ全長の二量体構造2017

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Dimerization of full-length Abeta peptides by the Hamiltonian replica-permutation method2017

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      日本生物物理学会第55回年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Replica-permutation method to obtain efficient sampling for biomolecules2017

    • Author(s)
      Satoru G. Itoh
    • Organizer
      The 2017 EMN Meeting on Computation and Theory
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Oligomer Formation Process of Abeta Fragments by Hamiltonian Replica-Permutation Methods2017

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      The 10th International Conference on Computational Physics
    • Place of Presentation
      Macau, China
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Oligomerization of Abeta(29-42) using Hamiltonian replica-permutation MD simulations2017

    • Author(s)
      Satoru G. Itoh
    • Organizer
      2017 NCTS March Workshop on Critical Phenomena and Complex Systems
    • Place of Presentation
      Hsinchu, Taiwan
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Hamiltonian replica-permutation molecular dynamics simulation studies on the oligomerization of amyloid-beta fragments2016

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      The 26th IUPAP International Conference on Statistical Physics
    • Place of Presentation
      Lyon, France
    • Year and Date
      2016-07-19
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research

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Published: 2016-04-21   Modified: 2020-03-30  

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