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Oligomerization of amyloid beta-peptides studies by computer simulations

Research Project

Project/Area Number 24740296
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics/Chemical physics
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) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2014: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2013: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2012: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywordsアミロイド線維形成 / 分子シミュレーション / アミロイド形成 / 国際情報交換
Outline of Final Research Achievements

I had developed new simulation methods, the replica-permutation method and the Hamiltonian replica-permutation method. By using these methods, efficient conformational sampling for biomolecules can be realized in comparison with existing simulation methods. I had studied the oligomerization process of amyloid-beta peptides by these new methods. As a result, it was shown that beta-hairpin structures were increased when the amyloid-beta peptides came close. When the amyloid-beta peptides got close sufficiently, intermolecular beta-sheet structures as seen in amyloid fibrils were readily created in the presence of intramolecular beta-sheet structures.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (32 results)

All 2015 2014 2013 2012

All Journal Article (10 results) (of which Peer Reviewed: 10 results,  Acknowledgement Compliant: 2 results) Presentation (22 results) (of which Invited: 4 results)

  • [Journal Article] Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation2015

    • Author(s)
      Koya Inagaki, Tadashi Satoh, Satoru G. Itoh, Hisashi Okumura, Koichi Kato
    • Journal Title

      Chemical Physics Letters

      Volume: 619 Pages: 203-207

    • DOI

      10.1016/j.cplett.2014.11.017

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Amyloid fibril disruption by ultrasonic cavitation: Nonequilibrium molecular dynamics simulations2014

    • Author(s)
      H. Okumura and S. G. Itoh
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 136 Issue: 30 Pages: 10549-10552

    • DOI

      10.1021/ja502749f

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations2014

    • Author(s)
      S. G. Itoh and H. Okumura
    • Journal Title

      J. Phys. Chem. B

      Volume: 118 Issue: 39 Pages: 11428-11436

    • DOI

      10.1021/jp505984e

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Manifold correction method for the Nose-Hoover and Nose-Poincare molecular dynamics simulations2014

    • Author(s)
      H. Okumura, S. G. Itoh, A. M. Ito, H. Nakamura, and T. Fukushima
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: 83 Issue: 2 Pages: 24003-24003

    • DOI

      10.7566/jpsj.83.024003

    • NAID

      40019984185

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Transformation of a design peptide between the alpha-helix and beta-hairpin structures by a helix-strand replica-exchange molecular dynamics simulation2013

    • Author(s)
      H. Okumura and S. G. Itoh
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 15 Issue: 33 Pages: 13852-13861

    • DOI

      10.1039/c3cp44443k

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Decomposition-order effects of time-integrator on ensemble averages for the Nose-Hoover thermostat2013

    • Author(s)
      S. G. Itoh, T. Morishita, and H. Okumura
    • Journal Title

      J. Chem. Phys.

      Volume: 139 Issue: 6 Pages: 64103-64103

    • DOI

      10.1063/1.4817194

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-beta (29-42) peptides2013

    • Author(s)
      S. G. Itoh and H. Okumura
    • Journal Title

      J. Comput. Chem.

      Volume: 34 Issue: 29 Pages: 2493-2497

    • DOI

      10.1002/jcc.23402

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Replica-permutation method with the Suwa-Todo algorithm beyond the replica-exchange method2013

    • Author(s)
      S. G. Itoh and H. Okumura
    • Journal Title

      J. Chem. Theory Comput.

      Volume: 9 Issue: 1 Pages: 570-581

    • DOI

      10.1021/ct3007919

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules2013

    • Author(s)
      S. G. Itoh and H. Okumura
    • Journal Title

      J. Comput. Chem.

      Volume: 34 Issue: 8 Pages: 622-639

    • DOI

      10.1002/jcc.23167

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics2013

    • Author(s)
      Tetsuya Morishita, Satoru. G. Itoh, Hisashi Okumura, Masuhiro Mikami
    • Journal Title

      Journal of Computational Chemistry

      Volume: 34 Issue: 16 Pages: 1375-1384

    • DOI

      10.1002/jcc.23267

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] Dimer formation of Abeta(29-42) studied by the Hamiltonian replica-permutation method2015

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      The 3rd International Symposium “Dynamical ordering of biomolecular systems for creation of integrated functions”
    • Place of Presentation
      合歓の郷(三重県志摩市)
    • Year and Date
      2015-01-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] クーロンレプリカ置換分子動力学シミュレーションによるAbeta(29-42)の二量体形成2014

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第28回分子シミュレーション討論会
    • Place of Presentation
      仙台市民会館(宮城県仙台市)
    • Year and Date
      2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] Dimerization of Abeta fragments by the Hamiltonian replica-permutation method2014

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nose Dynamics 30 Years
    • Place of Presentation
      慶應大学(東京都港区)
    • Year and Date
      2014-11-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] Applications of the Hamiltonian replica-permutation molecular dynamics simulations to Abeta fragments2014

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道札幌市)
    • Year and Date
      2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Hamiltonian replica-permutation method and its application to Abeta fragments2014

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      2014 International Biophysics Congress
    • Place of Presentation
      Brisbane, Australia
    • Year and Date
      2014-08-04
    • Related Report
      2014 Annual Research Report
  • [Presentation] ハミルトニアンレプリカ置換法によるA(29-42)の研究2014

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      横浜産貿ホール マリネリア(神奈川県横浜市)
    • Year and Date
      2014-06-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Free-energy calculation by the replica-permutation method for biomolecules2014

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      ICCMSE 2014 10th International Conference of Computational Methods in Sciences and Engineering
    • Place of Presentation
      Athens, Greece
    • Year and Date
      2014-04-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Replica-permutation method to enhance sampling efficiency2014

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      The 2nd International Symposium “Dynamical ordering of biomolecular systems for creation of integrated functions”
    • Place of Presentation
      Kyoto, Japan
    • Related Report
      2013 Research-status Report
  • [Presentation] ハミルトニアンレプリカ置換法を用いたAbetaフラグメントの研究2014

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      平成25年度生物物理中部支部会
    • Place of Presentation
      分子科学研究所(愛知県)
    • Related Report
      2013 Research-status Report
  • [Presentation] 新たな拡張アンサンブル法:レプリカ置換法2013

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第16回理論化学討論会
    • Place of Presentation
      福岡市健康づくりサポートセンター(福岡県)
    • Related Report
      2013 Research-status Report
  • [Presentation] レプリカ交換法からレプリカ置換法へ2013

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第13回日本蛋白質科学会年会
    • Place of Presentation
      とりぎん文化会館(鳥取県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Replica-Permutation Method for Biomolecules as a Better Alternative to Replica-Exchange Method2013

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      9th European Biophysics Congress
    • Place of Presentation
      Lisbon, Portugal
    • Related Report
      2013 Research-status Report
  • [Presentation] 諏訪・藤堂法を用いた拡張アンサンブル法:レプリカ置換法2013

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      日本物理学会2013年度秋季大会
    • Place of Presentation
      徳島大学(t徳島県)
    • Related Report
      2013 Research-status Report
  • [Presentation] 拡張アンサンブル法による効率的サンプリングに基づく自由エネルギー計算2013

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第4回計算統計物理学研究会
    • Place of Presentation
      山口大学(山口県)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Efficient sampling for biomolecules by the replica-permutation method2013

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      京都国際会議場(京都府)
    • Related Report
      2013 Research-status Report
  • [Presentation] New generalized ensemble algorithm without the detailed balance condition2013

    • Author(s)
      Satoru G. Itoh, Hisashi Okumura
    • Organizer
      3rd International Conference on Molecular Simulation
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2013 Research-status Report
  • [Presentation] クーロンレプリカ交換法のAβ(29-42)への応用2012

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      アジア連携分子研研究会「実験及び理論研究手法の開拓と新規物性探索への展開」
    • Place of Presentation
      分子科学研究所(愛知県)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] クーロンレプリカ交換法のAβフラグメントへの応用2012

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋国際会議場(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] クーロンレプリカ交換法によるAβ(29-42)の構造探索2012

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第6回分子科学討論会
    • Place of Presentation
      東京大学(東京都)
    • Related Report
      2012 Research-status Report
  • [Presentation] Studies on an Abeta fragment by the Coulomb replica-exchange method2012

    • Author(s)
      Satoru. G. Itoh, Hisashi Okumura
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学(愛知県)
    • Related Report
      2012 Research-status Report
  • [Presentation] Coulomb Replica-Exchange Method and Its Applications2012

    • Author(s)
      Satoru. G. Itoh
    • Organizer
      2012 NCTS November Workshop on Critical Phenomena and Complex Systems
    • Place of Presentation
      Taipei, TAIWAN
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 水中のAフラグメントに対するクーロンレプリカ交換分子動力学シミュレーション2012

    • Author(s)
      伊藤暁、奥村久士
    • Organizer
      第26回分子シミュレーション討論会
    • Place of Presentation
      九州大学西新プラザ(福岡県)
    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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