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Development of a Biomolecule Simulation System Using the Single Amino Acid Potential Force Field

Research Project

Project/Area Number 21200005
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research a proposed research project)

Allocation TypeSingle-year Grants
Research Field Biophysics
Bioinformatics/Life informatics
Research InstitutionTokai University

Principal Investigator

IWAOKA Michio  東海大学, 理学部, 教授 (30221097)

Co-Investigator(Kenkyū-buntansha) MINEZAKI Toshiya  東海大学, 理学部, 准教授 (30190713)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥24,180,000 (Direct Cost: ¥18,600,000、Indirect Cost: ¥5,580,000)
Fiscal Year 2011: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2010: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
Fiscal Year 2009: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Keywordsタンパク質 / アミノ酸 / 力場 / 分子シミュレーション / タンパク質構造データベース / ポテンシャル / 分子軌道計算 / フォールディング / 生物物理 / 蛋白質 / 構造・機能予測 / コンピュータシミュレーション / フオールデイング
Research Abstract

To elucidate the process of structural folding of proteins, four subjects were focused in this study. First, the Single Amino Acid Potential force field was improved, and the accuracy was evaluated. Second, the roles of the single amino acid potentials in protein structures were quantitatively analyzed. Third, the strain energy of protein structures was analyzed based on the single amino acid potentials. Fourth, the developed molecular simulation program was released on the web.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (60 results)

All 2012 2011 2010 2009 Other

All Journal Article (34 results) (of which Peer Reviewed: 27 results) Presentation (15 results) Book (4 results) Remarks (7 results)

  • [Journal Article] From Sulfur to Selenium. A New Research Arena in Chemical Biology and Biological Chemistry2012

    • Author(s)
      M. Iwaoka, K. Arai
    • Journal Title

      Curr. Chem. Biol.

      Volume: 6(In press)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic and Thermodynamic Analysis of the Conformational Folding Process of SS-Reduced Bovine Pancreatic Ribonuclease A Using a Selenoxide Reagent with High Oxidizing Ability2012

    • Author(s)
      K. Arai, F. Kumakura, M. Iwaoka
    • Journal Title

      FEBS Open Bio

      Volume: 2 Pages: 60-70

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] From Sulfur to Selenium. A New Research Arena in Chemical Biology and Biological Chemistry2012

    • Author(s)
      Michio Iwaoka, Kenta Arai
    • Journal Title

      Curr.Chem.Biol.

      Volume: 6(accepted)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic and Thermodynamic Analysis of the Conformational Folding Process of SS-Reduced Bovine Pancreatic Ribonuclease A Using a Selenoxide Reagent with High Oxidizing Ability2012

    • Author(s)
      Kenta Arai, Fumio Kumakura, Michio Iwaoka
    • Journal Title

      FEBS Open Bio

      Volume: 2(accepted) Issue: 1 Pages: 60-70

    • DOI

      10.1016/j.fob.2012.04.001

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rapid and Quantitative Disulfide Bond Formation for a Polypeptide Chain Using a Cyclic Selenoxide Reagent in an Aqueous Medium2011

    • Author(s)
      K. Arai, K. Dedachi, M. Iwaoka
    • Journal Title

      Chem. Eur. J.

      Volume: 17 Pages: 481-485

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] One-Pot Conversion of Serine and α-Methylserine Derivatives to the Corresponding Cysteines and Selenocystines by Using Chalcogenophosphate Reagents2011

    • Author(s)
      A. Makiyama, I. Komatsu, M. Iwaoka, M. Yatagai
    • Journal Title

      Phosph. Sulf. Silic. and The Related Elements

      Volume: 186 Pages: 125-133

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Antioxidative Glutathione Peroxidase Activity of Selenoglutathione2011

    • Author(s)
      S. Yoshida, F. Kumakura, I. Komatsu, K. Arai, Y. Onuma, H. Hojo, B. G. Singh, K. I. Priyadarsini, M. Iwaoka
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 50 Pages: 2125-2128

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Effect of Functional Groups on Antioxidant Properties of Substituted Selenoethers2011

    • Author(s)
      P. Prabhu, P. P. Bag, B. G. Singh, A. Hodage, V. K. Jain, M. Iwaoka, K. I. Priyadarsini
    • Journal Title

      Free Radical Res.

      Volume: 45 Pages: 461-468

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Rapid and Quantitative Disulfide Bond Formation for a Polypeptide Chain Using a Cyclic Selenoxide Reagent in an Aqueous Medium.2011

    • Author(s)
      Kenta Arai, Kenichi Dedachi, Michio Iwaoka
    • Journal Title

      Chem.Eur.J.

      Volume: 17 Pages: 481-485

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] One-Pot Conversion of Serine and α-Methylserine Derivatives to the Corresponding Cysteines and Selenocystines by Using Chalcogenophosphate Reagents.2011

    • Author(s)
      Akira Makiyama, Itsuki Komatsu, Michio Iwaoka, Masanobu Yatagai
    • Journal Title

      Phosph.Sulf.Silic.and The Related Elements

      Volume: 186 Pages: 125-133

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Antioxidative Glutathione Peroxidase Activity of Selenoglutathione.2011

    • Author(s)
      Sari Yoshida, Fumio Kumakura, Itsuki Komatsu, Kenta Arai, Yuko Onuma, Hironobu Hojo, Beena G.Singh, K.Indira Priyadarsini, Michio Iwaoka
    • Journal Title

      Angew.Chem.Int.Ed.

      Volume: 50 Pages: 2125-2128

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Water-Soluble Cyclic Selenide with Enhanced Glutathione Peroxidase-Like Catalytic Activities2010

    • Author(s)
      F. Kumakura, B. Mishra, K. I. Priyadarsini, M. Iwaoka
    • Journal Title

      Eur. J. Org. Chem.

      Pages: 440-445

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Role of Substrate Reactivity in the Glutathione Peroxidase (GPx) Activity of Selenocystine2010

    • Author(s)
      B. Singh, P. P. Bag, F. Kumakura, M. Iwaoka, K. I. Priyadarsini
    • Journal Title

      Bull. Chem. Soc. Jpn.

      Volume: 83 Pages: 703-708

    • NAID

      10026385460

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] 単一アミノ酸の構造2010

    • Author(s)
      岩岡道夫
    • Journal Title

      プロモイス

      Pages: 62-62

    • Related Report
      2011 Final Research Report 2009 Annual Research Report
  • [Journal Article] Synthesis of New Sulfoxide-Containing Diselenides and Unexpected Cyclization Reactions to 2,3-Dihydro-1,4-benzoseleno-thiine 1-Oxides2010

    • Author(s)
      D. M. Freudendahl, M. Iwaoka, T. Wirth
    • Journal Title

      Eur. J. Org. Chem.

      Pages: 3934-3944

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural Transitions and an Enzymatic Function of Ribonuclease A Encapsulated in Transparent Porous Silica Gel2010

    • Author(s)
      M. Iwaoka, N. Sano, N. Hasegawa, M. Yokokawa, S. Kunigami, H. Shirai
    • Journal Title

      Bull. Chem. Soc. Jpn.

      Volume: 83 Pages: 935-941

    • NAID

      10026510560

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] One-Electron Redox Processes in a Cyclic Selenide and a Selenoxide: A Pulse Radiolysis Study2010

    • Author(s)
      B. G. Singh, E. Thomas, F. Kumakura, K. Dedachi, M. Iwaoka, K. I. Priyadarsini
    • Journal Title

      J. Phys. Chem. A

      Volume: 114 Pages: 8271-8277

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Novel Cyclization Cascades to Functionalized Indanes and Tetrahydronaphthalenes2010

    • Author(s)
      Z. A. Khan, M. Iwaoka, T. Wirth
    • Journal Title

      Tetrahedron

      Volume: 66 Pages: 6639-6646

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of Kinetic and Thermodynamic Phases in the Pre-Folding Process of Bovine Pancreatic Ribonuclease A Coupled with Fast SS Formation and SS Reshuffling2010

    • Author(s)
      K. Arai, F. Kumakura, M. Iwaoka
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 10535-10542

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Synthesis of New Sulfoxide-Containing Diselenides and Unexpected Cyclization Reactions to 2,3-Dihydro-1,4-benzoselenothiine 1-Oxides.2010

    • Author(s)
      Diana M.Freudendahl, Michio Iwaoka, Thomas Wirth
    • Journal Title

      Eur.J.Org.Chem.

      Pages: 3934-3944

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural Transitions and an Enzymatic Function of Ribonuclease A Encapsulated in Transparent Porous Silica Gel.2010

    • Author(s)
      Michio Iwaoka, Nobukazu Sano, Norikazu Hasegawa, Mariko Yokokawa, Satoko Kunigami, Hiroyuki Shirai
    • Journal Title

      Bull.Chem.Soc.Jpn

      Volume: 83 Pages: 935-941

    • NAID

      10026510560

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] One-Electron Redox Processes in a Cyclic Selenide and a Selenoxide : A Pulse Radiolysis Study.2010

    • Author(s)
      Beena G.Singh, Elizabeth Thomas, Fumio Kumakura, Kenichi Dedachi, Michio Iwaoka, K.Indira Priyadarsini
    • Journal Title

      J.Phys.Chem.A

      Volume: 114 Pages: 8271-8277

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel Cyclization Cascades to Functionalized Indanes and Tetrahydrona phthalenes.2010

    • Author(s)
      Zulfiqar A.Khan, Michio Iwaoka, Thomas Wirth
    • Journal Title

      Tetrahedron

      Volume: 66 Pages: 6639-6646

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of Kinetic and Thermodynamic Phases in the Pre-Folding Process of Bovine Pancreatic Ribonuclease A Coupled with Fast SS Formation and SS Reshuffling.2010

    • Author(s)
      Kenta Arai, Fumio Kumakura, Michio Iwaoka
    • Journal Title

      Biochemistry

      Volume: 49 Pages: 10535-10542

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Water-Soluble Cyclic Selenide with Enhanced Glutathione Peroxidase-Like Catalytic Activities.2010

    • Author(s)
      F.Kumakura, B.Mishra, K.I.Priyadarsini, M.Iwaoka
    • Journal Title

      Eur.J.Org.Chem.

      Pages: 440-445

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of Substrate Reactivity in the Glutathione Peroxidase (GPx) Activity of Selenocystine.2010

    • Author(s)
      B.Sungh, P.P.Bag, F.Kumakura, M.Iwaoka, K.I.Priyadarsini
    • Journal Title

      Bull.Chem.Soc.Jpn. (In press)

    • NAID

      10026385460

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The SAAP Force Field. Development of the Single Amino Acid Potentials for Twenty Proteinogenic Amino Acids and Monte Carlo Molecular Simulation for Short Peptides2009

    • Author(s)
      M. Iwaoka, N. Kimura, D. Yosida, T. Minezaki
    • Journal Title

      J. Comput. Chem.

      Volume: 30 Pages: 2039-2055

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of Oxidative Folding of Ribonuclease A by Using Water-Soluble Selenoxide Reagent2009

    • Author(s)
      K. Arai, F. Kumakura, M. Iwaoka
    • Journal Title

      Amino Acids

      Volume: 37

    • Related Report
      2011 Final Research Report
  • [Journal Article] New Synthetic Strategies towards Selenocysteine and Selenomethionine Derivatives2009

    • Author(s)
      M. Iwaoka, S. Yoshida, S. Oishi, A. Makiyama, F. Kumakura
    • Journal Title

      Amino Acids

      Volume: 37

    • Related Report
      2011 Final Research Report
  • [Journal Article] Synthesis of Selnocysteine Derivatives and Their Antioxidant Catalytic Activities2009

    • Author(s)
      S. Yoshida, M. Iwaoka
    • Journal Title

      Amino Acids

      Volume: 37

    • Related Report
      2011 Final Research Report
  • [Journal Article] The SAAP Force Field. Development of the Single Amino Acid Potentials for Twenty Proteinogenic Amino Acids and Monte Carlo Molecular Simulation for Short Peptides.2009

    • Author(s)
      M.Iwaoka, N.Kimura, D.Yosida, T.Minezaki
    • Journal Title

      J.Comput.Chem. 30

      Pages: 2039-2055

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of Oxidative Folding of Ribonuclease A by Using Water-Soluble Selenoxide Reagent.2009

    • Author(s)
      K.Arai, F.Kumakura, M.Iwaoka
    • Journal Title

      Amino Acids 37

    • Related Report
      2009 Annual Research Report
  • [Journal Article] New Synthetic Strategies towards Selenocysteine and Selenomethionine Derivatives.2009

    • Author(s)
      M.Iwaoka, S.Yoshida, S.Oishi, A.Makiyama, F.Kumakura
    • Journal Title

      Amino Acids 37

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Synthesis of Selnocysteine Derivatives and Their Antioxidant Catalytic Activities.2009

    • Author(s)
      S.Yoshida, M.Iwaoka
    • Journal Title

      Amino Acids 37

    • Related Report
      2009 Annual Research Report
  • [Presentation] 単一アミノ酸ポテンシャル力場の改良と応用2012

    • Author(s)
      岩岡道夫、出立兼一、下里卓、峯崎俊哉
    • Organizer
      日本化学会第92春季年会(2012)
    • Place of Presentation
      慶応大日吉キャンパス
    • Year and Date
      2012-03-28
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 単一アミノ酸ポテンシャル力場を用いた非天然アミノ酸を含むペプチドの分子シミュレーション2012

    • Author(s)
      野村岳史、出立兼一、下里卓、峯崎俊哉、岩岡道夫
    • Organizer
      日本化学会第92春季年会(2012)
    • Place of Presentation
      慶応大日吉キャンパス
    • Year and Date
      2012-03-28
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 単一アミノ酸ポテンシャル力場を用いた低分子ペプチドの構造探索2011

    • Author(s)
      出立兼一、下里卓、峯崎俊哉、岩岡道夫
    • Organizer
      第25回分子シミュレーション討論会
    • Place of Presentation
      東工大大岡山キャンパス
    • Year and Date
      2011-12-05
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 単一アミノ酸力場を用いた非天然アミノ酸を含むペプチドの分子シミュレーション2011

    • Author(s)
      出立兼一、野村岳史、下里卓、峯崎俊哉、岩岡道夫
    • Organizer
      第48回ペプチド討論会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2011-09-28
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] Oxidative Folding Pathways of Proteins Investigated by Using Selenoxide Reagents2011

    • Author(s)
      M. Iwaoka
    • Organizer
      150 Years of German-Japanese Collaboration in GDCh-Wissenschaftsforum Chemie 2011
    • Place of Presentation
      Bremen, Germany
    • Year and Date
      2011-09-07
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] Molecular Simulation of Peptides Using the Single Amino Acid Potential Force Field2011

    • Author(s)
      K. Dedachi, M. Iwaoka
    • Organizer
      150 Years of German-Japanese Collaboration in GDCh-Wissenschaftsforum Chemie 2011
    • Place of Presentation
      Bremen, Germany
    • Year and Date
      2011-09-07
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 単一アミノ酸ポテンシャル(SAAP)力場を用いた生体分子の構造解析2011

    • Author(s)
      出立兼一, 下里卓, 峯崎俊哉, 岩岡道夫
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク
    • Year and Date
      2011-06-08
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] SAAP力場の開発とペプチド分子シミュレーションへの応用2011

    • Author(s)
      岩岡道夫, 出立兼一, 下里卓, 峯崎俊哉
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス
    • Year and Date
      2011-03-27
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] SAAP力場を用いたシニョリン及びC-ペプチドの構造解析2011

    • Author(s)
      出立兼一, 下里卓, 峯崎俊哉, 岩岡道夫
    • Organizer
      日本化学会第91春季年会
    • Place of Presentation
      神奈川大学横浜キャンパス
    • Year and Date
      2011-03-26
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] Single amino acid potentials as prominent determinants of protein structures2010

    • Author(s)
      M. Iwaoka
    • Organizer
      2010 International Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Honolulu, Hawaii
    • Year and Date
      2010-12-18
    • Related Report
      2011 Final Research Report
  • [Presentation] Single amino acid potentials as prominent determinants of protein structures.2010

    • Author(s)
      Michio Iwaoka
    • Organizer
      2010 International Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Honolulu, Hawaii
    • Year and Date
      2010-12-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] 単一アミノ酸ポテンシャル力場(SAAP力場)の開発と評価2010

    • Author(s)
      出立兼一, 下里卓, 峯崎俊哉, 岩岡道夫
    • Organizer
      第4回分子科学討論会
    • Place of Presentation
      大阪大学豊中キャンパス
    • Year and Date
      2010-09-17
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] 単一アミノ酸ポテンシャルを用いたタンパク質の歪みエネルギー解析2010

    • Author(s)
      岩岡道夫, 峯崎俊哉, 中村慎吾, 下里卓
    • Organizer
      日本化学会第90春季年会
    • Place of Presentation
      近畿大学
    • Year and Date
      2010-03-27
    • Related Report
      2011 Final Research Report 2009 Annual Research Report
  • [Presentation] Redox-Coupled Folding of Proteins by Using Small Organic Selenium Reagents2009

    • Author(s)
      M. Iwaoka
    • Organizer
      School and Symposium on Advanced Biological Inorganic Chemistry (SaBIC-2009)
    • Place of Presentation
      Mumbai, India
    • Year and Date
      2009-11-07
    • Related Report
      2011 Final Research Report
  • [Presentation] Redox-Coupled Folding of Proteins by Using Small Organic Selenium Reagents. (Invited Lecture)2009

    • Author(s)
      M.Iwaoka
    • Organizer
      School and Symposium on Advanced Biological Inorganic Chemistry (SaBIC-2009)
    • Place of Presentation
      Mumbai, India
    • Year and Date
      2009-11-07
    • Related Report
      2009 Annual Research Report
  • [Book] Nucleophilic Selenium in Organoselenium Chemistry: Synthesis and Reactions, T. Wirth編2012

    • Author(s)
      M. Iwaoka
    • Publisher
      Wiley-VCH Verlag GmbH & Co. KGaA
    • Related Report
      2011 Final Research Report
  • [Book] Organoselenium Chemistry : Synthesis and Reactions2012

    • Author(s)
      Michio Iwaoka, et al
    • Total Pages
      448
    • Publisher
      Wiley-VCH Verlag GmbH & Co.KGaA
    • Related Report
      2011 Annual Research Report
  • [Book] 化学辞典(第2版)2009

    • Author(s)
      安孫子誠也, 他112名
    • Total Pages
      1716
    • Publisher
      森北出版
    • Related Report
      2011 Final Research Report
  • [Book] 化学辞典(第2版)編集代表吉村壽次2009

    • Author(s)
      安孫子誠也, 他112名
    • Total Pages
      1716
    • Publisher
      森北出版
    • Related Report
      2009 Annual Research Report
  • [Remarks] 試作プログラムの配信

    • URL

      http://saap.sc.u-tokai.ac.jp

    • Related Report
      2011 Final Research Report
  • [Remarks] 研究成果の配信

    • URL

      http://www.sc.u-tokai.ac.jp/Iwaokalab.htm

    • Related Report
      2011 Final Research Report
  • [Remarks]

    • URL

      http://saap.sc.u-tokai.ac.jp

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.sc.u-tokai.ac.jp/Iwaokalab.htm

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://saap.sc.u-tokai.ac.jp

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.sc.u-tokai.ac.jp/Iwaokalab.htm

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.sc.u-tokai.ac.jp/IwaokaLab.htm

    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2018-03-28  

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