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Structural changes of hetero-oligomers in the Protein Data Bank

Research Project

Project/Area Number 18H03331
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionNagoya University

Principal Investigator

太田 元規  名古屋大学, 情報学研究科, 教授 (40290895)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2021: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2020: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2019: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2018: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Keywords立体構造 / 構造比較 / 構造機能相関 / バイオインフォマティクス / タンパク質・核酸の構造・動態・機能 / 構造変化
Outline of Annual Research Achievements

タンパク質のヘテロ複合体の多くは過渡的でアロステリーとも関連し,生理活性を高度に制御調節する.タンパク質の構造変化と機能発現は密接に関係しているので,ヘテロ複合体の構造変化には,その独特な機能発現機構を解く鍵が潜んでいる.本研究ではPDBに格納された全ヘテロ複合体を対象に立体構造比較を行い,構造変化を大規模,系統的に解析して運動を分類し,俯瞰する.この時,申請者らが開発した,複合体の構造比較法:SCPCと,立体構造変化の同定・記述法:Motion Treeを利用する.研究期間を通して,信頼できるヘテロ複合体の立体構造を取得する方法を考案した.立体構造データベース(PDB)のmmCIFフォーマットのファイルから,著者とコンピュータが生状態と判定した構造を同定し,それに対応するバイオロジカルユニットを得た.これを実施するに,mmCIFの鎖IDとPDBの鎖IDが異なる場合があるので対応表を作成したり,煩雑な作業が発生する.一連の作業をスムーズに実施するためのパイプラインを構築した.その後SwissProtのアクセッションを参照して,ヘテロマーを選択することでヘテロ複合体のデータを得た.本研究では第一歩としてヘテロダイマーに着目し,SCPCとMotionTreeを用いてプロトマーの相互作用面で運動が起きている場合(interface motion)や,プロトマーに渡るユニットが構成されて運動が起きている場合(subunit-spanning motion)の統計を取った.また,進化的類縁関係があるヘテロマーから構成されているホモロガスヘテロダイマーに着目し,構造の対称性が崩れる進化的イベントは配列置換ではなかなか起きず,そういう事例には挿入欠失が伴うことも発見した.

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Report

(4 results)
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(42 results)

All 2021 2020 2019 2018

All Journal Article (9 results) (of which Peer Reviewed: 8 results,  Open Access: 6 results) Presentation (31 results) (of which Int'l Joint Research: 8 results,  Invited: 8 results) Book (2 results)

  • [Journal Article] Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins2021

    • Author(s)
      Hijikata Atsushi、Shionyu Clara、Nakae Setsu、Shionyu Masafumi、Ota Motonori、Kanaya Shigehiko、Shirai Tsuyoshi
    • Journal Title

      BIOPHYSICS

      Volume: 18 Issue: 0 Pages: 226-240

    • DOI

      10.2142/biophysico.bppb-v18.025

    • NAID

      130008106407

    • ISSN
      2189-4779
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evaluating cepharanthine analogues as natural drugs against SARS‐CoV‐22021

    • Author(s)
      Hijikata Atsushi、Shionyu‐Mitsuyama Clara、Nakae Setsu、Shionyu Masafumi、Ota Motonori、Kanaya Shigehiko、Hirokawa Takatsugu、Nakajima Shogo、Watashi Koichi、Shirai Tsuyoshi
    • Journal Title

      FEBS Open Bio

      Volume: 12 Pages: 285-294

    • DOI

      10.1002/2211-5463.13337

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structure of human V-1 in the apo form2021

    • Author(s)
      Shuichi Takeda, Ryotaro Koike, Takayuki Nagae, Ikuko Fujiwara, Akihiro Narita, Yuichiro Maeda, Motonori Ota
    • Journal Title

      Acta Crystallographica Section F Structural Biology Communications

      Volume: 77 Pages: 13-21

    • DOI

      10.1107/s2053230x20016829

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Knowledge‐based structural models of SARS‐CoV‐2 proteins and their complexes with potential drugs2020

    • Author(s)
      Hijikata Atsushi、Shionyu‐Mitsuyama Clara、Nakae Setsu、Shionyu Masafumi、Ota Motonori、Kanaya Shigehiko、Shirai Tsuyoshi
    • Journal Title

      FEBS Letters

      Volume: 594 Pages: 1960-1973

    • DOI

      10.1002/1873-3468.13806

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins2020

    • Author(s)
      Koike Ryotaro、Amano Mutsuki、Kaibuchi Kozo、Ota Motonori
    • Journal Title

      Prot. Sci.

      Volume: 29 Pages: 564-571

    • DOI

      10.1002/pro.3789

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins2019

    • Author(s)
      Koike Ryotaro、Ota Motonori
    • Journal Title

      BIOPHYSICS

      Volume: 16 Issue: 0 Pages: 280-286

    • DOI

      10.2142/biophysico.16.0_280

    • NAID

      130007752770

    • ISSN
      2189-4779
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 天然変性タンパク質:既知のこと,未知のこと2019

    • Author(s)
      太田元規,福地佐斗志
    • Journal Title

      実験医学

      Volume: 37 Pages: 3077-3082

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Using 1HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method2018

    • Author(s)
      Okazaki Hiroki、Matsuo Naoki、Tenno Takeshi、Goda Natsuko、Shigemitsu Yoshiki、Ota Motonori、Hiroaki Hidekazu
    • Journal Title

      Protein Science

      Volume: 27 Pages: 1821-1830

    • DOI

      10.1002/pro.3485

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MICAN-SQ: A sequential protein structure alignment program that is applicable to monomers and all types of oligomers2018

    • Author(s)
      Shintaro Minami, Kengo Sawada, Motonori Ota, and George Chikenji
    • Journal Title

      Bioinformatics

      Volume: 34 Pages: 3324-3331

    • DOI

      10.1093/bioinformatics/bty369

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Directed Protein-Protein Interaction Network Representing Intracellular Signaling Pathways2021

    • Author(s)
      Wenruo Cao, Ryotaro Koike, Motonori Ota
    • Organizer
      第59回日本生物物理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Structural characterization of homologous hetero-oligomers2021

    • Author(s)
      Kota Ito, Clara Shionyu, Yasunobu Sugimoto, Ryotaro Koike, Motonori Ota
    • Organizer
      第59回日本生物物理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Relationship between Length of Intrinsically Disordered Regions and Protein Function2021

    • Author(s)
      Haruka Tanimoto, Ryotaro Koike, Motonori Ota
    • Organizer
      第59回日本生物物理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 異なる機能状態にあるアクチンの構造ゆらぎとその相関関係2021

    • Author(s)
      小池亮太郎,森次圭,太田元規
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Elastic network model analysis shows distinct flexibilities of capping protein bound to CARMIL or twinfilin2021

    • Author(s)
      Ryotaro Koike, Motonori Ota
    • Organizer
      第59回日本生物物理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Structural flexibility of actin in molecular dynamics simulation2021

    • Author(s)
      Ryotaro Koike, Motonori Ota
    • Organizer
      環太平洋国際化学会議2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Protein kinases phosphorylate long intrinsically disordered regions of substrate proteins2021

    • Author(s)
      Ryotaro Koike, Mutsuki Amano, Kozo Kaibuchi, Motonori Ota
    • Organizer
      環太平洋国際化学会議2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Small structural pattern common in chaperonin GroE substrate proteins2021

    • Author(s)
      S. Minami, T. Niwa, E. Uemura, R. Koike, H. Taguchi, M. Ota
    • Organizer
      第59回日本生物物理学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 天然変性タンパク質データベース:IDEAL (@2021)2021

    • Author(s)
      太田元規,嘉戸裕美子,坂本盛宇,細田和男,鹿間周子,大安裕美,高木大輔,安保勲人,山口敦子,畠中秀樹,小池亮太郎,廣明秀一,福地佐斗志
    • Organizer
      トーゴーの日シンポジウム2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] 液滴形成の生命情報解析2021

    • Author(s)
      太田元規,福地佐斗志
    • Organizer
      相分離メガネをかけて生命現象を見てみよう(トランスフォーマティブ化学生命融合大学院プログラム)
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] データベースアノテーションに基づく液滴の分析2020

    • Author(s)
      岩塚光輝,太田元規,福地佐斗志,安保勲人
    • Organizer
      第58回日本生物物理学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 液滴を作るタンパク質に見られる天然変性タンパク質2020

    • Author(s)
      太田元規,福地佐斗志
    • Organizer
      CBI学会2020年大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 天然変性タンパク質データベース:IDEAL2020

    • Author(s)
      太田元規,嘉戸裕美子,坂本盛宇,細田和男,山口敦子,畠中秀樹,小池亮太郎,廣明秀一,福地佐斗志
    • Organizer
      トーゴーの日シンポジウム2020
    • Related Report
      2020 Annual Research Report
  • [Presentation] Intrinsically disordered proteins (IDPs) included in droplets2020

    • Author(s)
      Motonori Ota, Satoshi Fukuchi
    • Organizer
      第43回日本分子生物学会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Structural flexibility of actin studied by molecular dynamics simulation2020

    • Author(s)
      Ryotaro Koike, Motonori Ota
    • Organizer
      第58回日本生物物理学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 全原子Motion Treeとドメイン運動に伴う側鎖の運動2019

    • Author(s)
      小池亮太郎,太田元規
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] タンパク質ータンパク質間相互作用の有向ネットワークが示す細胞内情報伝達2019

    • Author(s)
      葉山雄揮,小池亮太郎,太田元規
    • Organizer
      第19回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Full-atom Motion Tree detects side-chain motions and their coupling with domain motions2019

    • Author(s)
      Ryotaro Koike, Motonori Ota
    • Organizer
      第57回日本生物物理学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Structural flexibility of actin monomer in molecular dynamics simulation2019

    • Author(s)
      Ryotaro Koike, Motonori Ota
    • Organizer
      11th Toyota Riken International Workshop, Actin Workshop
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 天然変性タンパク質データベース:IDEAL2019

    • Author(s)
      太田元規.嘉戸裕美子,坂本盛宇,細田和男,山口敦子,畠中秀樹,小池亮太郎,廣明秀一,福地佐斗志
    • Organizer
      トーゴーの日シンポジウム2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Structural pattern that would be recognized by GroE2019

    • Author(s)
      Motonori Ota
    • Organizer
      Patterns in protein sequence and structure (reloaded)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A database of intrincially disordered proteins: IDEAL2019

    • Author(s)
      Motonori Ota
    • Organizer
      Elixir IDP user community meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] π-π相互作用と相分離現象2019

    • Author(s)
      葉山雄揮,太田元規
    • Organizer
      第2回LLPS研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 液滴を作るタンパク質に見られる天然変性タンパク質2019

    • Author(s)
      太田元規.福地佐斗志
    • Organizer
      大阪大学蛋白研セミナー(第3回LLPS研究会)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Description of structural changes by Motion Tree2019

    • Author(s)
      Ryotaro Koike, Kei Moritsugu, Motonori Ota
    • Organizer
      63rd Annual Meeting of the Biophysical Society
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] リン酸化部位を含む天然変性領域2018

    • Author(s)
      小池亮太郎,天野睦紀,貝淵弘三,太田元規
    • Organizer
      第18回日本蛋白質科学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] リン酸化によって誘起されるイベントのRDF記述フォーマット2018

    • Author(s)
      嘉戸裕美子,細田和男,坂本盛宇,小池亮太郎,福地佐斗志,太田元規
    • Organizer
      第18回日本蛋白質科学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 類縁タンパク質立体構造中の二次構造スワップの解析2018

    • Author(s)
      柴田哲郎,南慎太朗,小池亮太郎,太田元規
    • Organizer
      第18回日本蛋白質科学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] A database of intrinsically disordered protein: IDEAL (and its application to Protean segments)2018

    • Author(s)
      Motonori Ota
    • Organizer
      17th European Conference on Computational Biology Pre-meeting "Intrinsically disordered proteins: advances and state-of-the-art of the field"
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Property of intrinsically disordered "hub" proteins2018

    • Author(s)
      Motonori Ota
    • Organizer
      4th Symposium on non-globular proteins
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 天然変性タンパク質データベース:IDEAL2018

    • Author(s)
      太田元規,嘉戸裕美子,坂本盛宇,細田和男,小池亮太郎,廣明秀一,福地佐斗志
    • Organizer
      トーゴーの日シンポジウム2018
    • Related Report
      2018 Annual Research Report
  • [Book] 天然変性タンパク質の機能部位:理解の変容と進展(月刊細胞710号)2021

    • Author(s)
      福地佐斗志,太田元規
    • Total Pages
      78
    • Publisher
      ニューサイエンス社
    • Related Report
      2021 Annual Research Report
  • [Book] ドロプレット形成のデータベースと予測(相分離生物学の全貌 白木賢太郎編)2020

    • Author(s)
      太田元規,福地佐斗志
    • Total Pages
      402
    • Publisher
      東京化学同人
    • Related Report
      2020 Annual Research Report

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Published: 2018-04-23   Modified: 2022-12-28  

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