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Understanding the folding intermediate recognition mechanism by PDI

Research Project

Project/Area Number 17K15098
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionTohoku University

Principal Investigator

OKUMURA MASAKI  東北大学, 学際科学フロンティア研究所, 助教 (50635810)

Research Collaborator Inaba Kenji  
Project Period (FY) 2017-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Keywords小胞体 / フォールディング中間体 / 高速AFM / NMR / PDI / ジスルフィド結合 / PDIファミリー / 前駆体蛋白質 / 酸化的フォールディング / oxidative folding / folding intermediate / プロウログアニリン / 分子認識
Outline of Final Research Achievements

We directly observed the action of protein disulfide isomerase (PDI), the most versatile disulfide-introducing enzyme in the endoplasmic reticulum, during the catalysis of oxidative protein folding. High-speed AFM revealed that oxidized PDI is in rapid equilibrium between open and closed conformations, whereas reduced PDI is maintained in the closed state. In the presence of unfolded substrates, oxidized PDI, but not reduced PDI, assembles to form a face-to-face dimer, creating a central hydrophobic cavity with multiple redox-active sites. Such PDI dimers are diverse in shape and have different lifetimes depending on
substrates. We thus revealed the molecular mechanism by which PDI guides oxidative protein folding of various substrates.

Academic Significance and Societal Importance of the Research Achievements

パーキンソン病やアルツハイマー病など種々の神経変性疾患は体内で構造異常たんぱく質が過剰に蓄積することで引き起こされることが知られる。これまでにPDIの変異や機能欠損を引き起こす化学修飾が、さまざまな神経変性疾患の患者から見つかっている。今回新たにPDIの動的性質や二量体形成が、サイズやジスルフィド結合の数が異なるさまざまな基質のフォールディング状態を認識する上で、重要な役割を果たすことを明らかにした。本基礎的知見の獲得は、生体内における高効率・高精度なフォールディング促進機構の新たな解明につながり、神経変性疾患や2型糖尿病などのフォールディング病に関する有用な情報を提供するものと期待される。

Report

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

    (24 results)

All 2019 2018 2017

All Journal Article (9 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 9 results,  Open Access: 5 results) Presentation (9 results) (of which Int'l Joint Research: 2 results,  Invited: 8 results) Book (5 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding2019

    • Author(s)
      Okumura Masaki、Noi Kentaro、Kanemura Shingo、Kinoshita Misaki、Saio Tomohide、Inoue Yuichi、Hikima Takaaki、Akiyama Shuji、Ogura Teru、Inaba Kenji
    • Journal Title

      Nature Chemical Biology

      Volume: 15 Issue: 5 Pages: 499-509

    • DOI

      10.1038/s41589-019-0268-8

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Protein Disulfide Isomerase family: from Proteostasis to Pathogenesis2019

    • Author(s)
      Matsusaki M.#, Kanemura S.#, Kinoshita M.#, Lee Y.H., Inaba K.*, and Okumura M.* (#equal contribution *corresponding authors)
    • Journal Title

      Biochim Biophys Acta-general subjects

      Volume: in press Issue: 2 Pages: 30080-30087

    • DOI

      10.1016/j.bbagen.2019.04.003

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Coupling effects of thiol and urea-type groups for promotion of oxidative protein folding2019

    • Author(s)
      Shunsuke Okada, Motonori Matsusaki, Kenta AraiK , Yuji Hidaka, Kenji Inaba, Masaki Okumura, Takahiro Muraoka
    • Journal Title

      Chemical Communications

      Volume: 55(6) Issue: 6 Pages: 759-762

    • DOI

      10.1039/c8cc08657e

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ero1-mediated reoxidation of PDI accelerates the folding of cone-snail toxins2018

    • Author(s)
      O'Brien H., Kanemura S., Okumura M., Baskin P., Bandyopadhyay P., Ellgaard L., Inaba K., and Safavi-Hemami H.*
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 11 Issue: 11 Pages: 3418-3418

    • DOI

      10.3390/ijms19113418

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Energy landscape of polymorphic amyloid generation of β2-microglobulin revealed by calorimetry.2018

    • Author(s)
      Kinoshita M., Lin Y., Itoh D., Okumura M., Markova N., Ladbury J.E., Sterpone F., and Lee Y.H.*
    • Journal Title

      Chem Commun (Camb).

      Volume: 57 Issue: 57 Pages: 7995-7998

    • DOI

      10.1039/c8cc02718h

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Impact of membrane curvature on amyloid aggregation2018

    • Author(s)
      Terakawa Mayu S.、Lin Yuxi、Kinoshita Misaki、Kanemura Shingo、Itoh Dai、Sugiki Toshihiko、Okumura Masaki、Ramamoorthy Ayyalusamy、Lee Young-Ho
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Biomembranes

      Volume: - Issue: 9 Pages: 30130-30135

    • DOI

      10.1016/j.bbamem.2018.04.012

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Characterization and optimization of two-chain folding pathways of insulin via native chain assembly2018

    • Author(s)
      Arai Kenta、Takei Toshiki、Shinozaki Reina、Noguchi Masato、Fujisawa Shouta、Katayama Hidekazu、Moroder Luis、Ando Setsuko、Okumura Masaki、Inaba Kenji、Hojo Hironobu、Iwaoka Michio
    • Journal Title

      Communications Chemistry

      Volume: 1 Issue: 1 Pages: 26-26

    • DOI

      10.1038/s42004-018-0024-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Preparation of Selenoinsulin as a Long-Lasting Insulin Analogue2017

    • Author(s)
      Kenta Arai+, Toshiki Takei+, Masaki Okumura+, Satoshi Watanabe+, Yuta Amagai, Yuya Asahina, Luis Moroder, Hironobu Hojo, Kenji Inaba, and Michio Iwaoka
    • Journal Title

      Angew. Chem. Int. Ed.

      Volume: 印刷中 Issue: 20 Pages: 5522-5526

    • DOI

      10.1002/anie.201701654

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Highly Dynamic Nature of ERdj5 Is Key to Efficient Elimination of Aberrant Protein Oligomers through ER-Associated Degradation.2017

    • Author(s)
      Maegawa KI, Watanabe S#, Noi K#, Okumura M#, Amagai Y#, Inoue M, Ushioda R, Nagata K, Ogura T, Inaba K.(#equal contribution)
    • Journal Title

      Structure

      Volume: 25 Issue: 6 Pages: 846-857

    • DOI

      10.1016/j.str.2017.04.001

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Understanding the proteostasis mechanism in the endoplasmic reticulum2019

    • Author(s)
      M. Okumura
    • Organizer
      358th IMEG Seminar, Kumamoto Univ.
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 小胞体内局在酵素Protein Disulfide Isomerase familyによるタンパク質品質管理機構の理解2018

    • Author(s)
      奥村 正樹
    • Organizer
      北海道大学薬学部
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Understanding the proteotasis mechanism in the Endoplasmic Reticulum2018

    • Author(s)
      M. Okumura
    • Organizer
      KBSI seminar
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 酵素の構造ダイナミクスから紐解く基質認識の理解―Protein Disulfide Isomeraseを事例として2018

    • Author(s)
      奥村 正樹
    • Organizer
      第18回日本蛋白質科学会年会、ランチョンセミナ-
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Dynamic assembly and disassembly of protein disulfide isomerase in catalysis of oxidative protein folding2018

    • Author(s)
      M. Okumura
    • Organizer
      333th IMEG Seminar, Kumamoto Univ.
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Dynamic assembly and disassembly of Protein Disulfide Isomerase during guiding proper oxidative protein folding2018

    • Author(s)
      Masaki Okumura, Kentaro Noi, Shingo Kanemura, Shuji Akiyama,Teu Ogura, and Kenji Inaba
    • Organizer
      CLS, Tokyo Tech. International Forum 2018 Redox regulation of protein functions,transcription, translation and folding
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] How do PDI family member proteins act on nascent chains to catalyze their oxidative protein folding?2017

    • Author(s)
      奥村 正樹、平山 千尋、野井 健太郎、町田 幸大、今高 寛晃、小椋 光、稲葉 謙次
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Dynamic assembly/disassembly of Protein Disulfide Isomerase during the catalysis of oxidative protein folding2017

    • Author(s)
      奥村 正樹、野井 健太郎、金村 進吾、引間 孝明、秋山 修志、小椋 光、稲葉 謙次
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 高速原子間力顕微鏡が明らかにした基質に働きかけるProtein Disulfide Isomerase酵素の1分子動態2017

    • Author(s)
      奥村 正樹
    • Organizer
      最先端光計測とライフサイエンスの近未来 -Bio. Phys. Chem.三重点の探索-
    • Related Report
      2017 Research-status Report
    • Invited
  • [Book] 放射光利用の手引きー農水産・医療、エネルギー、環境、材料開発分野などへの応用ー細胞のタンパク質2019

    • Author(s)
      奥村正樹、稲葉謙次
    • Total Pages
      5
    • Publisher
      アグネ技術センター
    • Related Report
      2018 Annual Research Report
  • [Book] Oxidatve Folding of Peptides and Proteins 2nd Edition2018

    • Author(s)
      Okumura, M., Watanabe, S., Inaba, K.
    • Total Pages
      25
    • Publisher
      Royal Society of Chemistry
    • Related Report
      2018 Annual Research Report
  • [Book] アルツハイマー病ー発症メカニズムと新規診断法・創薬・治療開発2018

    • Author(s)
      奥村正樹、稲葉謙次
    • Total Pages
      5
    • Publisher
      NTS
    • Related Report
      2018 Annual Research Report
  • [Book] Structural insights into disulfide bond formation and protein quality control in the mammalian endoplasmic reticulum2018

    • Author(s)
      M. Okumura, S. Watanabe, and K. Inaba
    • Publisher
      Royal Society of Chemistry
    • Related Report
      2017 Research-status Report
  • [Book] X線小角散乱解析が明らかにしたPDIファミリータンパク質ERp46及びPDI酸化酵素Ero1αの構造ダイナミクスと機能2017

    • Author(s)
      金村 進吾、奥村 正樹、稲葉 謙次
    • Total Pages
      3
    • Publisher
      分子研レターズ
    • Related Report
      2017 Research-status Report
  • [Patent(Industrial Property Rights)] タンパク質のリフォールディング剤、タンパク質のリフォールディング方法及びタンパク質の再生方法2018

    • Inventor(s)
      奥村 正樹、村岡 貴博、岡田 隼輔、稲葉 謙次、松﨑 元紀
    • Industrial Property Rights Holder
      奥村 正樹、村岡 貴博、岡田 隼輔、稲葉 謙次、松﨑 元紀
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2018-109769
    • Filing Date
      2018
    • Related Report
      2018 Annual Research Report

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Published: 2017-04-28   Modified: 2020-03-30  

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