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Understanding the protein homeostasis mechanism by P5, a member of the PDI family

Research Project

Project/Area Number 19K06520
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
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)

Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2021: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000)
Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2019: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywordsタンパク質品質管理 / ジスルフィド結合 / X線小角散乱法 / 小胞体 / NMR / 二量体化モチーフ / 酸化的フォールディング / PDI family / P5 / シャペロン / SAXS / PDI / IRE1 / oxidative folding / 溶液散乱
Outline of Research at the Start

細胞内小器官の一つ小胞体には、厳正な蛋白質品質管理システムが存在する。近年、不良蛋白質の蓄積により誘導される小胞体ストレス応答因子の1つであるIRE1の機能制御に、PDIファミリー酵素の1つであるP5が関わっていることが報告された。しかしながら、P5は構造未知であり、機能的解析も十分に進んでいないため、同酵素による「フォールディング補助」および「小胞体ストレス応答因子の制御」の分子機構は未解明である。そこで本申請は、特に同酵素の酸化的フォールディング促進活性・シャペロン活性・小胞体ストレス応答因子の調節機構の詳細を構造生物学的、細胞生物学的手法により解明する。

Outline of Final Research Achievements

P5 is a PDI family member involved in the ER quality control. We discovered that P5 dimerizes via a unique adhesive motif contained in the N-terminal thioredoxin-like domain by SAXS and crystallographic anaylyses. A monomeric P5 mutant with the impaired adhesive motif showed structural instability and local unfolding. Disassembly of P5 to monomers compromised its ability to inactivate IRE1, one of ER stress sensor, via intermolecular disulfide bond reduction. Thus, the leucine-valine adhesive motif supports structure and function of P5. Furthermore, the enzymatic activity of P5-mediated oxidative folding is up-regulated by PDI, while the chaperone activity of P5 is stimulated by ERp72. Thus, we established molecular and mechanistic basis of P5-dependent protein quality control system in the endoplasmic reticulum.

Academic Significance and Societal Importance of the Research Achievements

細胞内の小胞体には新生タンパク質に、構造を安定化するためにジスルフィド結合を導入する仕組みが存在する。このジスルフィド結合の触媒を担っているのがPDIファミリー酵素である。特にPDIファミリー酵素のひとつP5は、癌などの疾患や小胞体ストレス応答、血液凝固といった様々な生理機能と関わることが報告されていたが、全体構造が不明なため詳しいメカニズムは不明であった。本課題では全長P5がユニークな構造モチーフを介して二量体構造をとることを明らかにし本モチーフが本酵素の機能発現にとって重要であることを提示した。従って本酵素の構造機能相関研究に基づき、本成果は医学的にも重要な知見をもたらす。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (53 results)

All 2022 2021 2020 2019 Other

All Int'l Joint Research (5 results) Journal Article (17 results) (of which Int'l Joint Research: 10 results,  Peer Reviewed: 17 results,  Open Access: 15 results) Presentation (25 results) (of which Int'l Joint Research: 7 results,  Invited: 17 results) Book (5 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] 韓国基礎科学研究所(韓国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of Glasgow(英国)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] KBSI(韓国)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] KBSI(韓国)

    • Related Report
      2019 Research-status Report
  • [Int'l Joint Research] University of Glasgow(英国)

    • Related Report
      2019 Research-status Report
  • [Journal Article] A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization2021

    • Author(s)
      Okumura M, Kanemura S., Matsusaki M., Kinoshita M., Saio T., Ito D., Hirayama C., Kumeta H., Watabe M., Amagai Y., Lee Y. H., Akiyama S. and Inaba K.
    • Journal Title

      Structure

      Volume: 29 Issue: 12 Pages: 1-14

    • DOI

      10.1016/j.str.2021.03.016

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Functional Interplay between P5 and PDI/ERp72 to Drive Protein Folding.2021

    • Author(s)
      Matsusaki M, Okada R, Tanikawa Y, Kanemura S, Ito D, Lin Y, Watabe M, Yamaguchi H, Saio T, Lee YH, Inaba K, and *Okumura M.
    • Journal Title

      Biology

      Volume: 10 Issue: 11 Pages: 1112-1112

    • DOI

      10.3390/biology10111112

    • NAID

      120007168792

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Ca2+ Regulates ERp57-Calnexin Complex Formation.2021

    • Author(s)
      Tanikawa Y,# Kanemura S,# Ito D, Lin Y, Matsusaki M, Kuroki K, Yamaguchi H, Maenaka K, Lee YH, Inaba K, and *Okumura M.
    • Journal Title

      Molecules

      Volume: 26 Issue: 10 Pages: 2853-2853

    • DOI

      10.3390/molecules26102853

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding2021

    • Author(s)
      Okada Shunsuke、Matsusaki Motonori、Okumura Masaki、Muraoka Takahiro
    • Journal Title

      Molecules

      Volume: 26 Issue: 4 Pages: 879-879

    • DOI

      10.3390/molecules26040879

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of nascent-chain disulfide bond formation2021

    • Author(s)
      Hirayama, C., Machida, K., Noi, K., Murakawa, T., Okumura, M., Ogura, T., Imataka, H., and Inaba, K.*
    • Journal Title

      iScience

      Volume: 4 Issue: 4 Pages: 102296-102296

    • DOI

      10.1016/j.isci.2021.102296

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization2021

    • Author(s)
      Okumura, M.,* Kanemura, S.,# Matsusaki, M., # Kinoshita, M., # Saio, T., Ito, D., Hirayama, C., Kumeta, H., Watabe, M., Amagai, Y., Lee, Y.H., Akiyama, S., and Inaba, K.*
    • Journal Title

      Structure

      Volume: in press

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Distinct roles and actions of protein disulfide isomerase family enzymes in catalysis of co-translational disulfide bond formation2021

    • Author(s)
      Hirayama, C., Machida, K., Noi, K., Murakawa, T., Okumura, M., Ogura, T., Imataka, H., and Inaba, K*.
    • Journal Title

      iScience

      Volume: 4 Pages: 102296-102296

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding2021

    • Author(s)
      Okada, S., Matsusaki, M., Okumura, M.,* and Muraoka, T.*
    • Journal Title

      molecules

      Volume: 26 Pages: 879-879

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding2021

    • Author(s)
      Okumura M, Noi K, and Inaba K*
    • Journal Title

      Current Opinion in Structural Biology

      Volume: 66 Pages: 49-57

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Visualization of structural dynamics of protein disulfide isomerase enzymes in catalysis of oxidative folding and reductive unfolding2020

    • Author(s)
      Okumura, M., Noi, K. and Inaba, K.*
    • Journal Title

      Curr. Opin. Struct. Biol.

      Volume: 66 Pages: 49-57

    • DOI

      10.1016/j.sbi.2020.10.004

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] PDI Family Members as Guides for Client Folding and Assembly2020

    • Author(s)
      Kanemura, S, Matsusaki, M, Inaba, K, and Okumura, M.*
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 21

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Antipsychotic olanzapine-induced misfolding of proinsulin in the ER accounts for atypical development of diabetes2020

    • Author(s)
      Ninagawa S*, Tada S,# Okumura M,# Inoguchi K,# Kinoshita M, Kanemura S, Imami K, Umezawa H, Ishikawa T, Okada T, Mackin R, Torii S, Ishihama Y, Inaba K, Anazawa T, Nagamine T, Mori K*
    • Journal Title

      eLife

      Volume: 9

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Biochemical characterization of ER-resident peroxidases, GPx7 and GPx8, reveals their different and regulated oxidative activities2020

    • Author(s)
      Kanemura S., Sofia E., Hirai N., Okumura M., Kadokura H., and Inaba K.*
    • Journal Title

      JOURNAL OF BIOLOGICAL CHEMISTRY

      Volume: 295 Pages: 12772-12785

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Solution NMR for investigation of liquid-liquid phase separation2020

    • Author(s)
      Saio T*, Okumura M, Lee Y.H*
    • Journal Title

      JKMRS

      Volume: 24 Pages: 47-52

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40)2019

    • Author(s)
      Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH
    • Journal Title

      ACS nano

      Volume: 27 Issue: 8 Pages: 8766-8783

    • DOI

      10.1021/acsnano.9b01578

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [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
      2019 Research-status 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
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Understanding the proteostasis network in the endoplasmic reticulum2022

    • Author(s)
      Masaki Okumura
    • Organizer
      Korea-Japan Joint Workshop on Biofunctional Chemistry
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] PDI familyの動的な会合による小胞体内タンパク質品質管理の理解2021

    • Author(s)
      奥村正樹
    • Organizer
      分子生物学会 WS
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 小胞体内で液滴を形成する因子の生理学的機能の理解2021

    • Author(s)
      奥村正樹
    • Organizer
      第5回LLPS研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 小胞体内酸化的フォールディングの触媒システムの理解2021

    • Author(s)
      奥村正樹
    • Organizer
      第21回 日本蛋白質科学会 年会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] プロテインジスルフィドイソメラーゼ群による基質触媒機構の解明2021

    • Author(s)
      奥村正樹
    • Organizer
      天野財団第22回酵素応用シンポジウム研究奨励賞受賞講演
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 液液相分離する小胞体内シャペロンの発見、機能、制御機構2020

    • Author(s)
      奥村 正樹
    • Organizer
      生化学会 年会 web セミナー
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 小胞体内ジスルフィド結合触媒ネットワークとインスリンフォールディングの品質管理2020

    • Author(s)
      奥村正樹、稲葉謙次
    • Organizer
      分子生物学会webフォーラム
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] Direct observation of actions of Protein Disulfide Isomerase in the catalysis of oxidative folding2020

    • Author(s)
      Masaki Okumura
    • Organizer
      KBSI seminar
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] PDIファミリーのシャペロン機能の新展開2019

    • Author(s)
      奥村正樹
    • Organizer
      第3回 タンパク質可塑性についての研究会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] PDIファミリーメンバーP5の新規構造と機能2019

    • Author(s)
      奥村正樹, 金村進吾, 松崎元紀, 木下岬, 荒井堅太, 平山千尋, 天貝佑太, 門倉広, 秋山修志, 稲葉謙次
    • Organizer
      第42回分子生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] PDIファミリー酵素によるヒト由来ガレクチンの構造機能制御機構の解明2019

    • Author(s)
      金村進吾, 黒井邦巧, 松崎元紀, 山口宏, 中林孝和, 稲葉謙次, 奥村正樹
    • Organizer
      第42回分子生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 小胞体内タンパク質の品質管理のフロンティア~温故知新~2019

    • Author(s)
      奥村正樹
    • Organizer
      関西学院大学理工学部講演会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] 小胞体内のタンパク質品質管理機構の解明2019

    • Author(s)
      奥村正樹
    • Organizer
      次世代研究者シンポジウム2019、名古屋大学
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Coupling effects of thiol and urea-type groups for promotion of oxidative folding2019

    • Author(s)
      Motonori Matsusaki, Shunsuke Okada, Kenji Inaba, Takahiro Muraoka, Masaki Okumura
    • Organizer
      International symposium on unfolded proteins, protein folding, and disease-causing aggregation, Korea
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Structural insights into the protein homeostasis mechanism in the endoplasmic reticulum2019

    • Author(s)
      Masaki Okumura
    • Organizer
      International symposium on unfolded proteins, protein folding, and disease-causing aggregation, Korea
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 新規レドックス分子のデザイン法確立と酸化的フォールディングへの応用2019

    • Author(s)
      松崎元紀, 岡田隼輔, 荒井堅太, 日高雄二, 稲葉謙次, 村岡貴博, 奥村正樹
    • Organizer
      第92回生化学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] PDIファミリーによるβ2-microglubulinの品質管理機構の解明2019

    • Author(s)
      木下岬, 金村進吾, 松崎元紀, 李映昊, 稲葉謙次, 奥村正樹
    • Organizer
      第92回生化学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] PDI family酵素によるヒト由来ガレクチンの機能制御機構の解明2019

    • Author(s)
      金村進吾, 黒井邦巧, 松崎元紀, 山口宏, 中林孝和, 稲葉謙次, 奥村正樹
    • Organizer
      第92回生化学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] PDIファミリーが触媒する前駆体タンパク質の酸化的フォールディング機構の解明2019

    • Author(s)
      増田光紀, 金村進吾, 木下岬, 山口宏, 日高雄二, 稲葉謙次, 奥村正樹
    • Organizer
      第92回生化学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] Understanding the mechanism by PDI family control proteostasis2019

    • Author(s)
      奥村正樹、稲葉謙次
    • Organizer
      第92回生化学会年会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Structures and functions of PDI family members involved in proteostasis2019

    • Author(s)
      Masaki Okumura
    • Organizer
      University of Glasgow, UK
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] PDIファミリーによる小胞体内品質管理機構の最前線2019

    • Author(s)
      奥村正樹
    • Organizer
      成蹊大学セミナー
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] 「可塑性」の学際的接点2019

    • Author(s)
      奥村正樹
    • Organizer
      第1回 タンパク質可塑性についての研究会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Newly developedthiol-disulfide exchange agent,guanidino-thiol2019

    • Author(s)
      Motonori Matsusaki, Shunsuke Okada, Kenta Arai, Yuji Hidaka, Kenji Inaba, Takahiro Muraoka, Masaki Okumura
    • Organizer
      14th ER redox club meeting, Herrsching am Ammersee, Germany
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Dynamic assembly/disassembly of Protein Disulfide Isomerase during the catalysis of oxidative protein folding2019

    • Author(s)
      Masaki Okumura, Kentaro Noi, Shingo Kanemura, Misaki Kinoshita, Tomohide Saio, Yuichi Inoue, Takaaki Hikima, Shuji Akiyama, Teru Ogura, Kenji Inaba
    • Organizer
      14th ER redox club meeting, Herrsching am Ammersee, Germany
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Book] 小胞体におけるMHCの品質管理2020

    • Author(s)
      金村 進吾、松崎 元紀、 前仲 勝実、 稲葉 謙次、 奥村 正樹
    • Total Pages
      8
    • Publisher
      臨床免疫・アレルギー科
    • Related Report
      2020 Research-status Report
  • [Book] 高速原子間力顕微鏡により明らかにされたプロテインジスルフィドイソメラーゼ(PDI)の構造ダイナミクス2020

    • Author(s)
      奥村 正樹、稲葉 謙次
    • Total Pages
      6
    • Publisher
      生化学会誌みにれびゅう
    • Related Report
      2020 Research-status Report
  • [Book] 生化学2020

    • Author(s)
      奥村正樹、稲葉謙次
    • Total Pages
      6
    • Publisher
      生化学会
    • Related Report
      2019 Research-status Report
  • [Book] 月間「細胞」構造生物学の最前線2019

    • Author(s)
      奥村正樹、稲葉謙次
    • Total Pages
      6
    • Publisher
      北隆館
    • Related Report
      2019 Research-status Report
  • [Book] 月刊「細胞」エレクトロンバイオダイナミクスが支える生命の生存戦略2019

    • Author(s)
      奥村正樹、稲葉謙次
    • Total Pages
      6
    • Publisher
      北隆館
    • Related Report
      2019 Research-status Report
  • [Patent(Industrial Property Rights)] 液滴及びその製造方法2020

    • Inventor(s)
      奥村 正樹、松﨑 元紀、金村 進吾、齋尾 智英、稲葉 謙次
    • Industrial Property Rights Holder
      奥村 正樹、松﨑 元紀、金村 進吾、齋尾 智英、稲葉 謙次
    • Industrial Property Rights Type
      特許
    • Filing Date
      2020
    • Related Report
      2020 Research-status Report

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Published: 2019-04-18   Modified: 2023-01-30  

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