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Ubiquitin structural biology providing the molecular basis for chemo-technologies

Planned Research

Project AreaNew frontier for ubiquitin biology driven by chemo-technologies
Project/Area Number 18H05501
Research Category

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

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionKyoto University (2020-2022)
The University of Tokyo (2018-2019)

Principal Investigator

Fukai Shuya  京都大学, 理学研究科, 教授 (10361792)

Project Period (FY) 2018-06-29 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥87,620,000 (Direct Cost: ¥67,400,000、Indirect Cost: ¥20,220,000)
Fiscal Year 2022: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2021: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2020: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2019: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2018: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
Keywords構造生物学 / 分子間相互作用 / ユビキチン / シグナル伝達 / タンパク質工学 / ケミカルバイオロジー / X線結晶構造解析 / キメラ化合物
Outline of Final Research Achievements

The ubiquitin modification, which was originally identified as a signal for protein degradation, is now known to play an essential role in the regulation of diverse cellular functions. Ubiquitin chains formed by covalently linking ubiquitin molecules are closely associated with the diversity of functions. Research aimed at understanding the molecular mechanisms of attachment, recognition, and removal of ubiquitin chains and artificially controlling cellular functions could contribute to therapeutic development for various diseases. In this study, we determined the three-dimensional structures of protein complexes associated with the ubiquitin chain modification to deepen the understanding of novel ubiquitin chain recognition mechanisms and molecular mechanisms involving ubiquitin chains. Furthermore, based on the obtained structural information, we attempted to design compounds that could control the function.

Academic Significance and Societal Importance of the Research Achievements

ユビキチン鎖と結合タンパク質の複合体(Npl4-K48鎖やTab2-K6鎖など)の立体構造解析によって新たなユビキチン鎖認識機構を明らかにした。また、ユビキチンリガーゼLUBACの触媒サブユニットHOIPの阻害剤HOIPINやUSPファミリーの脱ユビキチン化酵素を阻害する化合物Subquinocinといったユビキチン鎖が関与するタンパク質に結合する化合物の作用メカニズムを立体構造に基づいて理解し、共同研究も含めて原子・分子レベルから細胞・個体レベルまでの解析通じて免疫疾患に対する新たな治療法の可能性を示した。

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (14 results)

All 2023 2022 2021 2020 2019 2018 Other

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Open Access: 6 results) Presentation (5 results) (of which Int'l Joint Research: 2 results,  Invited: 5 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Journal Article] Structural basis for specific recognition of K6-linked polyubiquitin chains by the TAB2 NZF domain2021

    • Author(s)
      Li Yanjun、Okatsu Kei、Fukai Shuya、Sato Yusuke
    • Journal Title

      Biophysical Journal

      Volume: 120 Issue: 16 Pages: 3355-3362

    • DOI

      10.1016/j.bpj.2021.06.037

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Human DUB Protein Array for Clarification of Linkage Specificity of Polyubiquitin Chain and Application to Evaluation of Its Inhibitors. Biomedicines.2020

    • Author(s)
      Takahashi H, Yamanaka S, Kuwada S, Higaki K, Kido K, Sato Y, Fukai S, Tokunaga F, Sawasaki T.
    • Journal Title

      Biomedicines

      Volume: 4 Pages: 152-152

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Subquinocin, a small molecule inhibitor of CYLD and USP-family deubiquitinating enzymes, promotes NF-κB signaling2020

    • Author(s)
      Yamanaka Satoshi、Sato Yusuke、Oikawa Daisuke、Goto Eiji、Fukai Shuya、Tokunaga Fuminori、Takahashi Hirotaka、Sawasaki Tatsuya
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 524 Issue: 1 Pages: 1-7

    • DOI

      10.1016/j.bbrc.2019.12.049

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses.2020

    • Author(s)
      Oikawa D, Sato Y, Ohtake F, Komakura K, Hanada K, Sugawara K, Terawaki S, Mizukami Y, Phuong HT, Iio K, Obika S, Fukushi M, Irie T, Tsuruta D, Sakamoto S, Tanaka K, Saeki Y, Fukai S, Tokunaga F.
    • Journal Title

      Commun. Biol.

      Volume: 3 Issue: 1 Pages: 163-163

    • DOI

      10.1038/s42003-020-0882-8

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural insights into ubiquitin recognition and Ufd1 interaction of Npl42019

    • Author(s)
      Sato Yusuke、Tsuchiya Hikaru、Yamagata Atsushi、Okatsu Kei、Tanaka Keiji、Saeki Yasushi、Fukai Shuya
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1 Pages: 5708-5708

    • DOI

      10.1038/s41467-019-13697-y

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein2019

    • Author(s)
      Takahashi Tomio S、Sato Yusuke、Yamagata Atsushi、Goto-Ito Sakurako、Saijo Masafumi、Fukai Shuya
    • Journal Title

      Nucleic Acids Research

      Volume: 47 Issue: 7 Pages: 3784-3794

    • DOI

      10.1093/nar/gkz081

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural insights into ubiquitin phosphorylation by PINK12018

    • Author(s)
      Okatsu Kei、Sato Yusuke、Yamano Koji、Matsuda Noriyuki、Negishi Lumi、Takahashi Akiko、Yamagata Atsushi、Goto-Ito Sakurako、Mishima Masaki、Ito Yutaka、Oka Toshihiko、Tanaka Keiji、Fukai Shuya
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 10382-10382

    • DOI

      10.1038/s41598-018-28656-8

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 特定のユビキチン鎖を選択的に切断する脱ユビキチン化酵素の作動機構2022

    • Author(s)
      深井 周也
    • Organizer
      第27回日本病態プロテアーゼ学会学術集会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Structure-guided design of peptide derivatives that inhibit the Ufd1-Npl4 cofactor complex of p972022

    • Author(s)
      Shuya Fukai
    • Organizer
      The International Symposium in Tokyo 2022 Ubiquitin New Frontier “from Neo-Biology to Targeted Protein Degradation”
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ユビキチンコードの理解と制御のための構造生物学2021

    • Author(s)
      深井 周也
    • Organizer
      第94回 日本生化学会大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Structural and functional studies on factors associated with the ubiquitin-proteasome system2021

    • Author(s)
      Shuya Fukai
    • Organizer
      Pacifichem2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ユビキチンリガーゼRNF168によるK63結合型ユビキチン鎖の認識メカニズム2018

    • Author(s)
      深井 周也
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Remarks] 不要なタンパク質が分解を受ける前に解きほぐされる仕組み

    • URL

      https://www.u-tokyo.ac.jp/focus/ja/press/z0207_00021.html

    • Related Report
      2019 Annual Research Report
  • [Patent(Industrial Property Rights)] ユビキチンに対する人工抗体2023

    • Inventor(s)
      佐伯泰、他7名
    • Industrial Property Rights Holder
      佐伯泰、他7名
    • Industrial Property Rights Type
      特許
    • Filing Date
      2023
    • Related Report
      2022 Annual Research Report
    • Overseas

URL: 

Published: 2018-07-20   Modified: 2024-01-30  

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