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Elucidation of the mechanism of kinetically controlled reaction fields in cells

Planned Research

Project AreaKinetics-Driven Supramolecular Chemistry
Project/Area Number 21H05095
Research Category

Grant-in-Aid for Transformative Research Areas (B)

Allocation TypeSingle-year Grants
Review Section Transformative Research Areas, Section (II)
Research InstitutionTohoku University

Principal Investigator

Okumura Masaki  東北大学, 学際科学フロンティア研究所, 准教授 (50635810)

Project Period (FY) 2021-08-23 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥40,950,000 (Direct Cost: ¥31,500,000、Indirect Cost: ¥9,450,000)
Fiscal Year 2023: ¥11,830,000 (Direct Cost: ¥9,100,000、Indirect Cost: ¥2,730,000)
Fiscal Year 2022: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
Fiscal Year 2021: ¥18,200,000 (Direct Cost: ¥14,000,000、Indirect Cost: ¥4,200,000)
Keywords反応遅延制御 / LLPS / 酸化的フォールディング / 活性亢進剤 / フォールディング / potein assembly / レドックス反応場 / 小胞体 / protein assembly
Outline of Research at the Start

蛋白質の四次構造形成は、生体における非対称分子集合化反応である。この形成プロセス反応は、生物学において未解明である。試験管内、ポリペプチド鎖とシャペロンなど補助因子間での反応では、四次構造形成効率は大幅に低下する。つまりこの過程は、従来の概念では理解することができず、その解明には反応の概念を変革する必要がある。四次構造形成の起点は、複数種のポリペプチド鎖の局所濃縮である。本研究代表者は、小胞体内に形成される新たな反応場が基質を選択的に濃縮することを発見した。本研究における四次構造形成過程の詳細な機序解明は、人工環境での四次構造形成を可能にする人工遅延反応場構築の道を切り拓く

Outline of Final Research Achievements

Based on interdisciplinary collaborative research involving biochemistry, structural biology, cell biology, computational science, and organic synthetic chemistry, we discovered a new catalytic reaction field in cell for the kinetic-controlled folding catalysis. Furthermore, we developed de novo redox compounds that control enzyme activity, enabling chemical control of the reaction field to kinetically control protein folding. Taken together, this result paves the way to understanding the paradigm "multi-molecule-to-multi-molecule reaction of enzyme reaction field-substrate".

Academic Significance and Societal Importance of the Research Achievements

本課題ではオルガネラ内での液滴形成と、その内部での酵素反応遅延の発見に至った。遅延反応場としての液滴の新たな生命機能を示す革新的な研究と位置づけられ、シグナル伝達に限らず、様々な細胞内化学反応を制御するメゾスケール反応場として、液滴の概念を飛躍的に拡張する可能性を秘める。その学術的意義は遅延反応場としての液滴が「酵素-基質1対1反応」という従来酵素反応の常識を変革する、新たな「酵素反応場-基質の“多分子-対多分子”反応」と明示される上位概念を創出することが期待できる。本酵素が神経変性疾患やⅡ型糖尿病と関わることが指摘されていることから、新たな治療戦略に繋がる可能性があり、その社会的意義は高い。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (42 results)

All 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (4 results) Journal Article (14 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 13 results,  Open Access: 11 results) Presentation (20 results) (of which Int'l Joint Research: 6 results,  Invited: 20 results) Book (2 results) Remarks (2 results)

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

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] ケース・ウェスタン・リザーブ 大学(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 韓国基礎科学研究所(韓国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 韓国基礎科学研究所(韓国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Enzymatic and synthetic regulation of polypeptide folding2024

    • Author(s)
      Muraoka Takahiro、Okumura Masaki、Saio Tomohide
    • Journal Title

      Chemical Science

      Volume: 15 Issue: 7 Pages: 2282-2299

    • DOI

      10.1039/d3sc05781j

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Client recognition differences between PDI and ERp46 to guide oxidative folding2024

    • Author(s)
      Saio Tomohide、Ishii Kotone、Matsusaki Motonori、Kumeta Hiroyuki、Kanemura Shingo、Okumura Masaki
    • Journal Title

      bioRxiv

      Volume: 2024.03.04 Pages: 583432-583432

    • DOI

      10.1101/2024.03.04.583432

    • Related Report
      2023 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] Diselenide-bond replacement of the external disulfide bond of insulin increases its oligomerization leading to sustained activity2023

    • Author(s)
      Arai Kenta、Okumura Masaki、Lee Young-Ho、Katayama Hidekazu、Mizutani Kenji、Lin Yuxi、Park Sam-Yong、Sawada Kaichiro、Toyoda Masao、Hojo Hironobu、Inaba Kenji、Iwaoka Michio
    • Journal Title

      Communications Chemistry

      Volume: 6 Issue: 1 Pages: 258-258

    • DOI

      10.1038/s42004-023-01056-4

    • URL

      https://pure.teikyo.jp/en/publications/989906e3-9232-4d76-a01a-1831f1e863cd

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Semi-enzymatic acceleration of oxidative protein folding by <i>N</i>-methylated heteroaromatic thiols2023

    • Author(s)
      Okada Shunsuke、Matsumoto Yosuke、Takahashi Rikana、Arai Kenta、Kanemura Shingo、Okumura Masaki、Muraoka Takahiro
    • Journal Title

      Chemical Science

      Volume: 14 Issue: 28 Pages: 7630-7636

    • DOI

      10.1039/d3sc01540h

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dose-response relationship for the resistance of human insulin to degradation by insulin-degrading enzyme2023

    • Author(s)
      Okumura Masaki、Kuramochi Tsubura、Lin Yuxi、Furukawa Ran、Mizutani Kenji、Yokoyama Takeshi、Kim Mingeun、Lim Mi Hee、Yi Hyon-Seung、Arai Kenta、Yamaguchi Hiroshi、Hojo Hironobu、Iwaoka Michio、Tanaka Yoshikazu、Park Sam-Yong、Inaba Kenji、Kanemura Shingo、Lee Young-Ho
    • Journal Title

      bioRxiv

      Volume: 2023.04.08. Pages: 536135-536135

    • DOI

      10.1101/2023.04.08.536135

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Oxidative Protein Folding Promotion by Imidazoyl-conjugated Thiol2023

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

      Chem.Lett.

      Volume: 52 Pages: 202-205

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biophysical elucidation of neural network and chemical regeneration of neural tissue2022

    • Author(s)
      Takahiro Muraoka, Tomohide Saio, Masaki Okumura
    • Journal Title

      Biophysics and Physicobiology

      Volume: 19 Issue: 0 Pages: n/a

    • DOI

      10.2142/biophysico.bppb-v19.0024

    • ISSN
      2189-4779
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cysteine-based protein folding modulators for trapping intermediates and misfolded forms2022

    • Author(s)
      Nishino, H., Kitamura, M., Okada, S., Miyake, R., Okumura, M., and Muraoka, T.*
    • Journal Title

      RSC Advances

      Volume: 12 Pages: 26658-26664

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [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] 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
  • [Presentation] フォールディングとアンフォールディングの自在操作の実現2024

    • Author(s)
      奥村正樹
    • Organizer
      日本化学会第104春季年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 細胞における遅延制御反応場の形成機構と機能発現の探求2024

    • Author(s)
      奥村正樹
    • Organizer
      日本化学会第104春季年会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 小胞体内相分離の理解2023

    • Author(s)
      奥村正樹
    • Organizer
      第23回 日本蛋白質科学会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Discovery of a transient reaction field in the endoplasmic reticulum2023

    • Author(s)
      Masaki Okumura
    • Organizer
      International Cross-disciplinary Symposium
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] フォールディングの酵素学的速度制御2023

    • Author(s)
      奥村正樹
    • Organizer
      第46回分子生物学会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 小胞体局在因子による液滴の内部構造と機能の相関研究2023

    • Author(s)
      奥村正樹
    • Organizer
      大阪大学蛋白質研究所セミナー/第8回LLPS研究会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 各生物学的階層におけるタンパク質品質管理の理解2023

    • Author(s)
      奥村正樹
    • Organizer
      神戸学院大学セミナー 知の創造セミナー 4回目
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Understanding the mechanism by which Protein Disulfide Isomerase (PDI) family guide proper oxidative folding2023

    • Author(s)
      Masaki Okumura
    • Organizer
      Zoominar "Amyloid Symposium"
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 基質触媒におけるPDI酵素群の動的会合体形成の理解2023

    • Author(s)
      奥村正樹
    • Organizer
      日本化学会 第103春季年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 各階層における酸化的フォールディング触媒システムの理解2022

    • Author(s)
      奥村正樹
    • Organizer
      第22回 日本蛋白質科学会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Structural insights into the protein control system mechanism by PDI family, the endoplasmic reticulum-resident chaperone/enzyme2022

    • Author(s)
      Masaki Okumura
    • Organizer
      Protein Folding, Aggregation, Misfolding Disease, and Disease Crosstalk
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protein Disulfide Isomerase family; their molecular actions and functions2022

    • Author(s)
      Masaki Okumura
    • Organizer
      Redox Week in Sendai 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 小胞体内における酸化的フォールディング触媒ネットワークの理解2022

    • Author(s)
      奥村正樹
    • Organizer
      第95回 日本生化学会
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] PDIファミリーのシャペロン機能の理解:プロテオスタスと神経変性疾患2022

    • Author(s)
      奥村正樹
    • Organizer
      第45回 日本分子生物学会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] ホログラフィック顕微鏡を用いた相分離観察例の紹介2022

    • Author(s)
      奥村正樹
    • Organizer
      第45回 日本分子生物学会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [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
  • [Book] 月刊細胞 特集「LC(Low-Complexity)ドメインの生物学」2024

    • Author(s)
      渡部マイ, 金村進吾, 李映昊, 奥村正樹
    • Total Pages
      78
    • Publisher
      北隆館
    • Related Report
      2023 Annual Research Report
  • [Book] 小胞体ジスルフィド結合触媒ネットワークを支える酵素群の構造基盤2022

    • Author(s)
      金村進吾, 稲葉謙次, 奥村正樹
    • Total Pages
      2
    • Publisher
      日本結晶学会誌 64,209-210
    • Related Report
      2022 Annual Research Report
  • [Remarks] 東北大学奥村研

    • URL

      https://web.tohoku.ac.jp/okumura/#

    • Related Report
      2023 Annual Research Report
  • [Remarks] ラボホームページ

    • URL

      https://web.tohoku.ac.jp/okumura/

    • Related Report
      2022 Annual Research Report

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Published: 2021-10-22   Modified: 2025-01-30  

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