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Analysis of dynamic structural changes in a homotetrameric enzyme adapting its functions to environmental changes

Research Project

Project/Area Number 20K06509
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 InstitutionYokohama City University

Principal Investigator

Ikegami Takahisa  横浜市立大学, 生命医科学研究科, 教授 (20283939)

Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2022: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2020: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords解糖系 / GAPDH / アロステリック効果 / ホモ多量体 / NMR / GPADH / 四次構造 / Moon-lighting 蛋白質 / 神経変性疾患 / Moon-lighting蛋白質 / 核磁気共鳴
Outline of Research at the Start

グリセルアルデヒド3リン酸脱水素酵素(GAPDH)は解糖系に必須の酵素であるが、酸化還元状態などの状況に応じて、異なる相手分子と臨機応変に相互作用し種々の異なる機能を発揮することが知られている。申請者は、いつもはホモ四量体であるGAPDHがサブユニット数も含む四次構造を変化させることによって多機能性を発揮しているのではないかと考え、その新たな概念としてのアロステリック効果をNMR, native-MS, AUC などの物理的計測法を用いて解明する。

Outline of Final Research Achievements

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme that plays a crucial role in the glycolytic pathway and forms a homotetrameric structure composed of four identical subunits. GAPDH is known as a moon-lighting protein as it transforms into a protein with different functions from its original glycolytic function when cells age and are exposed to oxidative stress. The mechanism of this transformation was analyzed using NMR, thermal shift assay, and analytical gel filtration. The results suggest that the change in function is due to an alteration in the number of subunits. This was particularly evident when ATP was present in the absence of the coenzyme, NAD.

Academic Significance and Societal Importance of the Research Achievements

GAPDH は生化学的に長らく研究されてきた分子であり、従来よりサブユニット分裂が機能変化に関与する可能性が示唆されてきた。しかし、決定的な証拠はなく、議論の的となっていた。本研究では、分析ゲル濾過による分子レベルの解析とNMRによる原子レベルの解析を組み合わせることで、このサブユニット分裂を原子レベルで実証した。このサブユニット分裂は、老化や酸化ストレスによって引き起こされる。またGAPDH は、アルツハイマー病やパーキンソン病の発症に関わる分子との相互作用も報告されており、重要な役割をもつことが示唆されている。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (19 results)

All 2024 2023 2022 2021 2020

All Journal Article (13 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 13 results,  Open Access: 7 results) Presentation (6 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results)

  • [Journal Article] 1H, 13C and 15N backbone resonance assignments of hepatocyte nuclear factor-1-beta (HNF1β) POUS and POUHD2024

    • Author(s)
      Hokazono Sayaka、Imagawa Eri、Hirano Daishi、Ikegami Takahisa、Oishi Kimihiko、Konuma Tsuyoshi
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 18 Issue: 1 Pages: 59-63

    • DOI

      10.1007/s12104-024-10168-4

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy2024

    • Author(s)
      Imamura Kayo、Akagi Ken-Ichi、Miyanoiri Yohei、Tsujimoto Hirokazu、Hirokawa Takatsugu、Ashida Hideo、Murakami Kaori、Inoue Asuka、Suno Ryoji、Ikegami Takahisa、Sekiyama Naotaka、Iwata So、Kobayashi Takuya、Tochio Hidehito
    • Journal Title

      Structure

      Volume: 32 Issue: 3 Pages: 352-361

    • DOI

      10.1016/j.str.2023.12.008

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Analysis of the homodimeric structure of a D‐Ala‐D‐Ala metallopeptidase, VanX, from vancomycin‐resistant bacteria2024

    • Author(s)
      Konuma Tsuyoshi、Takai Tomoyo、Tsuchiya Chieko、Nishida Masayuki、Hashiba Miyu、Yamada Yudai、Shirai Haruka、Motoda Yoko、Nagadoi Aritaka、Chikaishi Eriko、Akagi Ken‐ichi、Akashi Satoko、Yamazaki Toshio、Akutsu Hideo、Ikegami Takahisa
    • Journal Title

      Protein Science

      Volume: 33 Issue: 6

    • DOI

      10.1002/pro.5002

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biophysical insights into the dimer formation of human Sirtuin 22024

    • Author(s)
      Suzuki Noa、Konuma Tsuyoshi、Ikegami Takahisa、Akashi Satoko
    • Journal Title

      Protein Science

      Volume: 33 Issue: 5

    • DOI

      10.1002/pro.4994

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CPMG pulse sequence for relaxation dispersion that cancels artifacts independently of spin states2023

    • Author(s)
      Konuma Tsuyoshi、Kurita Jun-ichi、Ikegami Takahisa
    • Journal Title

      Journal of Magnetic Resonance

      Volume: 352 Pages: 107489-107489

    • DOI

      10.1016/j.jmr.2023.107489

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain2023

    • Author(s)
      Kikuchi Masaki、Takase Shohei、Konuma Tsuyoshi、Noritsugu Kota、Sekine Saaya、Ikegami Takahisa、Ito Akihiro、Umehara Takashi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 120 Issue: 43

    • DOI

      10.1073/pnas.2304103120

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] ベクトルモデルはどのぐらい信じてよいのか?2023

    • Author(s)
      池上貴久
    • Journal Title

      NMR学会誌

      Volume: 13 Pages: 32-40

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemical conformation of the essential glutamate site of the c-ring within thermophilic bacillus FoF1-ATP synthase determined by solid-state NMR based on its isolated c-ring structure.2022

    • Author(s)
      Todokoro, Y., Kang, S.J., Suzuki, T., Ikegami, T., Kainosho, M., Yoshida, M., Fujiwara, T., Akutsu, H.
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 144 Issue: 31 Pages: 14132-14139

    • DOI

      10.1021/jacs.2c03580

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.2022

    • Author(s)
      Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland CB, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K
    • Journal Title

      Nucleic Acids Res.

      Volume: 50 Issue: 21 Pages: 12527-12542

    • DOI

      10.1093/nar/gkac1082

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Sensitivity enhancement by sequential data acquisition for 13C-direct detection NMR2021

    • Author(s)
      Furuita Kyoko、Sugiki Toshihiko、Takamuku Mika、Hattori Yoshikazu、So Masatomo、Kawata Yasushi、Ikegami Takahisa、Fujiwara Toshimichi、Kojima Chojiro
    • Journal Title

      Journal of Magnetic Resonance

      Volume: 322 Pages: 106878-106878

    • DOI

      10.1016/j.jmr.2020.106878

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of higher plant heme oxygenase-1 and its mechanism of interaction with ferredoxin2021

    • Author(s)
      Tohda Rei、Tanaka Hideaki、Mutoh Risa、Zhang Xuhong、Lee Young-Ho、Konuma Tsuyoshi、Ikegami Takahisa、Migita Catharina T.、Kurisu Genji
    • Journal Title

      Journal of Biological Chemistry

      Volume: 296 Pages: 100217-100217

    • DOI

      10.1074/jbc.ra120.016271

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata2020

    • Author(s)
      Kamata Kenichi、Mizutani Kenji、Takahashi Katsuya、Marchetti Roberta、Silipo Alba、Addy Christine、Park Sam-Yong、Fujii Yuki、Fujita Hideaki、Konuma Tsuyoshi、Ikegami Takahisa、Ozeki Yasuhiro、Tame Jeremy R. H.
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 22102-22102

    • DOI

      10.1038/s41598-020-78926-7

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 核磁気共鳴 NMR で飲み物を味わう2020

    • Author(s)
      池上貴久
    • Journal Title

      化学と教育(日本化学会)

      Volume: 68 Pages: 504-507

    • NAID

      130008123226

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Presentation] 解糖系moonlighting蛋白質GAPDHの環境変化に対応した立体構造変化の解析2023

    • Author(s)
      鈴木陽茉梨, 牧山ユキ, 元田容子, 小沼剛, 池上貴久
    • Organizer
      日本蛋白質科学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 多機能性タンパク質 GAPDH の立体構造変化と相互作用の解析2023

    • Author(s)
      鈴木陽茉梨、牧山ニコレユキ、元田容子、小沼 剛、池上貴久
    • Organizer
      NMR 討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria2022

    • Author(s)
      池上貴久
    • Organizer
      The 7th International Symposium on Drug Discovery and Design by NMR
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] AX3スピン系は訳分からないけど、やはり「メチル基」様様2022

    • Author(s)
      池上貴久
    • Organizer
      第61回NMR討論会チュートリアルコース
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] Methods of uniform or site-specific deuteration of proteins and their applications to NMR analyses2022

    • Author(s)
      池上貴久
    • Organizer
      J-PARC Workshop 2022 Deuterium Science Entering a New Phase
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] CPMG pulse sequence that cancels artifacts independently of spin states for relaxation dispersion2021

    • Author(s)
      池上貴久
    • Organizer
      22nd International Society of Magnetic Resonance Conference
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research

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Published: 2020-04-28   Modified: 2025-01-30  

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