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Protein structure analysis in human cell using advanced in-cell NMR techniques

Research Project

Project/Area Number 20H03191
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionYokohama National University

Principal Investigator

KOJIMA Chojiro  横浜国立大学, 大学院工学研究院, 教授 (50333563)

Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2022: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2021: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2020: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
KeywordsNMR / 蛋白質 / 立体構造解析 / 立体構造 / 細胞
Outline of Research at the Start

蛋白質の分子機能は立体構造によって制御されている。NMRは細胞内の蛋白質を細胞が生きている状態のまま構造解析できる唯一の手法である。しかし、生細胞内での蛋白質の構造解析は再現性や検出感度に問題があり、今までヒト細胞中での構造決定の成功例はない。そこで、本研究では独自技術で超高感度化に成功した生細胞内NMR技術を用いて、ヒト生細胞内蛋白質の立体構造解析に挑戦する。

Outline of Final Research Achievements

The molecular functions of proteins are regulated by their three-dimensional structures. NMR is the only technique capable of analyzing the structure of proteins inside living cells while maintaining their cellular environment. However, structural analysis of proteins within living cells has been challenging, and there was no report of protein structure determination in living human cells. In this study, we developed a technique for analyzing the three-dimensional structures of proteins in human living cells using an innovative technology that achieved ultra-high sensitivity, known as in vivo/in cell NMR. Furthermore, we expanded the ultra-high sensitivity in vivo/in cell NMR method to enable real-time measurements of structural changes in proteins and phosphorus metabolism within human living cells.

Academic Significance and Societal Importance of the Research Achievements

蛋白質の機能は立体構造によって制御されています。NMRは細胞内の蛋白質を細胞が生きている状態のまま構造解析できる唯一の手法ですが、生細胞内での蛋白質の立体構造解析技術には再現性や検出感度に問題がありました。本研究では独自技術で超高感度化に成功したNMR技術を用い、ヒト生細胞内蛋白質の立体構造決定に成功しました。この研究の成果は、生体内での蛋白質の構造解析において画期的な進展であり、蛋白質研究や医薬品開発における重要な貢献が期待されます。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (23 results)

All 2022 2021 Other

All Int'l Joint Research (4 results) Journal Article (12 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 12 results,  Open Access: 7 results) Presentation (4 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results) Book (3 results)

  • [Int'l Joint Research] UConn Health(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Czech Academy of Sciences/Czech Technical University(チェコ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Korea Basic Science Institute/University of Science and Technology/Chungnam National University(韓国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Korea Basic Science Institute/University of Science and Technology/Chungnam National University(韓国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Biological Magnetic Resonance Data Bank2022

    • Author(s)
      Hoch Jeffrey C、Baskaran Kumaran、Burr Harrison、Chin John、Eghbalnia Hamid?R、Fujiwara Toshimichi、Gryk Michael?R、Iwata Takeshi、Kojima Chojiro、Kurisu Genji、Maziuk Dmitri、Miyanoiri Yohei、Wedell Jonathan?R、Wilburn Colin、Yao Hongyang、Yokochi Masashi
    • Journal Title

      Nucleic Acids Research

      Volume: 51 Issue: D1 Pages: D368-D376

    • DOI

      10.1093/nar/gkac1050

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Multifunctional chemical inhibitors of the florigen activation?complex discovered by structure‐based high‐throughput screening2022

    • Author(s)
      Taoka Ken‐ichiro、Kawahara Ikumi、Shinya Shoko、Harada Ken‐ichi、Yamashita Eiki、Shimatani Zenpei、Furuita Kyoko、Muranaka Tomoaki、Oyama Tokitaka、Terada Rie、Nakagawa Atsushi、Fujiwara Toshimichi、Tsuji Hiroyuki、Kojima Chojiro
    • Journal Title

      The Plant Journal

      Volume: 112 Issue: 6 Pages: 1337-1349

    • DOI

      10.1111/tpj.16008

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA2022

    • Author(s)
      Yamada Takeshi、Furuita Kyoko、Sakurabayashi Shuhei、Nomura Makoto、Kojima Chojiro、Nakatani Kazuhiko
    • Journal Title

      Nucleic Acids Research

      Volume: 50 Issue: 17 Pages: 9621-9631

    • DOI

      10.1093/nar/gkac740

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Physicochemical characterization of the catalytic unit of hammerhead ribozyme and its relationship with the catalytic activity.2022

    • Author(s)
      Yoshiyuki Tanaka, Daichi Yamanaka, Saori Morioka, Taishi Yamaguchi, Masayuki Morikawa, Takashi S. Kodama, Vladimir Sychrovsky, Chojiro Kojima and Yoshikazu Hattori
    • Journal Title

      Biophysica

      Volume: 127 Issue: 3 Pages: 221-239

    • DOI

      10.3390/biophysica2030022

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] <sup>19</sup>F chemical library and <sup>19</sup>F-NMR for a weakly bound complex structure2022

    • Author(s)
      Shinya Shoko、Katahira Ritsuko、Furuita Kyoko、Sugiki Toshihiko、Lee Young-Ho、Hattori Yoshikazu、Takeshita Kohei、Nakagawa Atsushi、Kokago Aoi、Akagi Ken-ichi、Oouchi Muneki、Hayashi Fumiaki、Kigawa Takanori、Takimoto-Kamimura Midori、Fujiwara Toshimichi、Kojima Chojiro
    • Journal Title

      RSC Medicinal Chemistry

      Volume: 13 Issue: 9 Pages: 1100-1111

    • DOI

      10.1039/d2md00170e

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition2022

    • Author(s)
      Harada Ken-ichi、Furuita Kyoko、Yamashita Eiki、Taoka Ken-ichiro、Tsuji Hiroyuki、Fujiwara Toshimichi、Nakagawa Atsushi、Kojima Chojiro
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 11596-11596

    • DOI

      10.1038/s41598-022-15505-y

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 1H, 13C, and 15N resonance assignments of human glutathione peroxidase 42022

    • Author(s)
      Furuita Kyoko、Inomata Kouki、Sugiki Toshihiko、Kobayashi Naohiro、Fujiwara Toshimich、Kojima Chojiro
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 16 Issue: 2 Pages: 267-271

    • DOI

      10.1007/s12104-022-10090-7

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cooperative regulation of PBI1 and MAPKs controls WRKY45 transcription factor in rice immunity2022

    • Author(s)
      Ichimaru Kota、Yamaguchi Koji、Harada Kenichi、Nishio Yusaku、Hori Momoka、Ishikawa Kazuya、Inoue Haruhiko、Shigeta Shusuke、Inoue Kento、Shimada Keita、Yoshimura Satomi、Takeda Takumi、Yamashita Eiki、Fujiwara Toshimichi、Nakagawa Atsushi、Kojima Chojiro、Kawasaki Tsutomu
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 2397-2397

    • DOI

      10.1038/s41467-022-30131-y

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A hybrid strategy combining solution NMR spectroscopy and isothermal titration calorimetry to characterize protein-nanodisc interaction2022

    • Author(s)
      Sugiki Toshihiko、Lee Young-Ho、Alsanousi Nesreen、Murata Kaito、Kawamura Izuru、Fujiwara Toshimichi、Hanada Kentaro、Kojima Chojiro
    • Journal Title

      Analytical Biochemistry

      Volume: 639 Pages: 114521-114521

    • DOI

      10.1016/j.ab.2021.114521

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain2022

    • Author(s)
      Jibiki Kazuya、Liu Mo‐yan、Lei Chao‐sen、Kodama Takashi S.、Kojima Chojiro、Fujiwara Toshimichi、Yasuhara Noriko
    • Journal Title

      Genes to Cells

      Volume: 27 Issue: 3 Pages: 173-191

    • DOI

      10.1111/gtc.12917

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequence requirements of the FFAT‐like motif for specific binding to VAP‐A are revealed by NMR2021

    • Author(s)
      Furuita Kyoko、Hiraoka Marina、Hanada Kentaro、Fujiwara Toshimichi、Kojima Chojiro
    • Journal Title

      FEBS Letters

      Volume: 595 Issue: 17 Pages: 2248-2256

    • DOI

      10.1002/1873-3468.14166

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [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
      2020 Annual Research Report
    • Peer Reviewed
  • [Presentation] NMR tools developed for drug discovery and its application to DNA targeting small molecules2022

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 7th International Symposium on Drug Discovery and Design by NMR
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 19F-STD NMR for 3D structure modeling of a weakly bound protein-drug complex2022

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 4th International Symposium of Structure-Based Drug Discovery & 2022 Annual Conference of the Korean Society for Structural Biology Joint Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli and HeLa cells2021

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 2021 International Chemical Congress of Pacific Basin Societies (Pacifichem 2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 19F-STD NMR for 3D structure modeling of a weakly bound protein-drug complex2021

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 2021 International Chemical Congress of Pacific Basin Societies (Pacifichem 2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 創薬研究のための相互作用解析パーフェクト2021

    • Author(s)
      編集:津本 浩平、前仲 勝実
    • Total Pages
      368
    • Publisher
      羊土社
    • ISBN
      9784758122566
    • Related Report
      2021 Annual Research Report
  • [Book] NMRによる有機材料分析とその試料前処理、データ解釈2021

    • Author(s)
      執筆者:59名、技術情報協会
    • Total Pages
      676
    • Publisher
      技術情報協会
    • ISBN
      9784861048609
    • Related Report
      2021 Annual Research Report
  • [Book] 医学のあゆみ「構造生命科学による創薬への挑戦」2021

    • Author(s)
      編集:岩崎 憲治
    • Total Pages
      144
    • Publisher
      医歯薬出版
    • Related Report
      2021 Annual Research Report

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Published: 2020-04-28   Modified: 2024-01-30  

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