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Real-time observation of the biological events within living cells using in-cell NMR

Planned Research

Project AreaNovel measurement techniques for visualizing 'live' protein molecules at work
Project/Area Number 26119005
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 InstitutionThe University of Tokyo

Principal Investigator

Nishida Noritaka  東京大学, 大学院薬学系研究科(薬学部), 准教授 (50456183)

Co-Investigator(Kenkyū-buntansha) 甲斐荘 正恒  首都大学東京, 理学研究科, 客員教授 (20137029)
Research Collaborator Shimada Ichio  
Project Period (FY) 2014-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥173,160,000 (Direct Cost: ¥133,200,000、Indirect Cost: ¥39,960,000)
Fiscal Year 2018: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2017: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2016: ¥52,260,000 (Direct Cost: ¥40,200,000、Indirect Cost: ¥12,060,000)
Fiscal Year 2015: ¥28,340,000 (Direct Cost: ¥21,800,000、Indirect Cost: ¥6,540,000)
Fiscal Year 2014: ¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Keywords核磁気共鳴法 / in-cell NMR / 酸化ストレス / シグナル伝達 / 低分子量GTPase / バイオリアクター / SAIL法
Outline of Final Research Achievements

We have established the in-cell NMR methodology that enables the observation of the intracellular biological events in real-time manner. To observe the intracellular molecular response against oxidative stresses, we prepared the HeLa cells, in which both thioredoxin and glutathione were isotopically labeled, and monitored the redox status of Trx and glutathione by alternate in-cell NMR measurements. This study demonstrated the redox status of Trx is regulated not only by the intracellular redox potential but also by various endogenous regulatory molecules, such as Trx reductases. We also performed the in-cell NMR observation of small GTPase Ras and its oncogenic variants. We demonstrated that the GTP-bound ratio of Ras in the steady state is decreased in the cell for all Ras constructs, due to the increase of khy and the decrease of kex. We also succeeded in quantifying the contribution of the specific regulatory proteins by in-cell NMR experiments using the knockout cells.

Academic Significance and Societal Importance of the Research Achievements

細胞内は多種多様なタンパク質が複雑なネットワークを形成する分子混雑環境であり、細胞内のタンパク質はin vitroとは異なる構造や活性を示す。本研究ではin-cell NMR法を高度化し、細胞内タンパク質の構造や活性変化をリアルタイム観測する手法を確立して、細胞内酸化ストレスやシグナル伝達タンパク質の活性評価に適用した。本研究成果は、細胞内生命現象の可視化のみならず、細胞内で創薬標的タンパク質に対する候補化合物の薬効を直接評価するツールとしての応用が期待できる。

Report

(6 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (48 results)

All 2019 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (5 results) Journal Article (21 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 21 results,  Open Access: 8 results,  Acknowledgement Compliant: 9 results) Presentation (19 results) (of which Int'l Joint Research: 5 results,  Invited: 15 results) Book (1 results) Remarks (2 results)

  • [Int'l Joint Research] University of Toronto(カナダ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of Toronto(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] トロント大学(カナダ)

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Isotope-Aided Methods for Biological NMR Spectroscopy: Past, Present, and Future2018

    • Author(s)
      Kainosho Masatsune、Miyanoiri Yohei、Takeda Mitsuhiro
    • Journal Title

      Experimental Approaches of NMR Spectroscopy

      Volume: - Pages: 37-61

    • DOI

      10.1007/978-981-10-5966-7_2

    • ISBN
      9789811059650, 9789811059667
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Stable-Isotope-Aided NMR Spectroscopy2018

    • Author(s)
      Yohei Miyanoiri, Mitsuhiro Takeda and Masatsune Kainosho
    • Journal Title

      Modern Magnetic Resonance

      Volume: NA Pages: 469-486

    • DOI

      10.1007/978-3-319-28388-3_48

    • ISBN
      9783319283876, 9783319283883
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Numb-Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer chemoresistance and progression2018

    • Author(s)
      Ivan Nicola Colaluca, Andrea Basile, Veronica D’Uva, Davide Disalvatore, Manuela Vecchi, Stefano Confalonieri, Marina Mapelli, Salvatore Peace, Pier Paolo Di Fiore, Chun-Jiun Yang, Masatsune Kainosho, Michael Sattler
    • Journal Title

      J. Cell Biol.

      Volume: 217 Pages: 745-762

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Evolution and diversification of the plant gibberellin receptor GID12018

    • Author(s)
      Hideki Yoshida, Eiichi Tanimoto, Takaaki Hirai, Yohei Miyanoiri, Rie Mitani, Mayuko Kawamura, Mitsuhiro Takeda, Sayaka Takehara, Ko Hirano, Masatsune Kainosho, Takashi Akagi, Makoto Matsuoka, and Miyako Ueguchi-Tanaka
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 115 Pages: 7844-7853

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Perspective: next generation isotope-aided methods for protein NMR spectroscopy2018

    • Author(s)
      Kainosho Masatsune、Miyanoiri Yohei、Terauchi Tsutomu、Takeda Mitsuhiro
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 71 Issue: 3 Pages: 119-127

    • DOI

      10.1007/s10858-018-0198-x

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR2018

    • Author(s)
      Mochizuki Ayano、Saso Arata、Zhao Qingci、Kubo Satoshi、Nishida Noritaka、Shimada Ichio
    • Journal Title

      Journal of the American Chemical Society (selected as JACS Spotlights)

      Volume: 140 Issue: 10 Pages: 3784-3790

    • DOI

      10.1021/jacs.8b00426

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Numb-Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer2017

    • Author(s)
      Colaluca Ivan Nicola、Basile Andrea、Freiburger Lee、D'Uva Veronica、Disalvatore Davide、Vecchi Manuela、Confalonieri Stefano、Tosoni Daniela、Cecatiello Valentina、Malabarba Maria Grazia、Yang Chun-Jiun、Kainosho Masatsune、Sattler Michael、Mapelli Marina、Pece Salvatore、Di Fiore Pier Paolo
    • Journal Title

      J Cell Biol

      Volume: 217 Issue: 2 Pages: 745-762

    • DOI

      10.1083/jcb.201709092

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH22017

    • Author(s)
      Beck Erlach Markus、Koehler Joerg、Crusca Edson、Munte Claudia E.、Kainosho Masatsune、Kremer Werner、Kalbitzer Hans Robert
    • Journal Title

      J Biomol NMR

      Volume: 69 Issue: 2 Pages: 53-67

    • DOI

      10.1007/s10858-017-0134-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na + -Driven Flagella2017

    • Author(s)
      Miyanoiri Yohei、Hijikata Atsushi、Nishino Yuuki、Gohara Mizuki、Onoue Yasuhiro、Kojima Seiji、Kojima Chojiro、Shirai Tsuyoshi、Kainosho Masatsune、Homma Michio
    • Journal Title

      Structure

      Volume: 25 Issue: 10 Pages: 1540-1548

    • DOI

      10.1016/j.str.2017.08.010

    • NAID

      120006375873

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin.2016

    • Author(s)
      Huang S, Umemoto R, Tamura Y, Kofuku Y, Uyeda TQP, Nishida N, Shimada I
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 33690-33690

    • DOI

      10.1038/srep33690

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 13C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)2016

    • Author(s)
      Takeda M, Miyanoiri Y, Terauchi T, Kainosho M
    • Journal Title

      J Biomol NMR

      Volume: 66 Issue: 1 Pages: 37-53

    • DOI

      10.1007/s10858-016-0055-8

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Highly efficient residue-selective labeling with isotope-labeled Ile, Leu, and Val using a new auxotrophic E. coli strain2016

    • Author(s)
      Miyanoiri Y, Ishida Y, Takeda M, Terauchi T, Inouye M, Kainosho M
    • Journal Title

      J Biomol NMR

      Volume: 65 Issue: 2 Pages: 109-119

    • DOI

      10.1007/s10858-016-0042-0

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Mechanical force effect on the two-state equilibrium of the hyaluronan-binding domain of CD44 in cell rolling2015

    • Author(s)
      Suzuki T, Suzuki M, Ogino S, Umemoto R, Nishida N, Shimada I
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 112 Issue: 22 Pages: 6991-6996

    • DOI

      10.1073/pnas.1423520112

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Differential large-amplitude breathing motions in the interface of FKBP12-drug complexes2015

    • Author(s)
      Chun-Jiun Yang, Mitsuhiro Takeda, Tsutomu Terauchi, JunGoo Jee, Masatsune Kainosho
    • Journal Title

      Biochemistry

      Volume: 54 Issue: 47 Pages: 6983-95

    • DOI

      10.1021/acs.biochem.5b00820

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Nano-mole scale sequential signal assignment by 1H-detected protein solid-state NMR2015

    • Author(s)
      Songlin Wang, Sudhakar Parthasarathy, Yiling Xiao, Yusuke Nishiyama, Fei Long, Isamu Matsuda, Yuki Endo, Takahiro Nemoto, Kazuo Yamauchi, Tetsuo Asakura, Mitsuhiro Takeda, Tsutomu Terauchi, Masatsune Kainosho, Yoshitaka Ishii
    • Journal Title

      Chem. Commun. (Camb)

      Volume: 51 Issue: 81 Pages: 15055-8

    • DOI

      10.1039/c5cc04618a

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nano-mole scale side-chain assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling2015

    • Author(s)
      Songlin Wang, Sudhakar Parthasarathy, Yusuke Nishiyama, Yuki Endo, Takahiro Nemoto, Kazuo Yamauchi, Tetsuo Asakura, Mitsuhiro Takeda, Tsutomu Terauchi, Masatsune Kainosho, and Yoshitaka Ishii
    • Journal Title

      PLoS One

      Volume: 10 Issue: 4 Pages: 1-12

    • DOI

      10.1371/journal.pone.0122714

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional dynamics of cell surface membrane proteins2014

    • Author(s)
      Nishida N, Osawa M, Takeuchi K, Imai S, Stampoulis P, Kofuku Y, Ueda T, Shimada I
    • Journal Title

      J Magn Reson

      Volume: 241 Pages: 86-96

    • DOI

      10.1016/j.jmr.2013.11.007

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Cross-saturation and transferred cross-saturation experiments2014

    • Author(s)
      Ueda T, Takeuchi K, Nishida N, Stampoulis P, Kofuku Y, Osawa M, Shimada I
    • Journal Title

      Q Rev Biophys

      Volume: 47 Issue: 2 Pages: 143-187

    • DOI

      10.1017/s0033583514000043

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Backbone and side-chain 1H, 15N and 13C resonance assignments of the microtubule-binding domain of yeast cytoplasmic dynein in the high and low-affinity states2014

    • Author(s)
      Takarada O, Nishida N, Kikkawa M, Shimada I
    • Journal Title

      Biomol NMR assign

      Volume: 8 Issue: 2 Pages: 379-382

    • DOI

      10.1007/s12104-013-9522-2

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates2014

    • Author(s)
      Mitsuhiro Takeda, Yohei Miyanoiri, Tsutomu Terauchi, Chun-Jiun Yang, Masatsune Kainosho
    • Journal Title

      J. Magn. Reson.

      Volume: 241 Pages: 148-154

    • DOI

      10.1016/j.jmr.2013.10.001

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA.2014

    • Author(s)
      Schmidt, E., Ikeya, T., Takeda, M., Loehr, F., Buchner, L., Ito, Y., Kainosho, M., Guentert, P.
    • Journal Title

      J. Magn. Reson.

      Volume: 249 Pages: 88-93

    • DOI

      10.1016/j.jmr.2014.10.005

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] in-cell NMR法を用いた細胞内生命反応のリアルタイム観測2019

    • Author(s)
      Noritaka Nishida, Ichio Shimada
    • Organizer
      よこはまNMR研究会 第62回ワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Recent Advances in Isotope-Aided Methods for Studying Protein Structures and Dynamics-Historical Background and Future Perspectives2019

    • Author(s)
      Masatsune Kainosho
    • Organizer
      Advanced Isotope Labelling Methods for Integrated Structure Biology-AILM 2019
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] in-cell NMR法を用いた細胞内生命現象のリアルタイム観測2018

    • Author(s)
      Noritaka Nishida, Ichio Shimada
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ゲノム編集技術を活用した 細胞内Rasの活性制御機構のin-cell NMR観測2018

    • Author(s)
      Quinci Zhao, Ryu Fujimiya, Chris Mershall, Mitsuhiko Ikura, Noritaka Nishida, Ichio Shimada
    • Organizer
      第16回次世代を担う若手のためのフィジカル・ファーマフォーラム(PPF2018)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Real-time observation of the biological events within living cells using in-cell NMR2018

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      JST-Mirai kick-off symposium
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] in-cell NMR observation of oxidative stress induced response of thioredoxin2018

    • Author(s)
      望月綾野、佐宗新、久保智、趙慶慈、西田紀貴、嶋田一夫
    • Organizer
      第138回薬学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] in-cell NMR法による細胞内環境下におけるRasの活性状態の評価2018

    • Author(s)
      趙慶慈、藤宮璃勇、Chris Marshall、伊倉光彦、西田紀貴、嶋田一夫
    • Organizer
      第138回薬学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Real-time observation of the biological events within living cells using in-cell NMR2017

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      第16回蛋白質科学会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Real-time observation of the biological events within living cells using in-cell NMR2017

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] in-cell NMR法による細胞内環境下におけるRasの活性状態の評価2017

    • Author(s)
      趙慶慈、藤宮璃勇、Chris Marshall、伊倉光彦、西田紀貴、嶋田一夫
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] NMR observation of the biological events inside living cells2016

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      The 27th International Conference on Magnetic Resonance in Biological Systems (ICMRBS)
    • Place of Presentation
      京都国際会議場(京都府京都市)
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] NMR observation of the biological events within living cells2016

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      The 12th European Magnetic Resonance (EUROMAR) 2016
    • Place of Presentation
      オーフス(デンマーク)
    • Year and Date
      2016-07-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Bioreactor system for in-cell NMR observation of the biological events inside living cells2015

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      第38回 分子生物学会(BMB2015)
    • Place of Presentation
      神戸国際会議場(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] In-cell NMR observation of the biological events within living cells2015

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      The 25th Hot Spring Harbor International Symposium
    • Place of Presentation
      九州大学医学部馬出キャンパス(福岡県福岡市)
    • Year and Date
      2015-11-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生細胞内の生命現象を活写するin-cell NMR法の開発と応用2015

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      蛋白質科学会 第15回年会
    • Place of Presentation
      あわぎんホール(徳島県徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 生細胞内の生命現象を観測するバイオリアクター型in-cell NMR法の開発と応用2015

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      よこはまNMR研究会 第52回 ワークショップ
    • Place of Presentation
      理研鶴見キャンパス(神奈川県横浜市)
    • Year and Date
      2015-03-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A bioreactor for NMR observation of biological events inside living cells2014

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      第53回NMR討論会
    • Place of Presentation
      大阪大学コンベンションセンター(大阪府吹田市)
    • Year and Date
      2014-11-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 生細胞内の生命反応をリアルタイムに捉えるin-cell NMR法の開発と応用2014

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      新学術領域「動的構造生命」 第1回領域キックオフシンポジウム
    • Place of Presentation
      九州大学医学部馬出病院キャンパス(福岡県福岡市)
    • Year and Date
      2014-10-03
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A bioreactor system for observing biological eventsinside mammalian cells2014

    • Author(s)
      西田紀貴、嶋田一夫
    • Organizer
      In-cell NMRシンポジウム
    • Place of Presentation
      首都大学東京八王子キャンパス(東京都八王子市)
    • Year and Date
      2014-09-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Book] Discoidin domain receptor in health and disease2016

    • Author(s)
      Noritaka Nishida, Ichio Shimada
    • Total Pages
      355
    • Publisher
      Springer
    • Related Report
      2016 Annual Research Report
  • [Remarks] 東京大学薬学部 生命物理化学教室ホームページ

    • URL

      http://ishimada.f.u-tokyo.ac.jp/public_html/index_j.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] 東京大学薬学部生命物理化学教室

    • URL

      http://ishimada.f.u-tokyo.ac.jp/public_html/index_j.html

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report 2014 Annual Research Report

URL: 

Published: 2014-11-20   Modified: 2023-03-20  

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