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Analyses of the activation mechanisms of receptors of fatty acids and membrane receptors by in situ measurement

Planned Research

Project AreaIntegrative understanding of biological processes mediated by transient macromolecular complexes; New technology for visualizing physiologically metastable states.
Project/Area Number 21121006
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

Principal Investigator

SHIRAKAWA Masahiro  京都大学, 工学(系)研究科(研究院), 教授 (00202119)

Co-Investigator(Kenkyū-buntansha) MORIKAWA Kohsuke  財団法人国際高等研究所, チーフリサーチフェロー (80012665)
Co-Investigator(Renkei-kenkyūsha) TOCHIO Hidehito  京都大学, 大学院理学研究科, 教授 (70336593)
ARIYOSI Mariko  京都大学, 大学院工学研究科, 博士研究員 (80437243)
Project Period (FY) 2009-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥213,720,000 (Direct Cost: ¥164,400,000、Indirect Cost: ¥49,320,000)
Fiscal Year 2013: ¥40,560,000 (Direct Cost: ¥31,200,000、Indirect Cost: ¥9,360,000)
Fiscal Year 2012: ¥40,560,000 (Direct Cost: ¥31,200,000、Indirect Cost: ¥9,360,000)
Fiscal Year 2011: ¥30,420,000 (Direct Cost: ¥23,400,000、Indirect Cost: ¥7,020,000)
Fiscal Year 2010: ¥30,420,000 (Direct Cost: ¥23,400,000、Indirect Cost: ¥7,020,000)
Fiscal Year 2009: ¥71,760,000 (Direct Cost: ¥55,200,000、Indirect Cost: ¥16,560,000)
KeywordsNMR / 脂質シャペロン / 脂肪酸結合蛋白質 / In-cell NMR / 19F NMR / 細胞生物学 / FKBP12 / FK506 / ラパマイシン / 立体構造 / 細胞計測 / ESR / X線結晶法
Outline of Final Research Achievements

In this study, we were engaged to develop the methods for in-cell NMR of proteins and optically detected magnetic resonance (ODMR), aiming to create experimental techniques to provide structural and dynamics information of protein complexes formed transiently in cells or at cell membranes. For in-cell NMR, we used the signal transduction factor in immunological system FKBP12 and a chaperon protein for fatty acids, FABP4. We could measure in-cell 1H-15N correlation and 19F-NMR spectra of them, respectively. For ODMR, we have built methods to selectively detect fluorescence of diamond particles and to determine the directions of particles.

Report

(6 results)
  • 2014 Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (33 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (25 results) (of which Peer Reviewed: 25 results,  Open Access: 5 results,  Acknowledgement Compliant: 2 results) Presentation (8 results) (of which Invited: 6 results)

  • [Journal Article] The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates.2015

    • Author(s)
      Morimoto D,Walinda E, Fukada H, Sou YS, Kageyama S, Hoshino M, Fujii T, Tsuchiya H, Saeki Y, Arita K, Ariyoshi M, Tochio H, Iwai K, Namba K, Komatsu M, Tanaka K, Shirakawa M.
    • Journal Title

      Nat Commun.

      Volume: 6 Issue: 1 Pages: 6116-6116

    • DOI

      10.1038/ncomms7116

    • NAID

      120005528125

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR.2013

    • Author(s)
      Takaoka Y, Kioi Y, Morito A, Otani J, Arita K, Ashihara E, Ariyoshi M, Tochio H, Shirakawa M, Hamachi I.
    • Journal Title

      Chem Commun

      Volume: 49 Issue: 27 Pages: 2801-2803

    • DOI

      10.1039/c3cc39205h

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Pruning the ALS-associated protein SOD1 for in-cell NMR.2013

    • Author(s)
      Danielsson J, Inomata K, Murayama S, Tochio H, Lang L, Shirakawa M, Oliveberg M.
    • Journal Title

      Journal of the American Chemical Society

      Volume: 135(28) Issue: 28 Pages: 10266-10269

    • DOI

      10.1021/ja404425r

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of Fluorogenic Probes for Quick No-Wash Live-Cell Imaging of Intracellular Proteins2013

    • Author(s)
      Y. Hori, T. Norinobu, M. Sato, K. Arita, S. Shirakawa & K. Kikuchi
    • Journal Title

      J. Am. Chem. Soc

      Volume: 135 Issue: 33 Pages: 12360-12365

    • DOI

      10.1021/ja405745v

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An in-cell NMR study of monitoring stress-induced increase of cytosolic Ca2+ concentration in HeLa cells2013

    • Author(s)
      Dambarudhar Shiba Sankar Hembrama, Takahiro Haremakia, Jumpei Hamatsua, Jin Inouea, Hajime Kamoshidaa, Teppei Ikeyaa, Masaki Mishimaa, Tsutomu Mikawab, Nobuhiro Hayashic, Masahiro Shirakawad, Yutaka Ito
    • Journal Title

      Biochem Biophys Res Commun

      Volume: 438 Issue: 4 Pages: 653-659

    • DOI

      10.1016/j.bbrc.2013.07.127

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] High-resolution heteronuclear multidimensional NMR of proteins living insect cells using a baculovirus protein expression system ≪2013

    • Author(s)
      Jumpei Hamatsu, Daniel O'Donovan, Takashi Tanaka, Takahiro Shirai, Yuichiro Hourai, Tsutomu Mikawa, Teppei Ikeya, Masaki Mishima, Wayne Boucher, Brian O. Smith, Ernest D. Laue, Masahiro Shirakawa, Yutaka Ito 4
    • Journal Title

      Journal of the American Chemical Society

      Volume: 135 Issue: 5 Pages: 1688-1691

    • DOI

      10.1021/ja310928u

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4.2013

    • Author(s)
      Otani, J., Arita, K., Kato, T., Kinoshita, M., Kimura, H., Suetake, I., Tajima, S., Ariyoshi, M., Shirakawa, M.
    • Journal Title

      J Biol. Chem.

      Volume: 288 Issue: 9 Pages: 6351-6362

    • DOI

      10.1074/jbc.m112.431098

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Utilization of lysine ¹³C-methylation NMR for protein-protein interaction studies.2013

    • Author(s)
      Hattori Y, Furuita K, Ohki I, Ikegami T, Fukada H, Shirakawa M, Fujiwara T, Kojima C.
    • Journal Title

      J Biomol NMR.

      Volume: 55 Issue: 1 Pages: 19-31

    • DOI

      10.1007/s10858-012-9675-9

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes.2012

    • Author(s)
      Mishima Y, Watanabe M, Kawakami T, Jayasinghe CD, Otani J, Kikugawa Y, Shirakawa M, Kimura H, Nishimura O, Aimoto S, Tajima S, Suetake I.
    • Journal Title

      J Mol Biol.

      Volume: 425 Issue: 1 Pages: 54-70

    • DOI

      10.1016/j.jmb.2012.10.018

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Real-time background-free selective imaging of fluorescent nanodiamond in vivn2012

    • Author(s)
      Ryuji Igarashi, Yohsake Yoshinari, Riroaki Yokoia, Takuma Sugi, Fuminori Sugihara, Kazuhiro Ikeda, Hiroshi Sumiya, Shigenori Tsuji, Ikme Mori, Hidehito Tochio, Yoshie Rarada, Masahiro Shirakawa.
    • Journal Title

      Nano Letters

      Volume: 12 Issue: 11 Pages: 5726-5732

    • DOI

      10.1021/nl302979d

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF12012

    • Author(s)
      K.Arita, S.Isogai, T.Oda, M.Unoki, K.Sugita, N.Sekiyama, K.Kuwata, R.Hamamoto, H.Tochio, M.Sato, M.Ariyoshi, and M.Shirakawa
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 109 Issue: 32 Pages: 12950-12955

    • DOI

      10.1073/pnas.1203701109

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] TRAM is involved in IL-18 signaling and functions as a sorting adaptor for MyD88.2012

    • Author(s)
      Ohnishi H, Tochio H, Kato Z, Kawamoto N, Kimura T, Kubota K, Yamamoto T, Funasaka T, Nakano H, Wong RW, Shirakawa M, Kondo N.
    • Journal Title

      PLoS One.

      Volume: 7 Issue: 6 Pages: e38423-e38423

    • DOI

      10.1371/journal.pone.0038423

    • NAID

      120005540726

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular analysis of the binding mode of Toll/interleukin-1 receptor (TIR) domain proteins during TLR2 signaling.2012

    • Author(s)
      Nada M, Ohnishi H, Tochio H, Kato Z, Kimura T, Kubota K, Yamamoto T, Kamatari YO, Tsutsumi N, Shirakawa M, Kondo N.
    • Journal Title

      Mol Immunol.

      Volume: 52 Issue: 3-4 Pages: 108-116

    • DOI

      10.1016/j.molimm.2012.05.003

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80.2012

    • Author(s)
      Sekiyama N, Jee J, Isogai S, Akagi K, Huang TH, Ariyoshi M, Tochio H, Shirakawa M.
    • Journal Title

      J Biomol NMR.

      Volume: 52 Issue: 4 Pages: 339-350

    • DOI

      10.1007/s10858-012-9614-9

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effect of Ca^<2+> on microtubule severing enzyme katanin p60 ; insight into the substrate dependent activation mechanism2012

    • Author(s)
      N.Iwaya, et al
    • Journal Title

      FEBS J.

      Volume: 279 Issue: 7 Pages: 1339-1352

    • DOI

      10.1111/j.1742-4658.2012.08528.x

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural analysis of proteins in living eukaryotic cells using magnetic resonance spectroscopy2012

    • Author(s)
      Tochio H, Shirakawa M.
    • Journal Title

      Yakugaku Zasshi

      Volume: 132 Pages: 185-193

    • NAID

      130001872007

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Application of NMR spectroscopy in medicinal chemistry and drug discovery.2011

    • Author(s)
      Ohno A, Inomata K, Tochio H, Shirakawa M.
    • Journal Title

      Curr Top Med Chem.

      Volume: 11 Pages: 68-73

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and function of the N-terminal nucleolin binding domain of nuclear Valocin containing protein like 2 (NVL2) harboring a nucleolar localization signal2011

    • Author(s)
      Y.Fujiwara, et al
    • Journal Title

      J Biol Chem

      Volume: 286 Issue: 24 Pages: 21732-21741

    • DOI

      10.1074/jbc.m110.174680

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the UBA domain of p62 and its interaction with ubiquitin2011

    • Author(s)
      Isogai, S., Morimoto, D., Arita, K., Unzai, S., Tenno, T., Hasegawa, J., Sou, Y.S., Komatsu, M., Tanaka, K., Shirakawa, M., Tochio, H.
    • Journal Title

      J Biol Chem.

      Volume: 286 Issue: 36 Pages: 31864-318674

    • DOI

      10.1074/jbc.m111.259630

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug.2011

    • Author(s)
      Yamada H, Mizusawa K, Igarashi R, Tochio H, Shirakawa M, Tabata Y, Kimura Y, Kondo T, Aoyama Y, Sando S.
    • Journal Title

      ACS Chem Biol.

      Volume: 7 Issue: 3 Pages: 535-542

    • DOI

      10.1021/cb2003972

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distance Determination in Proteins inside Xenopus laevis Oocytes by Double Electron-Electron Resonance Experiments.2010

    • Author(s)
      Igarashi R, Sakai T, Hara H, Tenno T, Tanaka T, Tochio H, Shirakawa M.
    • Journal Title

      Journal of the American Chemical Society

      Volume: 132 Pages: 8228-8229

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45.2010

    • Author(s)
      Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M.
    • Journal Title

      Proteins : Structure Function and Bioinformatics

      Volume: 78 Pages: 1491-1502

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solution structure of a zinc-finger domain that binds to poly-ADP-ribose2010

    • Author(s)
      Isogai, S., Kanno, S.I., Ariyoshi, M., Tochio, H., Ito, Y., Yasui, A., Shirakawa, M.
    • Journal Title

      Genes to Cells

      Volume: 15 Pages: 101-110

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains2010

    • Author(s)
      Morimoto, D., Isogai, S., Tenno, T., Tochio, H., Shirakawa, M., Ariyoshi, M.
    • Journal Title

      Acta Crystallographica Section F

      Volume: 66 Pages: 834-837

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and Mutagenesis Studies of the C-terminal Region of Licensing Factor Cdt1 Enable the Identification of Key Residues for Binding to Replicative Helicase Mcm Proteins2010

    • Author(s)
      Jee, J., Mizuno, T., Kamada, K., Tochio, H., Chiba, Y., Yanagi, K., Yasuda, G., Hiroaki, H., Hanaoka, F., Shirakawa, M.
    • Journal Title

      J Biol Chem

      Volume: 285 Pages: 15931-15940

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] DNAメチル化の構造生物学とin-cell NMRによる細胞内でのタンパク質と薬剤の相互作用の観察2014

    • Author(s)
      白川 昌宏
    • Organizer
      日本薬学会医薬化学部会第32回メディシナルケミストリーシンポジウム
    • Place of Presentation
      神戸国際会議場
    • Year and Date
      2014-11-27
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Mechanics of cells and intracellular macromolecules measured by magnetic resonanceon2011

    • Author(s)
      Masahiro Shirakawa
    • Organizer
      Gordon Research Conference on Computational Aspects of Biomolecular NMR
    • Place of Presentation
      Il Ciocco Hotel and Resort, Italy
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Magnetic resonance techniques for observation of structure anddynamics of biomolecules in cells2011

    • Author(s)
      Masahiro Shirakawa
    • Organizer
      The 11th Annual Meeting of the protein Science Society of Japan
    • Place of Presentation
      Hotel Hankyu Expo-park, Osaka
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Plenary lecture2010

    • Author(s)
      Masahiro Shirakawa
    • Organizer
      APRU research symposium
    • Place of Presentation
      Kyoto University, Japan(招待講演)
    • Year and Date
      2010-11-24
    • Related Report
      2010 Annual Research Report
  • [Presentation] Magnetic Resonance for Investigation of structure and dynamics of proteins and membranes in live cells

    • Author(s)
      Shirakawa,M
    • Organizer
      The 25th International Conference on Magnetic Resonance in Biological Systems
    • Place of Presentation
      Lyon, France
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] In-Cell NMR Spectroscopy of Proteins Inside Living Cells

    • Author(s)
      Shirakawa,M
    • Organizer
      Keystone Symposium on Frontiers of NMR in Biology
    • Place of Presentation
      Utah, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] Magnetic resonance for cell biology:Mechanics of intra-cellar proteins and cells

    • Author(s)
      Masahiro Shirakawa
    • Organizer
      2011 KAIST chemical biology symposium
    • Place of Presentation
      Korea
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] 細胞内タンパク質・細胞膜の構造、運動性の磁気共鳴を使った計測手法の開発

    • Author(s)
      白川昌宏
    • Organizer
      理化学研究所 細胞システム研究コロキウム
    • Place of Presentation
      鈴木梅太郎ホール、理化学研究所和光キャンパス
    • Related Report
      2011 Annual Research Report
    • Invited

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Published: 2009-04-01   Modified: 2019-07-29  

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