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Towards generalized structure determination of in-cell NMR using the fully automated structure analysis

Research Project

Project/Area Number 22870026
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionTokyo Metropolitan University

Principal Investigator

IKEYA Teppei  首都大学東京, 理工学研究科, 助教 (30457840)

Project Period (FY) 2010 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥3,146,000 (Direct Cost: ¥2,420,000、Indirect Cost: ¥726,000)
Fiscal Year 2011: ¥1,508,000 (Direct Cost: ¥1,160,000、Indirect Cost: ¥348,000)
Fiscal Year 2010: ¥1,638,000 (Direct Cost: ¥1,260,000、Indirect Cost: ¥378,000)
Keywordsin-cell NMR / 蛋白質 / 自動構造解析 / In-cell NMR / 立体構造計算 / CYANA / 分子動力学計算 / NMRデータ自動解析 / FLYA / 構造計算
Research Abstract

Investigating proteins "at work" in a living environment is a major goal of molecular biology. New NMR methodology has enabled the measurement of multi-dimensional NMR spectra of proteins in living cells. Compared to in vitro spectra of purified proteins in-cell NMR spectra typically show a significant number of background signals, low signal-noise ratio, and broadened signals that lead to a much higher assignment ambiguity, which makes it difficult and cumbersome to check all possibilities manually. In this project, we developed a fully automated structure determination algorithm, NOESY-FLYA method, and optimized it to the in-cell NMR data.

Report

(3 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • Research Products

    (37 results)

All 2012 2011 2010 Other

All Journal Article (8 results) (of which Peer Reviewed: 4 results) Presentation (27 results) Remarks (2 results)

  • [Journal Article] Automated NMR chemical shift assignment and protein structure determination using exclusively NOESY spectra. J. Biomol2011

    • Author(s)
      Ikeya, T., Jee. J. G., Shigemitsu, Y., Hamatsu, J., Mishima, M., Ito, Y., Kainosho, M. & Guntert, P.
    • Journal Title

      NMR., published online ahead of print

    • Related Report
      2011 Final Research Report
  • [Journal Article] 高度好熱菌Thermus thermophilus HB8 TTHA1718遺伝子産物2011

    • Author(s)
      池谷鉄兵,伊藤隆
    • Journal Title

      eProS

    • URL

      http://www.pdbj.org/eprots/index_ja.cgi?PDB%3a2roe

    • Related Report
      2011 Final Research Report
  • [Journal Article] Exclusively NOESY-based automated NMR assignment and structure determination of proteins2011

    • Author(s)
      Ikeya, T., Jee, J.G., Shigemitsu, Y., Hamatsu, J., Mishima, M., Ito, Y., Kainosho, M., Guntert, P.
    • Journal Title

      J.Biomol.NMR

      Volume: 50(2) Issue: 2 Pages: 137-146

    • DOI

      10.1007/s10858-011-9502-8

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Automated NMR chemical shift assignment and protein structure deter mination using exclusively NOESY spectra.2011

    • Author(s)
      Ikeya, T., Jee.J.G., Shigemitsu, Y., Hamatsu, J., Mishima, M., Ito, Y., Kainosho, M., Guntert, P.
    • Journal Title

      J.Biomol.NMR.

      Volume: (published online ahead of print)

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NMR protein structure determination in living E. coli cells using nonlinear sampling2010

    • Author(s)
      Ikeya, T., Sasaki, A., Sakakibara, D., Shigemitsu, Y., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Nietlisbach, D., Walchli, M., Smith, B. O., Shirakawa, M., Guntert, P. & Ito, Y.
    • Journal Title

      Nature Protocols

      Volume: 5 Pages: 1051-1060

    • Related Report
      2011 Final Research Report
  • [Journal Article] Structural investigation of the C-terminal catalytic fragment of presenilin-12010

    • Author(s)
      Sobhanifar, S., Schneider, B., Lohr, F., Gottstein, D., Ikeya, T., Filipek, S., Guntert, P., Bernhard, F. & Dotsch, V.
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 107 Pages: 9644-9649

    • Related Report
      2011 Final Research Report
  • [Journal Article] NMR protein structure determination in living E.coli cells using non-linear sampling.2010

    • Author(s)
      Ikeya, T., Sasaki, A., Sakakibara, D., Shigemitsu, Y., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Nietlisbach, D., Walchli, M., Smith, B.O., Shirakawa, M., Guntert, P., Ito, Y.
    • Journal Title

      Nature Protocols

      Volume: 5 Pages: 1051-1060

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural investigation of the C-terminal catalytic fragment of presenilin-1.2010

    • Author(s)
      Sobhanifar, S., Schneider, B., Lohr, F., Gottstein, D., Ikeya, T., Filipek, S., Guntert, P., Bernhard, F., Dotsch, V.
    • Journal Title

      Proc.Natl.Acad.Sci.USA

      Volume: 107 Pages: 9644-9649

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] In-cell NMRによる細胞内蛋白質の分子動態解析2012

    • Author(s)
      濱津順平, Daniel Nietlispach,池谷鉄兵,三島正規,白川昌宏,伊藤隆
    • Organizer
      日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy2012

    • Author(s)
      Saori Hosoya, Tomomi Hanashima, Junmpei Hamatsu, Teppei Ikeya, Masaki Mishima, Peter Guentert, Masahiro Shirakawa and Yutaka Ito
    • Organizer
      日本分子生物学会年会
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 細胞内蛋白質構造の精密化2012

    • Author(s)
      池谷鉄兵
    • Organizer
      In cell NMR workshop 2012
    • Place of Presentation
      Osaka
    • Related Report
      2011 Final Research Report
  • [Presentation] 細胞内蛋白質構造の精密化2012

    • Author(s)
      池谷鉄兵
    • Organizer
      In cell NMR workshop 2012
    • Place of Presentation
      大阪
    • Related Report
      2011 Annual Research Report
  • [Presentation] NMR法による生きた細胞内での蛋白質の立体構造決定とダイナミクス解析2011

    • Author(s)
      池谷鉄兵
    • Organizer
      統計数理研究所研究会
    • Place of Presentation
      東京
    • Related Report
      2011 Final Research Report
  • [Presentation] NMR structure refinement by torsion angle moleculer dynamics simulation using a physical force field in CYANA2011

    • Author(s)
      Masaki Mishima, Yutaka Ito and Peter Guentert
    • Organizer
      ISNMR 2011
    • Place of Presentation
      Yokohama
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural and dynamics studies of proteins in living cells by in-cell NMR spectroscopy2011

    • Author(s)
      Junpei Hamatsu, Takahiro Shirai, Daniel Nietlispach, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa and Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      Yokohama
    • Related Report
      2011 Final Research Report
  • [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy2011

    • Author(s)
      Saori Hosoya, Tomomi Hanashima, Junmpei Hamatsu, Teppei Ikeya, Masaki Mishima, Peter Guentert, Masahiro Shirakawa and Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      Yokohama
    • Related Report
      2011 Final Research Report
  • [Presentation] Heteronuclear multidimensional NMR spectroscopy of proteins in human cultured cells2011

    • Author(s)
      Kaori Onishi, Jumpei Hamatsu, Dambarudhar Shiba Sanker Hembram, Takehiro Haremaki, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa and Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      Yokohama
    • Related Report
      2011 Final Research Report
  • [Presentation] NMR structure refinement by torsion angle moleculer dynamics Simulation using a physical force field in CYANA2011

    • Author(s)
      Teppei Ikeya, Masaki Mishima, Yutaka Ito, Peter Guentert
    • Organizer
      ISNMR 2011
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report
  • [Presentation] Structural and dynamics studies of proteins in living cells by in-cell NMR spectroscopy2011

    • Author(s)
      Junpei Hamatsu, Takahiro Shirai, Daniel Nietlispach, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa, Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report
  • [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy2011

    • Author(s)
      Saori Hosoya, Tomomi Hanashima, Junmpei Hamatsu, Teppei Ikeya, Masaki Mishima, Peter Guentert, Masahiro Shirakawa, Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report
  • [Presentation] Heteronuclear multidimensional NMR spectroscopy of proteins in human cultured cells2011

    • Author(s)
      Kaori Onishi, Jumpei Hamatsu, Dambarudhar Shiba Sanker Hembram, Takehiro Haremaki, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa, Yutaka Ito
    • Organizer
      ISNMR 2011
    • Place of Presentation
      横浜
    • Related Report
      2011 Annual Research Report
  • [Presentation] Automated protein structure determinations from minimal sets of spectra using FLYA2010

    • Author(s)
      池谷鉄兵, Jee JunGoo, 浜津順平, 三島正規, 伊藤隆, 甲斐荘正恒, Peter Guntert
    • Organizer
      NMR討論会
    • Place of Presentation
      東京
    • Year and Date
      2010-11-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] Structure and dynamics of proteins at work inside cells2010

    • Author(s)
      Ito, J. Hamatsu, T. Hanashima, M. Mishima, T. Mikawa, M. Waelchli, B. O. Smith, M. Shirakawa, T. Ikeya, P. Guentert
    • Organizer
      The 24th International Conference on Magnetic Resonance in Biological Systems
    • Place of Presentation
      Cairns, Commonwealth in Australia
    • Year and Date
      2010-08-22
    • Related Report
      2011 Final Research Report
  • [Presentation] NMR studies of 56 kDa E. coli periplasmic nickel binding protein NikA2010

    • Author(s)
      J. E. Jakus, Y. Tsuchie, T. Ikeya, M. Mishima, D. Nietlispach, J. R. H. Tame, Y. Ito
    • Organizer
      The 24th International Conference on Magnetic Resonance in Biological Systems
    • Place of Presentation
      Cairns, Commonwealth in Australia
    • Related Report
      2011 Final Research Report
  • [Presentation] Applications of nonlinear sampling scheme to 4D NOESY experiment2010

    • Author(s)
      Y. Shigemitsu, Y. Tsuchie, T. Ikeya, M. Mishima, D. Nietlispach, M. Waelchli, P. Guentert, B. O. Smith, Y. Ito
    • Organizer
      The 24th International Conference on Magnetic Resonance in Biological Systems
    • Place of Presentation
      Cairns, Commonwealth in Australia
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural evolution of oligomerization domains within the p53 family2010

    • Author(s)
      D. Coutandin, H. D. Ou, F. Lohr, T. Ikeya. J. Heering, G. Deutsch, T. Weber, P. Guntert, V. Dotsch
    • Organizer
      The 24th International Conference on Magnetic Resonance in Biological Systems
    • Place of Presentation
      Cairns, Commonwealth in Australia
    • Related Report
      2011 Final Research Report
  • [Presentation] FLYAによる最少スペクトルデータセットを用いた自動構造解析2010

    • Author(s)
      池谷鉄兵,池俊求,重光佳基,濱津順平,三島正規,伊藤隆,甲斐荘正恒, Peter Guentert
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] Nonlinear samplingと3D MaxEntを用いた迅速な4D NOESY測定の有用性の検証2010

    • Author(s)
      重光佳基,池谷鉄兵,土江祐介,三島正規, Daniel Nietlispach, Markus Waelchli, Peter Guentert, Brian O. Smith,伊藤隆
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] In-cell NMR法を用いた生細胞内におけるプロテインG B1ドメインの高次構造解析2010

    • Author(s)
      花島知美,濱津順平,池谷鉄兵,三島正規, Peter Guentert,白川昌宏,伊藤隆
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] NMRを用いた蛋白質の立体構造解析における非線形サンプリングの有用性の検証2010

    • Author(s)
      大西香穂里,重光佳基,土江祐介, Daniel Nietlispach,三島正規,池谷鉄兵,伊藤隆
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] In-cell NMRによる高度好熱菌TTHA1718蛋白質の生細胞動態解析2010

    • Author(s)
      濱津順平, Daniel Nietlispach,花島知美,池谷鉄兵,細谷沙織,三島正規,白川昌宏,伊藤隆
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] NMR studies of 56 kDa E. coli nickel binding protein NikA2010

    • Author(s)
      Joanna Jakus, Yuusuke Tsuchie, Teppei Ikeya, Masaki Mishima, Daniel Nietlispach, Jeremy R. H. Tame, Yutaka Ito
    • Organizer
      第49回NMR討論会
    • Place of Presentation
      船堀
    • Related Report
      2011 Final Research Report
  • [Presentation] NMRを用いた蛋白質の立体構造解析における非線形サンプリングの有用性の検証2010

    • Author(s)
      大西香穂里,重光佳基,土江祐介, Daniel Nieltispach,三島正規,池谷鉄兵,伊藤隆
    • Organizer
      第33回日本分子生物学会年会/第83回日本生化学会大会
    • Place of Presentation
      神戸ポートアイランド,兵庫県
    • Related Report
      2011 Final Research Report
  • [Presentation] In-cell NMRによるTTHA1718蛋白質の生細胞内分子動態解析2010

    • Author(s)
      濱津順平,花島知美,池谷鉄兵,細谷沙織,三島正規, Daniel Nieltispach,白川昌宏,伊藤隆
    • Organizer
      第33回日本分子生物学会年会/第83回日本生化学会大会
    • Place of Presentation
      神戸ポートアイランド,兵庫県
    • Related Report
      2011 Final Research Report
  • [Presentation] In-cell NMRを用いた生細胞内におけるプロテインG B1ドメインの高次構造解析2010

    • Author(s)
      花島知美,濱津順平,赤羽正寿,白川昌宏,三島正規,池谷鉄兵, Peter Guentert,伊藤隆
    • Organizer
      第33回日本分子生物学会年会/第83回日本生化学会大会
    • Place of Presentation
      神戸ポートアイランド,兵庫県
    • Related Report
      2011 Final Research Report
  • [Remarks]

    • URL

      http://www.comp.tmu.ac.jp/osbc/Group_Ito/index.html

    • Related Report
      2011 Final Research Report
  • [Remarks] 研究室紹介および, CYANAプログラムの実践的応用を紹介したページを作成.

    • URL

      http://www.cyana.org/wiki/index.php/Main_Page

    • Related Report
      2011 Final Research Report

URL: 

Published: 2010-08-27   Modified: 2016-04-21  

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