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Development of NMR data analysis methods for proten three-dimensional structure

Research Project

Project/Area Number 15K06979
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
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)

Co-Investigator(Renkei-kenkyūsha) ITO Yutaka  首都大学東京, 理工学研究科, 教授 (80261147)
GUENTERT Peter  首都大学東京, 理工学研究科, 客員教授 (20392110)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
KeywordsNMR立体構造計算 / ベイズ推定 / in-cell NMR / 高分子量蛋白質 / 蛋白質のダイナミクス / NMR / タンパク質立体構造決定 / 立体構造計算 / Bayes推定 / PCS / PRE
Outline of Final Research Achievements

In this project, we addressed to develop new computational methods for solution NMR with sparse data or low signal to noise ratio. We successfully improved a Bayesian-assisted structure determination method and determined accurate structures of proteins in living cells and a protein which a conventional method could not converge. In addition, we could synthesize a new lanthanide-binding tag that stably incorporates with a protein even in reduction environment such as inside of cells. Using a method of data analysis developed in this project, we could obtain sufficiently large pseudo-contact shifts (PCSs) and long-range structural information of proteins in living cells.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (48 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (7 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 7 results,  Open Access: 6 results,  Acknowledgement Compliant: 3 results) Presentation (36 results) (of which Int'l Joint Research: 10 results,  Invited: 5 results) Book (1 results)

  • [Int'l Joint Research] フランクフルトゲーテ大学(ドイツ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] スイス連邦工科大学(スイス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] フランクフルトゲーテ大学(ドイツ)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] レスター大学(英国)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Protein NMR Structure Refinement Based on Bayesian Inference for Dynamical Ordering of Biomacromolecules2018

    • Author(s)
      Teppei Ikeya and Yutaka Ito
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 1 Pages: 65-75

    • DOI

      10.2477/jccj.2018-0009

    • NAID

      130006555815

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Solution NMR views of dynamical ordering of biomacromolecules2018

    • Author(s)
      Ikeya Teppei、Ban David、Lee Donghan、Ito Yutaka、Kato Koichi、Griesinger Christian
    • Journal Title

      Biochim. Biophys. Acta-General Subjects

      Volume: 1862 Issue: 2 Pages: 287-306

    • DOI

      10.1016/j.bbagen.2017.08.020

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] In-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Guentert and Yutaka Ito
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 38312-38312

    • DOI

      10.1038/srep38312

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A new carbamidemethyl-linked lanthanide chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells.2016

    • Author(s)
      Yuya Hikone, Go Hirai, Masaki Mishima, Kohsuke Inomata, Teppei Ikeya, Souichiro Arai, Masahiro Shirakawa, Mikiko Sodeoka, and Yutaka Ito
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 66 Issue: 2 Pages: 99-110

    • DOI

      10.1007/s10858-016-0059-4

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A specific single-stranded DNA induces a distinct conformational change in the nucleoid-associated protein HU.2016

    • Author(s)
      Yuya Nishida, Teppei Ikeya, Tsutomu Mikawa, Jin Inoue, Yutaka Ito, Yasunori Shintani, Ryoji Masui, Seiki Kuramitsu, Seiji Takashima
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 8 Pages: 318-324

    • DOI

      10.1016/j.bbrep.2016.09.014

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Protein NMR Structure Refinement based on Bayesian Inference2016

    • Author(s)
      Teppei Ikeya, Shiro Ikeda, Takanori Kigawa, Yutaka Ito and Peter Guentert
    • Journal Title

      J. Phys.: Conf. Ser.

      Volume: 699 Pages: 012005-012005

    • DOI

      10.1088/1742-6596/699/1/012005

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] 生命分子のNMR計測・解析への応用2016

    • Author(s)
      葛西卓磨,池谷鉄兵,木川隆則
    • Journal Title

      電子情報通信学会

      Volume: -

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Presentation] NMR PROTEIN STRUCTURE ANALYSIS IN LIVING CELLS2017

    • Author(s)
      Teppei Ikeya, Peter Guentert, Yutaka Ito
    • Organizer
      The 5th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Place of Presentation
      東京大学 (東京)
    • Year and Date
      2017-01-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] NMRによるマルチドメイン蛋白質Drkの動態解析2017

    • Author(s)
      末元雄介,井上仁,新井崇一郎,鴨志田一,三島正規,猪股晃介,葛西卓磨,木川隆則,池谷鉄兵,伊藤隆
    • Organizer
      第17回日本蛋白質科学会年会, 仙台国際センター
    • Related Report
      2017 Annual Research Report
  • [Presentation] Protein structure determination in living eukaryotic cells by in-cell NMR spectroscopy2017

    • Author(s)
      Yusuke Suemoto, Takashi Tanaka, Hajime Kamoshida, Jin Inoue, Masaki Mishima, Peter Guentert, Teppei Ikeya and Yutaka Ito
    • Organizer
      19th International Union of Pure and Applied Biophysics (IUPAB) and 11th European Biophysical Societies' Association (EBSA) Congress, Edinburgh International Conference Centre, Edinburugh, UK
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structure determination of the locally disordered state of ubiquitin by high-pressure NMR spectroscopy2017

    • Author(s)
      Takuro Wakamoto, Soichiro Kitazawa, Teppei Ikeya, Tomoshi Kameda, Christian Roumestand, Nicola J. Baxter, Mike P. Williamson, Ryo Kitahara
    • Organizer
      ISMAR2017, Canada,Quebec
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NMRによるマルチドメイン蛋白質Drkの動態解2017

    • Author(s)
      末元雄介,井上仁,新井崇一郎,三島正規,猪股晃介,葛西卓磨,木川隆則,池谷鉄兵,伊藤隆
    • Organizer
      第18回若手NMR研究会, かんぽの宿紀伊田辺
    • Related Report
      2017 Annual Research Report
  • [Presentation] Protein structural refinement using paramagnetic effects in solution NMR2017

    • Author(s)
      岡田真由,池谷鉄兵,Rajesh Sundaresan,野尻英里,美川務,伊藤隆
    • Organizer
      第18回若手NMR研究会, かんぽの宿紀伊田辺
    • Related Report
      2017 Annual Research Report
  • [Presentation] NMRデータの自動解析および蛋白質立体構造計算の現状と創薬研究への応用の可能性2017

    • Author(s)
      池谷鉄兵
    • Organizer
      よこはまNMR研究会, 理研横浜キャンパス
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 常磁性効果を用いた溶液NMR法による蛋白質 の立体構造解析2017

    • Author(s)
      岡田真由,池谷鉄兵,Rajesh Sundaresan,野尻英里,美川務,伊藤隆
    • Organizer
      第56回NMR討論会, 首都大学東京・南大沢キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] NMRによるマルチ ドメイン蛋白質Drkの動態解析2017

    • Author(s)
      末元雄介,井上仁,鴨志田一,三島正規,猪股晃介,葛西卓磨,木川隆則,池谷鉄兵,伊藤隆
    • Organizer
      第56回NMR討論会, 首都大学東京・南大沢キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] ヒト培養細胞中の蛋白質の3D三重共鳴NMR測定2017

    • Author(s)
      鴨志田一,池谷鉄兵,三島正規,伊藤隆
    • Organizer
      第56回NMR討論会, 首都大学東京・南大沢キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] リン酸化ユビキチンの2つのコンフォメーションの立体構造 決定と圧力効果2017

    • Author(s)
      北沢創一郎, 青島佑, 伊賀 惇記, 池谷鉄兵, 北原亮
    • Organizer
      第56回NMR討論会, 首都大学東京・南大沢キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] 高圧力NMR法によるユビキチンの局所変性状態の立体構造決定2017

    • Author(s)
      若本拓朗,北沢創一郎, 池谷鉄兵, 亀田倫史,Roumestand Christian, Baxter Nichola, Willamson Mike, 北原亮
    • Organizer
      第56回NMR討論会, 首都大学東京・南大沢キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] スパースモデリングによるNMR計測・解析の高速高精度化2017

    • Author(s)
      葛西卓磨,池谷鉄兵,木川隆則
    • Organizer
      新学術領域「スパース モデリングの深化と高次元データ駆動科学の創成」第5回公開シンポジウム, 東京大学・本郷キャンパス
    • Related Report
      2017 Annual Research Report
  • [Presentation] In-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      池谷鉄兵,Peter Guentert, 伊藤隆
    • Organizer
      「ライフサイエンスの革新を目指した構造生命科学と先端的基盤技術」CREST・さきがけ合同領域会議
    • Place of Presentation
      京都国際会館 (京都)
    • Year and Date
      2016-12-14
    • Related Report
      2016 Research-status Report
  • [Presentation] スパースNMRデータを用いた細胞内蛋白質立体構造決定2016

    • Author(s)
      池谷 鉄兵, 池田 思朗, 木川 隆則, 伊藤 隆, Guentert Peter
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場 (茨城県・つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells2016

    • Author(s)
      彦根佑哉,平井剛,三島正規,猪股晃介,池谷鉄兵,新井崇一郎,白川昌宏,袖岡幹子,伊藤隆
    • Organizer
      第55回NMR討論会
    • Place of Presentation
      広島国際会議場 (広島)
    • Year and Date
      2016-11-16
    • Related Report
      2016 Research-status Report
  • [Presentation] In-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      Teppei Ikeya
    • Organizer
      The 42nd Naito Conference “In the Vanguard of Structural Biology: Revolutionizing Life Sciences”
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ (北海道・札幌)
    • Year and Date
      2016-10-04
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] In-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Guentert, Yutaka Ito
    • Organizer
      International Conference on Magnetic Resonance in Biological Systems 2016
    • Place of Presentation
      京都国際会館 (京都)
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells2016

    • Author(s)
      Yuya Hikone, Go Hirai, Masaki Mishima, Kohsuke Inomata, Teppei Ikeya, Souichiro Arai, Masahiro Shirakawa, Mikiko Sodeoka, Yutaka Ito
    • Organizer
      International Conference on Magnetic Resonance in Biological Systems 2016
    • Place of Presentation
      京都国際会館 (京都)
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Structure and dynamics of the locally disordered state of ubiqutin studied by high pressure NMR spectroscopy2016

    • Author(s)
      Takuro Wakamoto, Soichiro Kitazawa, Teppei Ikeya, Tomoshi Kameda, Maho Yagi-Utsumi, Koichi Kato, Christian Roumestand, Nicola J. Baxter, P.Mike Williamson, Ryo Kitahara
    • Organizer
      International Conference on Magnetic Resonance in Biological Systems 2016
    • Place of Presentation
      京都国際会館 (京都)
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] NMR snapshots of a fluctuating ubiquitin structure2016

    • Author(s)
      Soichiro Kitazawa, Takuro Wakamoto, Teppei Ikeya, Tomoshi Kameda, Maho Yagi-Utsumi, Koichi Kato, Christian Roumestand, Nicola J. Baxter, Mike P. Williamson, Ryo Kitahara
    • Organizer
      EUROMAR 2016
    • Place of Presentation
      Aarhus Concert Hall (Aarhus・Denmark)
    • Year and Date
      2016-07-03
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 生細胞内の秩序と蛋白質構造安定性の解明に向けた基盤技術2016

    • Author(s)
      池谷鉄兵
    • Organizer
      新学術領域「動的秩序と機能」第3回領域会議
    • Place of Presentation
      長浜ロイヤルホテル(滋賀県・長浜)
    • Year and Date
      2016-06-11
    • Related Report
      2016 Research-status Report
  • [Presentation] Structure determination of the locally disordered state of ubiquitin by high pressure NMR spectroscopy2016

    • Author(s)
      Takuro Wakamoto, Soichiro Kitazawa, Teppei Ikeya, Tomoshi Kameda, Nicola J. Baxter, Mike P. Williamson, Ryo Kitahara
    • Organizer
      第16回日本蛋白質科学会
    • Place of Presentation
      福岡国際会議場 (福岡)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 生命分子計測のスパースモデリング :限られた計測データから生命分子の構造情報を引き出す2016

    • Author(s)
      池谷鉄兵, 木川隆則
    • Organizer
      第16回日本蛋白質科学会
    • Place of Presentation
      福岡国際会議場 (福岡)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
  • [Presentation] スパースモデリングによるNMR計測・解析の高速高精度化2016

    • Author(s)
      木川隆則,葛西卓磨,池谷鉄兵
    • Organizer
      疎水モデリング 2015年度公開シンポジウム
    • Place of Presentation
      神戸
    • Year and Date
      2016-03-07
    • Related Report
      2015 Research-status Report
  • [Presentation] Improved in-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      Teppei Ikeya
    • Organizer
      UK-Japan Symposium “From single molecules to cells and tissues”
    • Place of Presentation
      University of Leicester (Leicester・UK)
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] スパースモデリングによるNMR計測・解析の高速高精度化2016

    • Author(s)
      木川隆則, 葛西卓磨, 池谷鉄兵
    • Organizer
      新学術領域「疎性モデリング」第四回領域会議
    • Place of Presentation
      東京大学 (東京)
    • Related Report
      2016 Research-status Report
  • [Presentation] Protein NMR Structure Refinement based on Bayesian Inference2015

    • Author(s)
      Teppei Ikeya, Shiro Ikeda, Takanori Kigawa, Yutaka Ito, Peter Guentert
    • Organizer
      High-Dimensional Data Driven Science
    • Place of Presentation
      京都
    • Year and Date
      2015-12-14
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ヒト培養細胞を用いた異種核多次元in-cell NMR測定2015

    • Author(s)
      鴨志田一,井上仁,猪俣晃介,池谷鉄兵, 三島 正規,伊藤隆
    • Organizer
      第38回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Year and Date
      2015-12-01
    • Related Report
      2015 Research-status Report
  • [Presentation] Three-dimensional protein structure and dynamics in living cells2015

    • Author(s)
      Teppei Ikeya, Jin Inoue, Peter Guentert, Yutaka Ito
    • Organizer
      動的秩序と生命 第4回国際シンポジウム
    • Place of Presentation
      福岡
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
  • [Presentation] Sf9細胞のin-cell NMRによる蛋白質の立体構造解析の試み2015

    • Author(s)
      田中孝,池谷鉄兵,濱津順平,三島正規,Peter Guentert,伊藤隆
    • Organizer
      第53回NMR討論会
    • Place of Presentation
      千葉
    • Year and Date
      2015-11-06
    • Related Report
      2015 Research-status Report
  • [Presentation] HeLa細胞およびSf9細胞のin-cell NMR測定のためのバイオリアクターシステムの検討2015

    • Author(s)
      石川真帆,鴨志田一,田中孝,池谷鉄兵,三島正規,伊藤隆
    • Organizer
      第54回NMR討論会
    • Place of Presentation
      千葉
    • Year and Date
      2015-11-06
    • Related Report
      2015 Research-status Report
  • [Presentation] ヒト培養細胞を用いた異種核3次元in-cell NMR測定2015

    • Author(s)
      鴨志田一,井上仁,猪俣晃介,新井祟一郎,池谷鉄兵, 三島 正規,伊藤隆
    • Organizer
      第54回NMR討論会
    • Place of Presentation
      千葉
    • Year and Date
      2015-11-06
    • Related Report
      2015 Research-status Report
  • [Presentation] 複数の正則化項を用いた圧縮センシングによるNMRスペクトルの再構成2015

    • Author(s)
      Kazuya Sumikoshi, Teppei Ikeya, Yutaka Ito, Kentaro Shimizu
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] ヒト培養細胞を用いた異種核多次元in-cell NMR測定2015

    • Author(s)
      鴨志田一,井上仁,猪俣晃介,池谷鉄兵, 三島 正規,伊藤隆
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      徳島
    • Year and Date
      2015-06-24
    • Related Report
      2015 Research-status Report
  • [Presentation] ベイズ推定を用いた立体構造計算と in-cell NMR データへのアプローチ2015

    • Author(s)
      池谷鉄兵
    • Organizer
      In-cell NMR シンポジウム
    • Place of Presentation
      東京 秋葉原
    • Year and Date
      2015-04-24
    • Related Report
      2015 Research-status Report
    • Invited
  • [Book] Experimental Approaches of NMR Spectroscopy2018

    • Author(s)
      Teppei Ikeya and Yutaka Ito
    • Publisher
      Springer
    • ISBN
      9789811059667
    • Related Report
      2017 Annual Research Report

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Published: 2015-04-16   Modified: 2022-02-16  

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