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Initiative for faster and more precise NMR data measurement and analysis with sparse modeling

Planned Research

Project AreaInitiative for High-Dimensional Data-Driven Science through Deepening of Sparse Modeling
Project/Area Number 25120003
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 InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Kigawa Takanori  国立研究開発法人理化学研究所, 生命システム研究センター, チームリーダー (20270598)

Co-Investigator(Kenkyū-buntansha) 池谷 鉄兵  首都大学東京, 理工学研究科, 助教 (30457840)
Co-Investigator(Renkei-kenkyūsha) Kasai Takuma  国立研究開発法人理化学研究所, 生命システム研究センター, 研究員 (70446516)
Project Period (FY) 2013-06-28 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥72,540,000 (Direct Cost: ¥55,800,000、Indirect Cost: ¥16,740,000)
Fiscal Year 2017: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Fiscal Year 2016: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Fiscal Year 2015: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Fiscal Year 2014: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Fiscal Year 2013: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000)
Keywordsスパースモデリング / NMR / 圧縮センシング / スペクトル解析 / ベイズ統計 / レプリカ交換モンテカルロ法 / テンソル分解 / 安定同位体標識
Outline of Final Research Achievements

In this project, focusing on the sparseness of NMR data and structure information of biomolecule, we have aimed to achieve faster and more precise NMR measurement and analysis of biomolecules by solving the issues arising from complexity and complicatedness of NMR analysis with the sparse modeling. In the subproject 1, we have successfully developed the spectrum reconstruction method with high reproducibility. In the subproject 2, decoding process of “SiCode” was dramatically improved by concurrently deconvoluting spectra and identifying amino-acid assignment. In the subproject 3, the method for faster and more precise biomolecular structure calculation was established by using Bayesian inference, and was successfully applied to de novo structure determination of proteins in living eukaryotic cells. In later introduced subproject 4, we have successfully developed a novel method enabling concurrent signal identification and structural dynamics analysis.

Report

(6 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (56 results)

All 2018 2017 2016 2015 2014 2013

All Journal Article (13 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 11 results,  Open Access: 9 results,  Acknowledgement Compliant: 4 results) Presentation (42 results) (of which Int'l Joint Research: 18 results,  Invited: 29 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Protein NMR Structure Refinement based on Bayesian Inference for dynamical ordering of biomacromolecules2018

    • Author(s)
      T.Ikeya, Y. Ito
    • Journal Title

      J. Comput. Chem. Jpn.

      Volume: 印刷中

    • NAID

      130006555815

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [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] Advances in stable isotope assisted labeling strategies with information science2017

    • Author(s)
      Kigawa Takanori
    • Journal Title

      Archives of Biochemistry and Biophysics

      Volume: 628 Pages: 17-23

    • DOI

      10.1016/j.abb.2017.06.014

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Impact of cellular health conditions on the protein folding state in mammalian cells2017

    • Author(s)
      Inomata Kohsuke、Kamoshida Hajime、Ikari Masaomi、Ito Yutaka、Kigawa Takanori
    • Journal Title

      Chemical Communications

      Volume: 53 Issue: 81 Pages: 11245-11248

    • DOI

      10.1039/c7cc06004a

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 無細胞タンパク質合成系による安定同位体標識利用NMR解析 - 情報科学を融合した標識技術 : SiCode2017

    • Author(s)
      木川 隆則
    • Journal Title

      医学のあゆみ

      Volume: 262 Pages: 461-466

    • Related Report
      2017 Annual Research Report
  • [Journal Article] NMR Analyses of Proteins with Stable Isotope Labeling Based on Information Sciences2017

    • Author(s)
      葛西卓磨、木川隆則
    • Journal Title

      Seibutsu Butsuri

      Volume: 57 Issue: 3 Pages: 153-156

    • DOI

      10.2142/biophys.57.153

    • NAID

      130005678945

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [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

      電子情報通信学会誌

      Volume: 99 Pages: 439-443

    • Related Report
      2016 Annual Research Report
  • [Journal Article] NMR spectral analysis using prior knowledge2016

    • Author(s)
      Takuma Kasai, Kenji Nagata, Masato Okada, Takanori Kigawa
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 699 Pages: 012003-012003

    • DOI

      10.1088/1742-6596/699/1/012003

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [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
      2016 Annual Research 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 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Stable isotope labeling strategy based on coding theory.2015

    • Author(s)
      Kasai T, Koshiba S, Yokoyama J, Kigawa T
    • Journal Title

      J. Biomol. NMR

      Volume: 63 Issue: 2 Pages: 213-221

    • DOI

      10.1007/s10858-015-9978-8

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Influence of incomplete NOESY peaks of the interface residues on structure determinations of homodimeric proteins.2014

    • Author(s)
      Lin, Y. J., Ikeya, T., Kirchner, D. K. & Guentert, P.
    • Journal Title

      J. Chin. Chem. Soc.

      Volume: 61 Issue: 12 Pages: 1297-1306

    • DOI

      10.1002/jccs.201400095

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] タンパク質試料への情報の符号化を用いたNMR解析法2018

    • Author(s)
      葛西卓磨
    • Organizer
      2018年電子情報通信学会総合大会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Protein production platform for rational design engineering2018

    • Author(s)
      Kigawa Takanori
    • Organizer
      PepTalk 2018
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Selective isotope labeling strategy and computational interpretation of spectra for protein NMR analyses2017

    • Author(s)
      Kasai Takuma
    • Organizer
      International Meeting on “High-Dimensional Data-Driven Science” (HD3-2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Rapid production in milligram quantities of a hundred kinds of newly generated mutant proteins2017

    • Author(s)
      Kasai Takuma
    • Organizer
      PEGS2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 困難な条件でのタンパク質NMR解析のための情報科学を活用した安定同位体標識法2017

    • Author(s)
      葛西卓磨
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Stable isotope labeling strategy based on information science applied to in-cell NMR2017

    • Author(s)
      Kasai Takuma
    • Organizer
      ISMAR 2017 (20th Meeting of the International Society of Magnetic Resonance)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 低感度NMRスペクトルから情報を得るための安定同位体標識法のin-cell NMRへの応用2017

    • Author(s)
      葛西卓磨
    • Organizer
      日本生物物理学会第55回年会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] in-cell NMRなど困難な実験系を対象としたアミノ酸選択的安定同位体標識法2017

    • Author(s)
      葛西卓磨
    • Organizer
      第56回NMR討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 細胞環境での分子構造動態の理解に向けて2016

    • Author(s)
      木川隆則
    • Organizer
      シンポジウム「細胞環境における蛋白質の動態解析のためのNMRおよび計算科学的アプローチ」
    • Place of Presentation
      京都大学吉田キャンパス・(京都府・京都市)
    • Year and Date
      2016-03-28
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 分子構造動態の細胞内リアルタイムモニタリングに向けて2016

    • Author(s)
      木川隆則
    • Organizer
      よこはまNMR研究会第55回ワークショップ「リアルタイムモニタリング」
    • Place of Presentation
      理化学研究所横浜キャンパス・(神奈川県・横浜市)
    • Year and Date
      2016-03-23
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] In-cell NMR of intracellular signaling proteins2016

    • Author(s)
      Kigawa Takanori
    • Organizer
      The 5th International Symposium on Drug Discovery and Design by NMR
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protein dynamics in cellular environment analyzed by stable isotope-aided NMR spectroscopy2016

    • Author(s)
      Kigawa Takanori
    • Organizer
      The 42nd Naito Conference
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Improved in-cell structure determination of proteins at near-physiological concentration2016

    • Author(s)
      Ikeya Teppei
    • Organizer
      UK/Japan international Symposium
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] NMRスペクトルから正しい情報を得るための変数探索による解析法2016

    • Author(s)
      葛西卓磨
    • Organizer
      第16回日本蛋白質科学会年会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Protein NMR structure determination for sparse data set derived from living cells2016

    • Author(s)
      池谷鉄兵
    • Organizer
      第54回日本生物物理学会年会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 情報科学を活用したシグナル帰属法のin-cell NMRへの応用2016

    • Author(s)
      葛西卓磨
    • Organizer
      第55回NMR討論会
    • Related Report
      2016 Annual Research Report
  • [Presentation] タンパク質のNMR解析が困難な系にも有効なシグナル帰属法2016

    • Author(s)
      葛西卓磨
    • Organizer
      第54回日本生物物理学会年会
    • Related Report
      2016 Annual Research Report
  • [Presentation] Structure and dynamics analyses of proteins in cellular environment with advanced stable-isotope labeling2016

    • Author(s)
      木川隆則
    • Organizer
      第39回日本分子生物学会年会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] NMR spectral analysis using prior knowledge2015

    • Author(s)
      葛西卓磨
    • Organizer
      International Meeting on “High-Dimensional Data Driven Science” (HD3-2015)
    • Place of Presentation
      メルパルク京都・(京都府・京都市)
    • Year and Date
      2015-12-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protein NMR Structure Refinement based on Bayesian Inference2015

    • Author(s)
      Teppei Ikeya
    • Organizer
      International Meeting on “High-Dimensional Data Driven Science” (HD3-2015)
    • Place of Presentation
      メルパルク京都・(京都府・京都市)
    • Year and Date
      2015-12-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protein dynamics in molecular crowding environment elucidated by an extended model-free analysis of NMR relaxation data2015

    • Author(s)
      木川隆則
    • Organizer
      BMB2015
    • Place of Presentation
      神戸ポートアイランド・(兵庫県・神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Three-dimensional protein structure and dynamics in living cells2015

    • Author(s)
      Teppei Ikeya
    • Organizer
      動的秩序と生命 第4回国際シンポジウム
    • Place of Presentation
      九州大学西新プラザ・(福岡県・福岡市)
    • Year and Date
      2015-11-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 安定同位体標識率等の事前知識を活用するNMRスペクトル解析法2015

    • Author(s)
      葛西卓磨
    • Organizer
      第54回NMR討論会
    • Place of Presentation
      千葉工業大学津田沼キャンパス・(千葉県・習志野市)
    • Year and Date
      2015-11-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] NMRデータ解析法の改良による効率的な細胞内蛋白質構造決定2015

    • Author(s)
      池谷鉄兵
    • Organizer
      第54回NMR討論会
    • Place of Presentation
      千葉工業大学津田沼キャンパス・(千葉県・習志野市)
    • Year and Date
      2015-11-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] NMR Analysis of Protein Structure and Dynamics with Computational and Information Sciences.2015

    • Author(s)
      木川隆則
    • Organizer
      29th Annual Symposium of the Protein Society
    • Place of Presentation
      Barcelona・Spain
    • Year and Date
      2015-07-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 符号化標識法を用いたNMRシグナル帰属戦略2015

    • Author(s)
      葛西卓磨
    • Organizer
      in-cell NMRシンポジウム “Computational aspects in biomolecular & in-cell NMR”
    • Place of Presentation
      首都大学東京秋葉原サテライトキャンパス・(東京都・千代田区)
    • Year and Date
      2015-04-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [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 “Computational aspects in biomolecular & in-cell NMR”
    • Place of Presentation
      首都大学東京秋葉原サテライトキャンパス・(東京都・千代田区)
    • Year and Date
      2015-04-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Stable Isotope Labeling Strategy Based on Coding Theory2015

    • Author(s)
      Takanori Kigawa
    • Organizer
      The 4th International Symposium on Drug Discovery and Design by NMR
    • Place of Presentation
      理化学研究所横浜キャンパス・(神奈川県・横浜市)
    • Year and Date
      2015-02-05
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SiCode: A novel stable isotope labeling strategy suitable for difficult targets2014

    • Author(s)
      Takanori Kigawa
    • Organizer
      International NMR Symposium on Pharmaceutical NMR
    • Place of Presentation
      大阪大学蛋白質研究所・(大阪府・吹田市)
    • Year and Date
      2014-12-20
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Three-Dimensional Protein Structure and Dynamics in Living Cells2014

    • Author(s)
      Teppei Ikeya
    • Organizer
      7th Korea-Japan Seminars on Biomolecular Sciences
    • Place of Presentation
      Soul・Korea
    • Year and Date
      2014-11-27
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Protein dynamics in molecular crowding environment analyzed by stable isotope-aided NMR spectroscopy2014

    • Author(s)
      Takanori Kigawa
    • Organizer
      International Conference on Analytical Science & Technology
    • Place of Presentation
      Daejeon・Korea
    • Year and Date
      2014-11-20
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生きた細胞内での蛋白質の立体構造とダイナミクス2014

    • Author(s)
      池谷鉄兵
    • Organizer
      構造活性相関シンポジウム
    • Place of Presentation
      くまもと森都心プラザ・(熊本県・熊本市)
    • Year and Date
      2014-11-13
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ベイズ推定を利用したNMR蛋白質構造最適化法の開発2014

    • Author(s)
      池谷鉄兵
    • 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
      2014-11-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] 誤り検出符号によるノイズに強いアミノ酸選択標識法2014

    • Author(s)
      葛西卓磨
    • 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
  • [Presentation] Analysis of protein dynamics under molecular crowding environment by using stable isotope aided NMR spectroscopy2014

    • Author(s)
      Takanori Kigawa
    • Organizer
      In-cell NMRシンポジウム Protein biophysics under physiological condition
    • Place of Presentation
      首都大学東京国際交流会館・(東京都・八王子市)
    • Year and Date
      2014-09-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ベイズ推定を用いた NMR 立体構造計算法の開発2014

    • Author(s)
      Teppei Ikeya
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター・(北海道・札幌市)
    • Year and Date
      2014-09-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 生きた細胞中の天然変性蛋白質の動態2014

    • Author(s)
      池谷鉄兵
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター・(北海道・札幌市)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] タンパク質の立体構造計算におけるNMRデータの可視化2014

    • Author(s)
      池谷鉄兵
    • Organizer
      日本分光学会NMR分科会 2014
    • Place of Presentation
      東京大学・薬学部・(東京都・文京区)
    • Year and Date
      2014-09-11
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A refinement method for NMR protein structure determination based on Bayesian inference2014

    • Author(s)
      Teppei Ikeya
    • Organizer
      XXVIth ICMRBS
    • Place of Presentation
      Dalas・USA
    • Year and Date
      2014-08-29
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cell-Free Protein Synthesis and Stable Isotope Labeling2014

    • Author(s)
      Takanori Kigawa
    • Organizer
      XXVIth ICMRBS
    • Place of Presentation
      Dalas・USA
    • Year and Date
      2014-08-27
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Amino-acid Selective Stable Isotope Labeling Strategy Based on the Coding Theory2014

    • Author(s)
      Takuma Kasai
    • Organizer
      XXVIth ICMRBS
    • Place of Presentation
      Dalas・USA
    • Year and Date
      2014-08-25
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A NMR structure calculation algorithm based on Bayesian inference2014

    • Author(s)
      池谷鉄兵
    • Organizer
      大阪大学蛋白質研究所セミナー IPR Seminar
    • Place of Presentation
      名古屋大学東山キャンパス・(愛知県・名古屋市)
    • Year and Date
      2014-06-19
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Patent(Industrial Property Rights)] タンパク質解析装置、タンパク質解析方法、および、プログラム2013

    • Inventor(s)
      木川隆則、葛西卓磨
    • Industrial Property Rights Holder
      研究開発法人理化学研究所
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013
    • Acquisition Date
      2017
    • Related Report
      2017 Annual Research Report

URL: 

Published: 2013-07-10   Modified: 2019-03-29  

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