Selective labeling strategy, tolerant of amino-acid scrambling, for various expression systems

• Project/Area Number: 26650027
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: 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): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2014: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
• Keywords: 蛋白質 / NMR / アミノ酸選択的安定同位体標識 / 符号化標識法 / ピークフィッティング / レプリカ交換モンテカルロ法 / タンパク質 / アミノ酸選択的安定同位体標識法

Outline of Final Research Achievements

Amino-acid selective stable isotope labeling is a powerful method for signal assignment processes for protein analyses with NMR. This method relies on expression systems with suppressed amino-acid scrambling, such as cell-free protein synthesis. The basic idea of this study is to estimate change of isotope labeling ratio derived from the amino-acid scrambling as unknown parameters from NMR spectra. Such approach requires a method for searching huge parameter space. Therefore we developed a parameter-optimization method for analyses of NMR spectra of amino-acid selectively isotope labeled proteins, using replica exchange Monte Carlo. This method also enabled analyses of low signal-to-noise-ratio spectra.

Research Products

• [Journal Article] 情報科学を活用した安定同位体標識によるタンパク質NMR解析法 (2017)
  • Author(s): 葛西卓磨、木川隆則
  • Journal Title: 生物物理 Volume: 印刷中
  • NAID: 130005678945
  • Peer Reviewed / Open Access
• [Journal Article] NMR spectral analysis using prior knowledge (2016)
  • 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
  • Peer Reviewed / Open Access / 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: 電子情報通信学会誌 Volume: 99 Pages: 439-443
• [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
  • Peer Reviewed / Open Access
• [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、樋口佳恵、猪股晃介、木川隆則
  • Organizer: 第17回日本蛋白質科学会年会
  • Place of Presentation: 仙台国際センター（宮城県仙台市）
• [Presentation] Spectral analysis using prior knowledge (2016)
  • Author(s): Takuma Kasai, Kenji Nagata, Masato Okada, Takanori Kigawa
  • Organizer: The 57th Experimental Nuclear Magnetic Resonance Conference
  • Place of Presentation: Wyndham Grand Hotel（アメリカ合衆国ピッツバーグ）
  • Year and Date: 2016-04-11
  • Int'l Joint Research
• [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、永田賢二、岡田真人、木川隆則
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場（福岡県福岡市）
  • Invited
• [Presentation] Model Fitting Method for Accurate Analyses of NMR Spectra (2016)
  • Author(s): Takuma Kasai, Kenji Nagata, Masato Okada, Takanori Kigawa
  • Organizer: 27th International Conference on Magnetic Resonance in Biological Systems
  • Place of Presentation: 国立京都国際会館（京都府京都市）
  • Int'l Joint Research
• [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、樋口佳恵、猪股晃介、木川隆則
  • Organizer: 第55回NMR討論会
  • Place of Presentation: 広島国際会議場（広島県広島市）
• [Presentation] Signal assignment strategy for protein NMR under challenging conditions (2016)
  • Author(s): Takuma Kasai, Kae Higuchi, Kohsuke Inomata, Takanori Kigawa
  • Organizer: 第54回日本生物物理学会大会
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
• [Presentation] NMR spectral analysis using prior knowledge (2015)
  • Author(s): Takuma Kasai, Kenji Nagata, Masato Okada, Takanori Kigawa
  • Organizer: International Meeting on "High-Dimensional Data Driven Science"
  • Place of Presentation: メルパルク京都（京都府・京都市）
  • Year and Date: 2015-12-14
  • Int'l Joint Research / Invited
• [Presentation] NMR spectrum analysis with error detection mechanism (2015)
  • Author(s): Takuma Kasai, Takanori Kigawa
  • Organizer: International Meeting on "High-Dimensional Data Driven Science"
  • Place of Presentation: メルパルク京都（京都府・京都市）
  • Year and Date: 2015-12-14
  • 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、永田 賢二、岡田 真人、木川 隆則
  • 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
• [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: 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
  • Invited
• [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、小柴生造、横山順、木川隆則
  • 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
  • Invited
• [Presentation] Amino-acid Selective Stable Isotope Labeling Strategy Based on the Coding Theory (2014)
  • Author(s): Takuma Kasai, Seizo Koshiba, Jun Yokoyama, Takanori Kigawa
  • Organizer: International Conference on Magnetic Resonance in Biological Systems 2014
  • Place of Presentation: テキサス州ダラス（アメリカ合衆国）
  • Year and Date: 2014-08-25 – 2014-08-28