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

• Project/Area Number: 22870026
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Tokyo 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: ¥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)
• Keywords: in-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.

Research Products

• [Journal Article] Automated NMR chemical shift assignment and protein structure determination using exclusively NOESY spectra. J. Biomol (2011)
  • 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
• [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
• [Journal Article] Exclusively NOESY-based automated NMR assignment and structure determination of proteins (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: 50(2) Issue: 2 Pages: 137-146
  • DOI: 10.1007/s10858-011-9502-8
  • 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)
  • Peer Reviewed
• [Journal Article] NMR protein structure determination in living E. coli cells using nonlinear 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
• [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
• [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
  • 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
  • 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
• [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy (2012)
  • 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
• [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
• [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
• [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
• [Presentation] NMR structure refinement by torsion angle moleculer dynamics simulation using a physical force field in CYANA (2011)
  • Author(s): Masaki Mishima, Yutaka Ito and Peter Guentert
  • Organizer: ISNMR 2011
  • Place of Presentation: Yokohama
• [Presentation] Structural and dynamics studies of proteins in living cells by in-cell NMR spectroscopy (2011)
  • Author(s): Junpei Hamatsu, Takahiro Shirai, Daniel Nietlispach, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa and Yutaka Ito
  • Organizer: ISNMR 2011
  • Place of Presentation: Yokohama
• [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy (2011)
  • 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
• [Presentation] Heteronuclear multidimensional NMR spectroscopy of proteins in human cultured cells (2011)
  • 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
• [Presentation] NMR structure refinement by torsion angle moleculer dynamics Simulation using a physical force field in CYANA (2011)
  • Author(s): Teppei Ikeya, Masaki Mishima, Yutaka Ito, Peter Guentert
  • Organizer: ISNMR 2011
  • Place of Presentation: 横浜
• [Presentation] Structural and dynamics studies of proteins in living cells by in-cell NMR spectroscopy (2011)
  • Author(s): Junpei Hamatsu, Takahiro Shirai, Daniel Nietlispach, Teppei Ikeya, Masaki Mishima, Masahiro Shirakawa, Yutaka Ito
  • Organizer: ISNMR 2011
  • Place of Presentation: 横浜
• [Presentation] Structure determination of the protein G B1 domain in living cells yb in-cell NMR spectroscopy (2011)
  • 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
• [Presentation] Heteronuclear multidimensional NMR spectroscopy of proteins in human cultured cells (2011)
  • 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
• [Presentation] Automated protein structure determinations from minimal sets of spectra using FLYA (2010)
  • 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
• [Presentation] Structure and dynamics of proteins at work inside cells (2010)
  • 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
• [Presentation] NMR studies of 56 kDa E. coli periplasmic nickel binding protein NikA (2010)
  • 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
• [Presentation] Applications of nonlinear sampling scheme to 4D NOESY experiment (2010)
  • 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
• [Presentation] Structural evolution of oligomerization domains within the p53 family (2010)
  • 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
• [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
• [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
• [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
• [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
• [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
• [Presentation] NMR studies of 56 kDa E. coli nickel binding protein NikA (2010)
  • 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
• [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
• [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
• [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
• [Remarks]
  • URL: http://www.comp.tmu.ac.jp/osbc/Group_Ito/index.html
• [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