Development of automating completely NMR structure system that uses SAIL protein

• Project/Area Number: 18207007
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tokyo Metropolitan University (2007-2008); The Institute of Physical and Chemical Research (2006)
• Principal Investigator: PETER Guentert Tokyo Metropolitan University, 戦略研究センター, 客員教授 (20392110)
• Co-Investigator(Kenkyū-buntansha): JEE Jungoo 首都大学東京, 戦略研究センター, 准教授 ; 池 [ジュン]求 首都大学東京, 戦略研究センター, 准教授 (50381554)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥49,010,000 (Direct Cost: ¥37,700,000、Indirect Cost: ¥11,310,000); Fiscal Year 2008: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000); Fiscal Year 2007: ¥14,950,000 (Direct Cost: ¥11,500,000、Indirect Cost: ¥3,450,000); Fiscal Year 2006: ¥20,930,000 (Direct Cost: ¥16,100,000、Indirect Cost: ¥4,830,000)
• Keywords: NMR / SAIL法 / NMRデータの自動帰属 / 構造計算 / NMRデータ自動解析 / タンパク質立体構造計算

Research Abstract

SAIL-FLYA法は、NMR法でのタンパク質の三次元立体構造を、人手による介在をまったく必要とせずに高精度に決定できる全自動解析システムである。SAIL-FLYA法を用いれば、従来法で必要とされるNMRスペクトルより格段に少ないデータ数でも、正確な構造決定が可能となる。本研究では、このシステムを開発、改良を加え、比較的低分子量のタンパク質であるユビキチンを例としてその性能評価を行った。加えて、さらなる性能向上のために、CYANA計算法の改良、及びFLYA法に適用可能な新たな自動化学シフト帰属法の開発等も行った。また、従来難しいかったタンパク質にSAIL-CYANA法を適用し、その構造決定に成功した。

Research Products

• [Journal Article] Protein structure determination in living cells by in-cell NMR spectroscopy (2009)
  • Author(s): Sakakibara, D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Walchli, M., Smith, B.O., Shirakawa, M., Guntert, P. & Ito, Y.
  • Journal Title: Nature 458 Pages: 102-105
• [Journal Article] Solution structure of the cysteine-rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily (2009)
  • Author(s): He, F., Dang, W., Saito, K., Watanabe, S., Kobayashi, N., Guntert, P., Kigawa, T, Tanaka, A., Muto, Y. & Yokoyama, S.
  • Journal Title: Protein Sci 18 Pages: 650-656
• [Journal Article] The βE-domain of Ec-1 metallothionein : A metal-binding domain with a distinctive structure (2009)
  • Author(s): Peroza, E. A., Schmucki, R., Guntert, P., Freisinger, E. & Zerbe O.
  • Journal Title: J. Mol. Biol 387 Pages: 207-218
• [Journal Article] Solution structure of the RNA binding domain in the human muscleblind-like protein 2. (2009)
  • Author(s): He, F., Dang, W., Abe, C., Tsuda, K., Inoue, M., Watanabe, S., Kobayashi, N., Kigawa, T, Matsuda, T., Yabuki, T., Aoki, M., Seki, E., Harada, T., Tomabechi, Y., Terada, T., Shirouzu, M., Tanaka, A., Guntert, P., Muto, Y. & Yokoyama, S.
  • Journal Title: Protein Sci 18 Pages: 80-91
• [Journal Article] Automated structure determination from NMR Spectra (2009)
  • Author(s): Guntert, P.
  • Journal Title: Eur. Biophys 38 Pages: 129-143
• [Journal Article] Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm (2009)
  • Author(s): Schmucki, R., Yokoyama, S. & Guntert, P.
  • Journal Title: J. Biomol. NMR. 43 Pages: 97-109
• [Journal Article] Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions (2009)
  • Author(s): Ohnishi, S., Paakkonen, K., Koshiba, S., Tochio, N., Sato, M., Kobayashi, N., Harada, T., Watanabe, S., Muto, Y., Guntert, P., Tanaka, A., Kigawa, T., & Yokoyama, S.
  • Journal Title: Proteins 74 Pages: 133-144
• [Journal Article] Protein structure determination in living cells by in-cell NMR spectroscopy. (2009)
  • Author(s): Sakakibara, D., Sasaki, A., Ikeya, T., Hamatsu, J., Hanashima, T., Mishima, M., Yoshimasu, M., Hayashi, N., Mikawa, T., Walchli, M., Smith, B, O., Shirakawa, M., Guntert, P. & Ito, Y.
  • Journal Title: Nature 458 Pages: 102-105
  • Peer Reviewed
• [Journal Article] Automated assignment of NMR chemical shifts using peak-partide dynamics simulation with the DYNASSIGN algorithm. (2009)
  • Author(s): Schmucki, R., Yokoyama, S. & Guntert, P.
  • Journal Title: J. Biomol. NMR 43 Pages: 97-109
  • Peer Reviewed
• [Journal Article] Structure of the putative 32 kDa myrosinase binding protein from Arabidopsis (At3g16450.1)as determined by the SAIL-NMR method (2008)
  • Author(s): Takeda, M., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A. M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Jee, J., Guntert, P., Aceti, D.J., Markley, J.L. & Kainosho, M.
  • Journal Title: FEBS J. 275 Pages: 5873-5884
• [Journal Article] Structural basis of the role of the NikA ribbon-helix-helix domain in initiating bacterial conjugation (2008)
  • Author(s): Yoshida, H., Furuya, N., Lin, Y. J., Guntert, P., Komano, T. & Kainosho, M.
  • Journal Title: J. Mol. Biol 384 Pages: 690-701
• [Journal Article] Solution structure of the extraterminal domain of the bromodomain-containing protein BRD4. (2008)
  • Author(s): Lin, Y.J., Umehara, T., Inoue, M., Saito, K., Kigawa, T., Jang, M. K., Ozato, K., Yokoyama, S., Padmanabhan, B., Guntert, P.
  • Journal Title: Protein Sci. 17 Pages: 2174-2179
• [Journal Article] Structural basis for the selectivity of the external thioesterase of the surfactin-synthetase (2008)
  • Author(s): Koglin, A., Lohr, F., Bernhard, F., Rogov, V.R., Frueh, D.P., Strieter, E.R., Mofid, M.R., Guntert, P., Wagner, G., Walsh, C.T., Marahiel, M.A. & Dotsch, V.
  • Journal Title: Nature 454 Pages: 907-911
• [Journal Article] The RRM domain of poly(A)-specific ribonuclease(PARN)has a non-canonical binding site for mRNA cap analog recognition (2008)
  • Author(s): Nagata, T., Suzuki, S., Endo, R., Shirouzu, M., Terada, T., Inoue, M., Kigawa, T, Guntert, P., Hayashizaki, Y., Muto, Y. & Yokoyama, S.
  • Journal Title: Nucl. Acids Res 36 Pages: 4754-4767
• [Journal Article] Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method (2008)
  • Author(s): Takeda, M., Chang, C.K., Ikeya, T., Guntert, P., Chang, Y.H., Hsu, Y.L., Huang, T.H. & Kainosho, M.
  • Journal Title: J. Mol. Biol 380 Pages: 608-622
• [Journal Article] Transmembrane segment enhanced labeling as a tool for the backbone assignment of helical membrane proteins (2008)
  • Author(s): Reckel, S., Sobhanifar, S., Schneider, B., Junge, F., Schwarz, D., Durst, F., Lohr, F., Guntert, P., Bernhard, F. & Dotsch, V.
  • Journal Title: Proc. Natl. Acad. Sci. USA 105 Pages: 8262-8267
• [Journal Article] Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode (2008)
  • Author(s): Kuwasako, K., Takahashi, M., Tochio, N., Abe, C., Tsuda, K., Inoue, M., Terada, T., Shirouzu, M., Kobayashi, N., Kigawa, T., Taguchi, S., Tanaka, A., Hayashizaki, Y., Guntert, P., Muto, Y. & Yokoyama, S.
  • Journal Title: Biochemistry 47 Pages: 6437-6450
• [Journal Article] Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses. (2008)
  • Author(s): Kuwasako, K., Dohmae, N., Inoue, M., Shirouzu, M., Taguchi, S., Guntert, P., Seraphin, B., Muto, Y. & Yokoyama, S.
  • Journal Title: Proteins 71 Pages: 1617-1636
• [Journal Article] Structure of the putative 32 kDa myrosinase binding protein from Arabidopsis (At3gl6450.1)as determined by the SAIL-NMR method. (2008)
  • Author(s): Takeda, M., Sugimori, N, Torizawa, T., Terauchi, T., Ono, A. M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Jee, J., Guntert, P., Aceti, D. J, Markley, J. L. & Kainosho, M.
  • Journal Title: FEBS J. 275 Pages: 5873-5884
  • Peer Reviewed
• [Journal Article] Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method. Implications for RNA packaging as revealed by nucleic acid interactions (2008)
  • Author(s): Takeda, M., Chang, C. K., Ikeya, T., Guntert, P., Chang, Y. H., Hsu, Y. L., Huang, T. H. & Kainosho, M.
  • Journal Title: Journal of Molecular Biology (in press)
  • Peer Reviewed
• [Journal Article] NMRによる蛋白質構造決定の自動化.In計算シミュレーションと分析データ解析 (2007)
  • Author(s): Ikeya, T., Guntert, P. & Kainosho, M.
  • Journal Title: Maruzen(inJapanese)(Tokyo) Pages: 148-166
• [Journal Article] Automated structure determination of proteins with the SAIL-FLYA NMR method (2007)
  • Author(s): Takeda, M., Ikeya, T., Guntert, P. & Kainosho, M.
  • Journal Title: Nature Protocols 2 Pages: 2896-2902
• [Journal Article] a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies (2007)
  • Author(s): Kobayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Guntert, P., Kigawa, T. & Yokoyama, S. KUJIRA
  • Journal Title: J. Biomol. NMR 39 Pages: 31-52
• [Journal Article] Structural insight into dimeric interaction of the SARAH domains from Mst1 and RASSF family proteins in the apoptosis pathway (2007)
  • Author(s): Hwang, E., Ryu, K.S., Paakkonen, K., Guntert, P., Cheong, H.K., Lim, D.S., Lee, J.O., Jeon, Y.H. & Cheong, C
  • Journal Title: Proc. Natl. Acad. Sci. USA 104 Pages: 9236-9241
• [Journal Article] Solution structure of an atypical WW domain in a novel β-clam-like dimeric form (2007)
  • Author(s): Ohnishi, S., Guntert, P., Koshiba, S., Tomizawa, T., Akasaka, R., Tochio, N., Sato, M., Inoue, M., Harada, T., Watanabe, S., Tanaka, T., Shirouzu, M., Kigawa, T. & Yokoyama, S.
  • Journal Title: FEBS Lett 581 Pages: 462-468
• [Journal Article] Automated structure determination of proteins with the SAIL-FLYA NMR method. (2007)
  • Author(s): Takeda, M., Ikeya, T., Guntert, P. & Kainosho, M.
  • Journal Title: Nature Protocols 2 Pages: 2896-2902
  • Peer Reviewed
• [Journal Article] Structural insight into dimeric interaction of the SARAH domains from Mst1 and RASSF family proteins in the apoptosis pathway (2007)
  • Author(s): Hwang, E., Ryu, K. S., Paakkonen, K., Guntert, P., Cheong, H. K., Lim, D. S., Lee, J. O., Jeon, Y. H. & Cheong, C.
  • Journal Title: Proc. Natl. Acad. Sci. USA 104 Pages: 9236-9241
  • Peer Reviewed
• [Journal Article] A photoswitchable miniprotein based on the sequence of avian pancreatic polypeptide (2006)
  • Author(s): Jurt, S., Aemissegger, A., Guntert, P., Zerbe, O. & Hilvert, D.
  • Journal Title: Angew. Chem. Int. Ed. 45 Pages: 6297-6300
• [Journal Article] Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP (2006)
  • Author(s): Kuwasako, K., He, F., Inoue, M., Tanaka, A., Sugano, S., Guntert, P., Muto, Y. & Yokoyama, S.
  • Journal Title: Structure 14 Pages: 1677-1689
• [Journal Article] Automated protein structure determination from NMR spectra (2006)
  • Author(s): Lopez-Mendez, B. & Guntert, P.
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 13112-13122
• [Journal Article] Solution structures of the first and fourth TSR domains of F-spondin (2006)
  • Author(s): Paakkonen, K., Tossavainen, H., Permi, P., Rakkolainen, H., Rauvala, H., Raulo, E., Kilpelainen, I. & Guntert, P.
  • Journal Title: Proteins 64 Pages: 665-672
• [Journal Article] 高分子量タンパク質のNMR構造決定-より速く、より正確に : タンパク質NMRの常識を覆す革新技術SAIL法 (2006)
  • Author(s): Kainosho, M. & Guntert, P.
  • Journal Title: Stereo-array isotope labeling for faster and more accurate NMR structure determinations of high molecular weight proteins Biotechnology J. (in Japanese)(Tokyo) 6 Pages: 467-470
• [Journal Article] Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra (2006)
  • Author(s): Scott, A., Lopez-Mendez, B. & Guntert, P.
  • Journal Title: Magn. Reson. Chem. 44
• [Journal Article] Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA. (2006)
  • Author(s): Ikeya, T., Terauchi, T., Guntert, P., Kainosho, M.
  • Journal Title: Magn. Reson. Chem 44
• [Journal Article] Solution structure of the antifreeze-like domain of human sialic acid synthase (2006)
  • Author(s): Hamada, T., Ito, Y., Abe, T., Hayashi, F., Guntert, P., Inoue, M., Kigawa, T., Terada, T., Shirouzu, M., Yoshida, M., Tanaka, A., Sugano, S., Yokoyama, S. & Hirota, H.
  • Journal Title: Protein Sci. 15 Pages: 1010-1016
• [Journal Article] NMR structure of the R-module-A parallel β-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase (2006)
  • Author(s): Aachmann, F.L., Svanem, B.I. G., Guntert, P., Petersen, S.B., Valla, S. & Wimmer, R.
  • Journal Title: J. Biol. Chem 281 Pages: 7350-7356
• [Journal Article] Optimal isotope labeling for NMR protein structure determinations (2006)
  • Author(s): Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Ono, A.M. & Guntert, P.
  • Journal Title: Nature 440 Pages: 52-57
• [Journal Article] Symbolic NMR product operator calculations (2006)
  • Author(s): Guntert, P.
  • Journal Title: Int. J. Quant. Chem 106 Pages: 344-350
• [Journal Article] Optimal isotope labelling for NMR protein structure determinations (2006)
  • Author(s): Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Ono, A., M., Gontert, P.
  • Journal Title: Nature 440 Pages: 52-57
• [Journal Article] Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA (2006)
  • Author(s): Ikeya, T., Terauchi, T., Guntert, P., Kainosho, M.
  • Journal Title: Magnetic Resonance in Chemistry 44
• [Journal Article] Automated protein structure determination from NMR spectra (2006)
  • Author(s): Lopez-Mendez, B., Guntert, P.
  • Journal Title: Journal of the American Chemical Society 128 Pages: 13112-13122
• [Journal Article] Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra (2006)
  • Author(s): Scott, A., Lopez-Mendez, B., Guntert, P.
  • Journal Title: Magnetic Resonance in Chemistry 44
• [Journal Article] 高分子量タンパク質のNMR構造決定-より速く、より正確に : タンパク質NMRの常識を覆す革新技術SAIL法 (2006)
  • Author(s): 甲斐荘 正恒, Guntert, P.
  • Journal Title: バイオテクノロジージャーナル 6 Pages: 467-470
• [Book] 計算シミュレーションと分析データ解析(分担執筆項目:NMRによる蛋白質構造決定の自動化) (2007)
  • Author(s): 池谷 鉄兵, Guntert Peter, 甲斐荘 正恒(分担執筆者)
  • Total Pages: 18
  • Publisher: 丸善株式会社