Applications, Development, and Dissemination of the SAIL-FLYA NMR Method for Fully Automated Protein Structure Analysis

• Project/Area Number: 21370045
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Tokyo Metropolitan University
• Principal Investigator: PETER Guentert 首都大学東京, 理工学研究科, 特任教授 (20392110)
• Co-Investigator(Kenkyū-buntansha): JEE Jungoo 首都大学東京, 戦略研究センター, 准教授 (50381554)
• Co-Investigator(Renkei-kenkyūsha): 甲斐荘 正恒 名古屋大学, 大学院・理学研究科構造生物学センター, GCOE特別招へい教授 (20137029)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥18,850,000 (Direct Cost: ¥14,500,000、Indirect Cost: ¥4,350,000); Fiscal Year 2011: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2010: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2009: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
• Keywords: NMR, SAIL法 / 自動帰属 / 構造計算 / SAIL法 / NMRデータの自動帰属 / CYANA / FLYA / proteorhodopsin / membrane protein

Research Abstract

We have successfully applied the SAIL method to solve the structure of the integral membrane protein proteorhodopsin[Angew. Chem. Int. Ed. 50, 11942? 11946(2011)]. This was the first de novo NMR structure determination of a seven-transmembrane-helix membrane protein. Using the cell-free system we could employ SAIL variants of Leu and Val with the advantage that only one of the prochiral methyl groups is detectable and signal overlap is considerably reduced. SAIL permitted the side-chain assignment of all Val and 60% of the Leu residues. This was crucial for obtaining NOE distance restraints that were used in conjunction with paramagnetic relaxation enhancement data for the structure calculation with CYANA.
We published our NOESY-FLYA method for the exclusively NOESY-based structure determination of proteins[J. Biomol. NMR. 50, 137-146(2011)], which does not require any other NMR spectra than NOESY for obtaining the resonance assignments and the conformational restraints for the NMR structure calculation with CYANA. This approach was successfully applied to SAIL-ubiquitin. The CYRANGE algorithm for the objective and automated identification of residue ranges for the superposition of protein structures[BMC Bioinformatics 12, 170(2011)], and a method for the simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space[J. Biomol. NMR 52, 351-364(2012)] were developed.
The program CYANA was applied in the CASD-NMR project, a blind testing of methods for the automated determination of protein structures from NMR data.[Structure 20, 227-236(2012)].

Research Products

• [Journal Article] Solution structure of the Splicing Factor Motif(SFM) of the human Prp18 protein (2012)
  • Author(s): He, F., Inoue, M., Kigawa, T., Takahashi, M., Kuwasako, K., Tsuda, K., Kobayashi, N., Terada, T., Shirouzu, M., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S. & Muto, Y.
  • Journal Title: Proteins Volume: 80 Pages: 968-974
• [Journal Article] Simultaneous single-structure and bundle representation of prote in NMR structures in torsion angle space (2012)
  • Author(s): Gottstein, D., Kirchner, D. K. & Guntert, P.
  • Journal Title: J. Biomol Volume: 52 Pages: 351-364
• [Journal Article] Protein structure validation by generalized linear model RMSD prediction (2012)
  • Author(s): Bagaria, A., Jaravine, V., Huang, Y. J., Montelione, G. T. & Guntert, P.
  • Journal Title: Protein Sci Volume: 21 Pages: 229-238
• [Journal Article] Blind testing of routine, fully automated determination of protein structures from NMR data (2012)
  • Author(s): Rosato, A., Aramini, J. M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J. F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Guntert, P., He. Y. F., Herrmann, T., Huang, Y. J., Jaravine, V., Jonker, H. R. A., Kennedy, M. A.
  • Journal Title: Structure Volume: 20 Pages: 227-236
• [Journal Article] Solution structure of the Splicing Factor Motif (SFM) of the human Prp18 protein (2012)
  • Author(s): He, F., Inoue, M., Kigawa, T., Takahashi, M., Kuwasako, K., Tsuda, K., Kobayashi, N., Terada, T., Shirouzu, M., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S., Muto, Y.
  • Journal Title: Proteins Volume: 80 Issue: 3 Pages: 968-974
  • DOI: 10.1002/prot.24003
  • Peer Reviewed
• [Journal Article] Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space (2012)
  • Author(s): Gottstein, D., Kirchner, D.K., Guntert, P.
  • Journal Title: J.Biomol.NMR Volume: 52(4) Issue: 4 Pages: 351-364
  • DOI: 10.1007/s10858-012-9615-8
  • Peer Reviewed
• [Journal Article] Protein structure validation by generalized linear model RMSD prediction (2012)
  • Author(s): Bagaria, A., Jaravine, V., Huang, Y.J., Montelione, G.T., Guntert, P.
  • Journal Title: Protein Sci. Volume: 21(2) Issue: 2 Pages: 229-238
  • DOI: 10.1002/pro.2007
  • Peer Reviewed
• [Journal Article] Blind testing of routine, fully automated determination of protein structures from NMR data.Structure 20, 227-236 (2012) (2012)
  • Author(s): Rosato, A., Aramini, J.M., Arrowsmith, C, Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J.F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Guntert, P., He, Y.F., Herrmann, T., Huang, Y.J., Jaravine, V., Jonker, H.R.A., Kennedy, M.A., Lange, O.F., Liu, G., Malliavin, T.E., Mani, R., Mao, B., Montelione, G.T., Nilges, M., Rossi, P., van der Schot, G., Schwalbe, H., Szyperski, T., Vendruscolo, M., Vernon, R., Vranken, W.F., de Vries, S., Vuister, G.W., Wu, B., Yang, Y., Bonvin, A.M.J.J.
  • Journal Title: Structure Volume: 20(2) Issue: 2 Pages: 227-236
  • DOI: 10.1016/j.str.2012.01.002
  • Peer Reviewed
• [Journal Article] Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution-and solid-state NMR with the UPLABEL algorithm (2011)
  • Author(s): Hefke, F., Bagaria, A., Reckel, S., Ullrich, S. J., Dotsch, V., Glaubitz, C. & Guntert, P.
  • Journal Title: J. Biomol. NMR Volume: 49 Pages: 75-84
• [Journal Article] Solution NMR structure of proteorhodopsin (2011)
  • Author(s): Reckel, S., Gottstein, D., Stehle, J., Lohr, F., Verhoefen, M. K., Takeda, M., Silvers, R., Kainosho, M., Glaubitz, C., Guntert, P. & Dotsch, V.
  • Journal Title: Angew. Chem. Int. Ed Volume: 50 Pages: 11942-11946
• [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 Pages: 137-146
• [Journal Article] Determination of optimal residue ranges for the superposition of protein structures (2011)
  • Author(s): Kirchner, D. K. & Guntert, P.
  • Journal Title: BMC Bioinformatics Volume: 12 Pages: 170-170
• [Journal Article] Structural basis for the dual RNA-recognition modes of human Tra2-βRRM. Nucl (2011)
  • Author(s): Tsuda, K., Someya, T., Kuwasako, K., Takahashi, M., Fahu, H., Inoue, M., Harada, T., Watanabe, S., Terada, T., Kobayashi, N., Shirouzu, M., Kigawa, T., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S. & Muto, Y.
  • Journal Title: Acids Res Volume: 39 Pages: 1538-1553
• [Journal Article] Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein (2011)
  • Author(s): Yamashita, S., Nagata, T., Kawazoe, M., Takemoto, C., Kigawa, T., Guntert, P., Kobayashi, N., Terada, T., Shirouzu, M., Wakiyama, M., Muto, Y. & Yokoyama, S.
  • Journal Title: Protein Sci Volume: 20 Pages: 118-130
• [Journal Article] Solution NMR structure of proteorhodopsin (2011)
  • Author(s): Reckel, S., Gottstein, D., Stehle, J., Lohr, E, Verhoefen, M.K., Takeda, M., Silvers, R., Kainosho, M., Glaubitz, C., Wachtveitl, J., Bernhard, F., Schwalbe, H., Guntert, P., Dotsch, V.
  • Journal Title: Angew.Chem.Int.Ed. Volume: 50(50) Issue: 50 Pages: 11942-11946
  • DOI: 10.1002/anie.201105648
  • Peer Reviewed
• [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] Objective identification of residue ranges for the superposition of protein structures (2011)
  • Author(s): Kirchner, D.K., Guntert, P.
  • Journal Title: BMC Bioinformatics Volume: 12 Issue: 1 Pages: 170-170
  • DOI: 10.1186/1471-2105-12-170
  • Peer Reviewed
• [Journal Article] Structural basis for the dual RNA-recognition modes of human Tra2-β RRM (2011)
  • Author(s): Tsuda, K., Someya, T., Kuwasako, K., Takahashi, M., Fahu, H., Inoue, M., Harada, T., Watanabe, S., Terada, T., Kobayashi, N., Shirouzu, M., Kigawa, T., Tanaka, A., Sugano, S., Guntert, P., Yokoyama, S., Muto, Y.
  • Journal Title: Nucl.Acids Res. Volume: 39(4) Issue: 4 Pages: 1538-1553
  • DOI: 10.1093/nar/gkq854
  • Peer Reviewed
• [Journal Article] Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein (2011)
  • Author(s): Yamashita, S., Nagata, T., Kawazoe, M., Takemoto, C., Kigawa, T, Guntert, P., Kobayashi, N., Terada, T., Shirouzu, M., Wakiyama, M., Muto, Y., Yokoyama, S.
  • Journal Title: Protein Sci. Volume: 20(1) Issue: 1 Pages: 118-130
  • DOI: 10.1002/pro.543
  • Peer Reviewed
• [Journal Article] Optimization of amino acid type-specific ^<13>C and ^<15>N labeling for the backbone assignment of membrane proteins by solution(-)and solid-state NMR with the UPLABEL algorithm{HYPERLINK "http://www.bpc.uni-frankfurt.de/guentert/Reprints/Hefke11-UPLABEL.pdf" \o "http://www.bpc.uni-frankfurt.de/guentert/Reprints/Hefke11-UPLABEL.pdf"} (2011)
  • Author(s): Hefke, F., Bagaria, A., Reckel, S., Ullrich, S.J., Dotsch, V., Glaubitz, C., Guntert, P.
  • Journal Title: J.Biomol.NMR Volume: 49(2) Pages: 75-84
  • 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., Mlynarczyk, K., Pulawski, W., Ghoshdastider, U., Kolinski, M., 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 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., Nietlispach, D., Walchli, M., Smith, B. O., Shirakawa, M., Guntert, P. & Ito, Y.
  • Journal Title: Nature Protocols Volume: 5 Pages: 1051-1060
• [Journal Article] Solution structure of polytheonamide B, a highly cytotoxic non-ribosomal polypeptide from marine sponge (2010)
  • Author(s): Hamada, T., Matsunaga, S., Fujiwara, M., Fujita, K., Hirota, H., Schmucki, R., Guntert, P., Fusetani, N.
  • Journal Title: J. Am. Chem. Soc Volume: 132 Pages: 12941-12945
• [Journal Article] Structural insight into the zinc finger CW domain as a novel histone modification reader (2010)
  • Author(s): He, F., Umehara, T., Inoue, M., Harada, T., Watanabe, S., Kigawa, T, Takahashi, M., Kuwasako, K., Tsuda, K., Matsuda, T., Aoki, M., Seki, E., Kobayashi, N., Tanaka, A., Sugano, S., Guntert, P., Muto, Y. & Yokoyama, S.
  • Journal Title: Structure Volume: 18 Pages: 1127-1139
• [Journal Article] Solution structure of the mitochondrial protein ICT1 that is essential for cell vitality (2010)
  • Author(s): Handa, Y., Hikawa, Y., Tochio, N., Kogure, H., Inoue, M., Koshiba, S., Guntert, P., Inoue, Y., Kigawa, T., Yokoyama, S. & Nameki, N.
  • Journal Title: J. Mol. Biol Volume: 404 Pages: 260-273
• [Journal Article] Solution structure of the mitochondrial protein ICT1 that is essential for cell vitality{HYPERLINK "http://www.bpc.uni-frankfurt.de/guentert/Reprints/Handa_JMolBiol_2010.pdf" \o "http://www.bpc.uni-frankfurt.de/guentert/Reprints/Handa_JMolBiol_2010.pdf"} (2010)
  • Author(s): Handa, Y., Hikawa, Y., Tochio, N., Kogure, H., Inoue, M., Koshiba, S., Guntert, P., Inoue, Y., Kigawa, T., Yokoyama, S., Nameki, N.
  • Journal Title: J.Mol.Biol. Volume: 404(2) Pages: 260-273
  • Peer Reviewed
• [Journal Article] Structural insight into the zinc finger CW domain as a histone modify-cation reader. (2010)
  • Author(s): He, F., Umehara, T., Saito, K., Harada, T., Watanabe, S., Yobuki, T., Kigawa, T., Takahashi, M., Kuwasako, K., Tsuda, K., Matsuda, T., Aoki, M., Seki, E., Kobayashi, N., Guntert, P., Yokoyama, S., Muto, Y.
  • Journal Title: Structure Volume: 18(9) Pages: 1127-1139
  • Peer Reviewed
• [Journal Article] Solution structure of polytheonamide B, a highly cytotoxic nonribosomal polypeptide from marine sponge{HYPERLINK "http://www.bpc.uni-frankfurt.de/guentert/Reprints/HamadaJACS2010.pdf" \o "http://www.bpc.uni-frankfurt.de/guentert/Reprints/HamadaJACS2010.pdf"} (2010)
  • Author(s): Hamada, T., Matsunaga, S., Fujiwara, M., Fujita, K., Hirota, H., Schmucki, R., Guntert, P., Fusetani, N.
  • Journal Title: J.Am.Chem.Soc. Volume: 132(37) Pages: 12941-12945
  • Peer Reviewed
• [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
• [Journal Article] SAIL-Stereo-array isotope labeling. (2010)
  • Author(s): Kainosho, M., Guntert, P.
  • Journal Title: Q.Rev.Biophys. Volume: 42 Pages: 247-300
  • Peer Reviewed
• [Journal Article] Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system (2009)
  • Author(s): Ikeya, T., Takeda, M., Yoshida, H., Terauchi, T., Jee, J., Kainosho, M. & Guntert, P.
  • Journal Title: J. Biomol. Volume: 44 Pages: 261-272
• [Journal Article] Conformational stability and activity of p73 require a second helix in the tetramerization domain (2009)
  • Author(s): Coutandin, D., Lohr, F., Niesen, F. H., Ikeya, T., Weber, T. A., Schafer, B., Bullock, A. N., Yang, A., Guntert, P., Knapp, S., McKeon, F., Der Ou, H. & Dotsch, V.
  • Journal Title: Cell Death Diff Volume: 16 Pages: 1582-1589
• [Journal Article] Structure of the Cdt1 C-terminal domain : Conservation of the winged helix fold in replication licensing factors (2009)
  • Author(s): Khayrutdinov, B. I., Bae, W. J., Yun, Y. M., Lee, J. H., Tsuyama, T., Kim, J. J., Hwang, E., Ryu, K. S., Cheong, H. K., Cheong, C., Ko, J. S., Enomoto, T., Karplus, P. A., Guntert, P., Tada, S., Jeon, Y. H., Cho, Y.
  • Journal Title: Prot. Sci Volume: 18 Pages: 2252-2264
• [Journal Article] A. M. J. J. CASD-NMR : a rolling experiment for the critical assessment of automated structure determination of proteins from NMR data (2009)
  • Author(s): Rosato, A., Bagaria, A., Baker, D., Bardiaux, B., Cavalli, A., Doreleijers, J. F., Giachetti, A., Guerry, P., Guntert, P., Herrmann, T., Huang, Y. J., Jonker, H. R. A., Mao, B., Malliavin, T. E., Montelione, G. T., Nilges, M., Raman, S., van der Schot, G.
  • Journal Title: Nature Methods Volume: 6 Pages: 625-626
• [Journal Article] Structural basis for the sequence specific RNA-recognition mechanism of human CUG-BP1 RRM3 (2009)
  • Author(s): Tsuda, K., Kuwasako, K., Takahashi, M., Someya, T., Inoue, M., Terada, T., Kobayashi, N., Shirouzu, M., Kigawa, T., Tanaka, A., Sugano, S., Guntert, P., Muto, Y. & Yokoyama, S.
  • Journal Title: Nucl. Acids Res Volume: 37 Pages: 5151-5166
• [Journal Article] SAIL-Stereo-array isotope labeling (2009)
  • Author(s): Kainosho, M. & Guntert, P.
  • Journal Title: Q. Rev. Biophys Volume: 42 Pages: 247-300
• [Journal Article] Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. (2009)
  • Author(s): Ikeya T, Takeda M, Yoshida H, Terauchi T, Jee JG, Kainosho M, Guntert P.
  • Journal Title: J. Biomol. NMR. 44(4) Pages: 261-272
  • Peer Reviewed
• [Journal Article] Conformational stability and activity of p73 require a second helix in the tetramerization domain (2009)
  • Author(s): Coutandin D, Lohr F, Niesen F H, Ikeya T, Weber TA, Schafer B, Zielonka EM, Bullock AN, Yang A, Guntert P, Knapp S, McKeon F, Ou HD, Dotsch V.
  • Journal Title: Cell Death Differ. 16(12) : Pages: 1582-1589
  • Peer Reviewed
• [Journal Article] Structure of the Cdt1 C-terminal domain: conservation of the winged helix fold in replication licensing factors. (2009)
  • Author(s): Khayrutdinov BI, Bae WJ, Yun YM, Lee JH, Tsuyama T, Kim JJ, Hwang E, Ryu KS, Cheong HK, Cheong C, Ko JS, Enomoto T, Karplus PA, Guntert P, Tada S, Jeon YH, Cho Y.
  • Journal Title: Protein Sci. 18(11) Pages: 2252-2264
  • Peer Reviewed
• [Journal Article] CASD-NMR : critical assessment of automated structure determination by NMR. (2009)
  • Author(s): Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Guntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Monterlione GY, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM.
  • Journal Title: Nat. Methods 6(9) Pages: 625-626
  • Peer Reviewed
• [Journal Article] Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3. (2009)
  • Author(s): Tsuda K, Kuwasako K, Takahashi M, Someya T, Inoue M, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Guntert P, Muto Y, Yokoyama S.
  • Journal Title: Nucleic Acids Res. 37(15) : Pages: 5151-5166
  • Peer Reviewed