Optimization of automated NMR data analysis for in-cell NMR structure determination

• Project/Area Number: 25440032
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• 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, 教授 (20392110)
• Co-Investigator(Kenkyū-buntansha): Ikeya Teppei 首都大学東京, 理工学研究科, 助教 (30457840)
• Co-Investigator(Renkei-kenkyūsha): Ito Yutaka 首都大学東京, 理工学研究科, 教授 (80261147)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2015: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2014: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2013: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: NMR立体構造計算 / NMR信号自動解析 / NMR 立体構造計算 / CYANA / NOE自動解析 / eNOE / NMR^2 / ベイズ推定 / 蛋白質-リガンド複合体 / In-cell NMR / NMRデータの自動帰属 / 構造計算 / FLYA

Outline of Final Research Achievements

In-cell NMR has enabled the direct observation of proteins in living cells. We developed the CYANA software specifically for in-cell NMR. The automated chemical shift and NOE assignment algorithms in CYANA were adapted for better handling of in-cell NMR spectra processed with nonlinear sampling techniques.The automated chemical shifts assignment is significantly more robust and efficient than previous methods, and NMR structure calculation algorithm based on Bayesian inference are cornerstones for this. Compared to spectra of purified proteins, in-cell NMR ones typically show a significant number of background signals, low signal-noise ratio, and broadened signals that lead to much higher assignment ambiguity, which makes it difficult and cumbersome to check all possibilities manually. An algorithm can exhaustively search all candidates and determine assignments more quickly and more objectively. The viability of the in-cell CYANA approach was shown by applying it to in-cell NMR data.

Research Products

• [Journal Article] NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment. (2016)
  • Author(s): Orts, J., Waelti, M. A., Marsh, M., Vera, L., Gossert, A. D., Guentert, P. & Riek, R.
  • Journal Title: J. Am. Chem. Soc. Volume: 138 Issue: 13 Pages: 4393-4400
  • DOI: 10.1021/jacs.5b12391
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Protein NMR Structure Refinement based on Bayesian Inference (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Solid-state NMR sequential assignments of the N-terminal domain of HpDnaB helicase. (2016)
  • Author(s): Wiegand, T., Gardiennet, C., Ravotti, F., Bazin, A., Kunert, B., Lacabanne, D., Cadalbert, R., Guentert, P., Terradot, L., Boeckmann, A. & Meier, B. H.
  • Journal Title: Biomol. NMR Assign. Volume: 10 Issue: 1 Pages: 13-23
  • DOI: 10.1007/s12104-015-9629-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The exact NOE as an alternative in ensemble structure determination. (2016)
  • Author(s): Voegeli, B., Olsson, S., Guentert, P. & Riek, R.
  • Journal Title: Biophys. J. Volume: 110 Issue: 1 Pages: 113-126
  • DOI: 10.1016/j.bpj.2015.11.031
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3. (2015)
  • Author(s): Voegeli, B., Olsson, S., Riek, R. & Guentert, P.
  • Journal Title: Data in Brief Volume: 5 Pages: 99-106
  • DOI: 10.1016/j.dib.2015.08.020
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A structural ensemble of the enzyme cyclophilin reveals an orchestrated mode of action at atomic resolution. (2015)
  • Author(s): Chi, C. N., Voegeli, B., Bibow, S., Strotz, D., Orts, J., Guentert, P. & Riek, R.
  • Journal Title: Angew. Chem. Volume: 54 Issue: 40 Pages: 11657-11661
  • DOI: 10.1002/anie.201503698
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. (2015)
  • Author(s): Yilmaz Maden, E. & Guentert, P.
  • Journal Title: J. Biomol. NMR Volume: 63 Issue: 1 Pages: 21-37
  • DOI: 10.1007/s10858-015-9959-y
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics. (2015)
  • Author(s): Voegeli, B., Olsson, S., Riek, R. & Guentert, P.
  • Journal Title: J. Struct. Biol. Volume: 191 Issue: 3 Pages: 306-317
  • DOI: 10.1016/j.jsb.2015.07.008
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Combined automated NOE assignment and structure calculation with CYANA. (2015)
  • Author(s): Guentert, P. & Buchner, L.
  • Journal Title: J. Biomol. NMR Volume: 62 Issue: 4 Pages: 453-471
  • DOI: 10.1007/s10858-015-9924-9
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] NMR Exchange Format: a unified and open standard for representation of NMR restraint data. (2015)
  • Author(s): Gutmanas, A., Adams, P. D., Bardiaux, B., Berman, H. M., Case, D. A., Fogh, R. H. Guentert, P., et.al
  • Journal Title: Nat. Struct. Mol. Biol. Volume: 22 Issue: 6 Pages: 433-434
  • DOI: 10.1038/nsmb.3041
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Combined automated NOE assignment and structure calculation with CYANA. (2015)
  • Author(s): Guentert, P. & Buchner
  • Journal Title: J. Biomol. NMR Volume: ?
  • Peer Reviewed
• [Journal Article] Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. (2015)
  • Author(s): Buchner, L. & Guentert, P.
  • Journal Title: J. Biomol. NMR Volume: ?
  • Peer Reviewed
• [Journal Article] The RING domain of human promyelocytic leukemia protein (PML). (2015)
  • Author(s): Huang, S. Y., Chang, C. F., Fan, P. J., Naik, M. T., Guentert, P., Shih, H. M. & Huang, T. H.
  • Journal Title: J. Biomol. NMR Volume: 61 Issue: 2 Pages: 173-180
  • DOI: 10.1007/s10858-015-9901-3
  • Peer Reviewed
• [Journal Article] Increased reliability of NMR protein structures by consensus structure bundles. (2015)
  • Author(s): Buchner, L. & Guentert, P.
  • Journal Title: Structure Volume: 23 Issue: 2 Pages: 425-434
  • DOI: 10.1016/j.str.2014.11.014
  • Peer Reviewed
• [Journal Article] Atomic-resolution three-dimensional structure of amyloid β fibrils bearing the Osaka mutation. (2015)
  • Author(s): Schuetz, A. K., Vagt, T., Huber, M., Ovchinnikova, O. Y., Cadalbert, R., Wall, J., Guentert, P., Boeckmann, A., Glockshuber, R., and Meier, B. H.
  • Journal Title: Angew. Chem. Int. Ed. Volume: 54 Issue: 1 Pages: 331-335
  • DOI: 10.1002/anie.201408598
  • Peer Reviewed
• [Journal Article] Automated structure determination from NMR spectra. (2015)
  • Author(s): Schmidt, E. & Guentert, P.
  • Journal Title: Meth. Mol. Biol. Volume: 1261 Pages: 303-329
  • DOI: 10.1007/978-1-4939-2230-7_16
  • ISBN: 9781493922291, 9781493922307
  • Peer Reviewed
• [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
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Novel RNA recognition motif domain in cytoplasmic polyadenylation element binding protein 3. (2014)
  • Author(s): Tsuda, K., Kuwasako, K., Nagata, T., Takahashi, M., Kigawa, T., Kobayashi, N., Guentert, P., Shirouzu, M., Yokoyama, S. & Muto, Y.
  • Journal Title: Proteins Volume: 82 Issue: 10 Pages: 2879-2886
  • DOI: 10.1002/prot.24651
  • Peer Reviewed
• [Journal Article] RBFOX and SUP-12 sandwich a guanine base to form a stable complex and regulate tissue-specific splicing. (2014)
  • Author(s): Kuwasako K, Takahashi M, Unzai S, Tsuda K, Yoshikawa S, He F, Kobayashi N, Guntert P, Shirouzu M, Ito T, Tanaka A, Yokoyama S, Hagiwara M, Kuroyanagi H, and Muto Y.
  • Journal Title: Nat. Struct. Mol. Biol. Volume: 21(9) Issue: 9 Pages: 778-86
  • DOI: 10.1038/nsmb.2870
  • Peer Reviewed / Open Access
• [Journal Article] Structural features of peptoid-peptide hybrids in lipid-water interfaces. (2014)
  • Author(s): Uggerhoej, L. E., Munk, J. K., Hansen, P. R., Guentert, P. & Wimmer, R.
  • Journal Title: FEBS Lett. Volume: 588 Issue: 17 Pages: 3291-3297
  • DOI: 10.1016/j.febslet.2014.07.016
  • Peer Reviewed
• [Journal Article] Spontaneous self assembly of fragments of engineered Armadillo repeat proteins into a folded structure. (2014)
  • Author(s): Watson, R. P., Christen, M. T., Bumbak, F., Ewald, C., Reichen, C. Mihajlovic, M., Schmidt, E., Guentert, P., Caflisch, A., Plueckthun, A., Zerbe, O.
  • Journal Title: Structure Volume: 22 Issue: 7 Pages: 985-995
  • DOI: 10.1016/j.str.2014.05.002
  • Peer Reviewed
• [Journal Article] Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments. (2014)
  • Author(s): Kraehenbuehl, B., El Bakkali, I., Schmidt, E., Guentert, P. & Wider, G.
  • Journal Title: J. Biomol. NMR Volume: 59 Issue: 2 Pages: 87-93
  • DOI: 10.1007/s10858-014-9829-z
  • Peer Reviewed
• [Journal Article] Crystal structure of a PCP/Sfp complex reveals the structural basis for carrier protein posttranslational modification. (2014)
  • Author(s): Tufar, P., Rahighi, S., Kraas, F. I., Kirchner, D. K., Loehr, F., Henrich, E., Koepke, J., Dikic, I., Guentert, P., Marahiel, M. A. & Doetsch, V.
  • Journal Title: Chem. Biol. Volume: 21 Issue: 4 Pages: 552-562
  • DOI: 10.1016/j.chembiol.2014.02.014
  • Peer Reviewed
• [Journal Article] Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs. (2014)
  • Author(s): Voegeli, B., Orts, J., Strotz, D., Chi, C., Minges, M., Waelti, M. A., Guentert, P. & Riek, R.
  • Journal Title: J. Magn. Reson. Volume: 241 Pages: 53-59
  • DOI: 10.1016/j.jmr.2013.11.016
  • Peer Reviewed
• [Journal Article] Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. (2014)
  • Author(s): Kogure, H., Handa, H., Nagata, M., Kanai, N., Guntert, P., Kubota, K., Nameki, N.
  • Journal Title: Nucleic Acids Research Volume: 42 Issue: 5 Pages: 3152-3163
  • DOI: 10.1093/nar/gkt1280
  • Peer Reviewed
• [Journal Article] Peak picking NMR spectral data using non-negative matrix factorization (2014)
  • Author(s): Tikole, S., Jaravine, V., Rogov, V., Doetsch, V. & Guentert, P.
  • Journal Title: BMC Bioinformatics Volume: 15 Issue: 1 Pages: 46-46
  • DOI: 10.1186/1471-2105-15-46
  • Peer Reviewed
• [Journal Article] Stereospecific assignments in proteins using exact NOEs. (2013)
  • Author(s): Orts, J., Vaegeli, B., Riek, R. & Guentert, P.
  • Journal Title: J. Biomol. NMR Volume: 57 Issue: 3 Pages: 211-218
  • DOI: 10.1007/s10858-013-9780-4
  • Peer Reviewed
• [Journal Article] Automated and assisted RNA resonance assignment using NMR chemical shift statistics. (2013)
  • Author(s): Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Guentert, P. & Schubert, M.
  • Journal Title: Nucl. Acids Res. Volume: 41 Issue: 18 Pages: e172-e172
  • DOI: 10.1093/nar/gkt665
  • Peer Reviewed
• [Journal Article] Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. (2013)
  • Author(s): Schmidt, E. & Guentert, P.
  • Journal Title: J. Biomol. NMR Volume: 57 Issue: 2 Pages: 193-204
  • DOI: 10.1007/s10858-013-9779-x
  • Peer Reviewed
• [Journal Article] Effects of NMR spectral resolution on protein structure calculation. (2013)
  • Author(s): Tikole, S., Jaravine, V., Orekhov, V. Yu. & Guentert, P.
  • Journal Title: PLoS ONE Volume: 8 Issue: 7 Pages: e68567-e68567
  • DOI: 10.1371/journal.pone.0068567
  • Peer Reviewed
• [Journal Article] Estimating structure quality trends in the Protein Data Bank by equivalent resolution. (2013)
  • Author(s): Bagaria, A., Jaravine, V. & Guentert, P.
  • Journal Title: Comp. Biol. Chem. Volume: 46 Pages: 8-15
  • DOI: 10.1016/j.compbiolchem.2013.04.004
  • Peer Reviewed
• [Journal Article] Molecular crowding drives active Pin1 into nonspecific complexes with endogenous proteins prior to substrate recognition. (2013)
  • Author(s): Luh, L. M., Haensel, R., Loehr, F., Kirchner, D. K., Krauskopf, K., Pitzius, S., Schaefer, B., Tufar, P., Corbeski, I., Guentert, P. & Doetsch, V.
  • Journal Title: J. Am. Chem. Soc. Volume: 135 Issue: 37 Pages: 13796-13803
  • DOI: 10.1021/ja405244v
  • Peer Reviewed
• [Journal Article] 1H, 13C, and 15N resonance assignments of the dsRBDs of mouse RNA helicase A (2013)
  • Author(s): Takashi Nagata T, Kengo Tsuda, Naohiro Kobayashi, Peter Guntert, Shigeyuki Yokoyama, and Yutaka Muto
  • Journal Title: Biomolecular NMR Assignment Volume: 7巻 Issue: 1 Pages: 69-72
  • DOI: 10.1007/s12104-012-9380-3
  • Peer Reviewed
• [Journal Article] Recommendations of the wwPDB NMR Validation Task Force. (2013)
  • Author(s): Montelione, G. T., Nilges, M., Bax, A., Guentert, P., Herrmann, T., Richardson, J. S., Schwieters, C., Vranken, W. F., Vuister, G. W., Wishart, D. S., Berman, H. M., Kleywegt, G. J.& Markley, J. L.
  • Journal Title: Structure Volume: 21 Issue: 9 Pages: 1562-1570
  • DOI: 10.1016/j.str.2013.07.021
  • Peer Reviewed
• [Presentation] Automated assignment of NMR spectra with FLYA (2016)
  • Author(s): Guentert, P.
  • Organizer: ライデン大学セミナー
  • Place of Presentation: オランダ ライデン
  • Year and Date: 2016-03-30
  • Invited
• [Presentation] NMR structure analysis with CYANA (2016)
  • Author(s): Guentert, P.
  • Organizer: 2nd G-NMR School
  • Place of Presentation: ドイツ フランクフルト
  • Year and Date: 2016-02-29
  • Invited
• [Presentation] Molecular multibody dynamics (2016)
  • Author(s): Guentert, P.
  • Organizer: 京都大学セミナー
  • Place of Presentation: 京都
  • Year and Date: 2016-02-15
  • Invited
• [Presentation] CYANA: A tool for structure calculation (2016)
  • Author(s): Guentert, P.
  • Organizer: NMR Meets Biology
  • Place of Presentation: インド ケララ
  • Year and Date: 2016-02-14
  • Invited
• [Presentation] Computation methods to study biomolecular systems (2016)
  • Author(s): Guentert, P.
  • Organizer: 京都大学セミナー
  • Place of Presentation: 京都
  • Year and Date: 2016-02-09
  • Invited
• [Presentation] Insight into protein structure and dynamics from solution- and solid-state NMR (2015)
  • Author(s): Guentert, P.
  • Organizer: WPI-NEXT Workshop on High Resolution Cell Biology
  • Place of Presentation: 名古屋
  • Year and Date: 2015-10-01
  • Invited
• [Presentation] Automated NMR resonance assignment and structure calculation (2015)
  • Author(s): Guentert, P.
  • Organizer: 名古屋大学セミナー
  • Place of Presentation: 名古屋
  • Year and Date: 2015-09-30
  • Invited
• [Presentation] Consensus structure bundles and the information content of NMR restraints (2015)
  • Author(s): Guentert, P.
  • Organizer: 第16回若手NMR研究会
  • Place of Presentation: 神奈川
  • Year and Date: 2015-09-27
  • Invited
• [Presentation] NMR structure calculation (2015)
  • Author(s): Guentert, P.
  • Organizer: EMBO Practical Course on Structure Determination of Biological Macromolecules by Solution NMR
  • Place of Presentation: ドイツ
  • Year and Date: 2015-07-31
  • Invited
• [Presentation] Advances in automated assignment and structure determination of difficult proteins (2015)
  • Author(s): Guentert, P.
  • Organizer: Paulo Foundation Symposium
  • Place of Presentation: フィンランド ヘルシンキ
  • Year and Date: 2015-06-09
  • Invited
• [Presentation] Advances in automated assignment and structure determination of difficult proteins (2015)
  • Author(s): Guentert, P.
  • Organizer: Symposium on in-cell NMR studies
  • Place of Presentation: 東京 秋葉原
  • Year and Date: 2015-04-24
  • Invited