Use of contact prediction-based restraints for protein structure determination from sparse NMR data

• Project/Area Number: 20K06508
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 43020:Structural biochemistry-related
• Research Institution: Tokyo Metropolitan University
• Principal Investigator: GUENTERT Peter 東京都立大学, 理学研究科, 客員教授 (20392110)
• Co-Investigator(Kenkyū-buntansha): 池谷 鉄兵 東京都立大学, 理学研究科, 准教授 (30457840) ; 伊藤 隆 東京都立大学, 理学研究科, 教授 (80261147)
• Project Period (FY): 2020-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: machine learning / NMR / protein structure / automated assignment / contact prediction / distance restraints

Outline of Research at the Start

In this project, we propose to improve NMR protein structure determination using machine learning methods that can predict distances between atoms in proteins. The aim is to enable structure determination of larger or more challenging proteins than hitherto possible, including the study of proteins in living cells, large methyl-labeled proteins, multi-domain systems, membrane proteins, and generally proteins with low stability or at low concentrations, for which it is difficult to measure a sufficient amount of NMR data.

Outline of Final Research Achievements

We have incorporated the use of protein structures predicted by AlphaFold2 into our fully automated NMR spectra analysis algorithm ARTINA, which yields peak lists, chemical shift assignments, and three-dimensional protein structures directly from a set of multidimensional NMR spectra without any manual work. The AlphaFold2 structures can be used in ARTINA for the structure-based prediction of approximate chemical shifts and for generating the cross peaks expected in NOESY-type spectra. It could be shown that the AlphaFold2 structures enable to obtain reliable chemical shift assignments from smaller sets of NMR spectra than without structures. Thus, NMR measurement times can be significantly reduced and the NMR studies of proteins becomes more efficient. The ARTINA algorithm has been made available in the NMRtist webserver that allows scientists to obtain assignments and structures of proteins within a few hours of computation time rather than weeks or months of manual analysis.

Academic Significance and Societal Importance of the Research Achievements

Nuclear magnetic resonance spectroscopy (NMR) provides detailed information on structure, dynamics and interactions of proteins. The method developed in this project will accelerate virtually any biological NMR studies that require the analysis of protein NMR spectra and chemical shift assignments.

Research Products

• [Journal Article] NMRtist: an online platform for automated biomolecular NMR spectra analysis (2023)
  • Author(s): Klukowski Piotr, Riek Roland, Guentert Peter
  • Journal Title: Bioinformatics Volume: 39 Issue: 2
  • DOI: 10.1093/bioinformatics/btad066
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA (2022)
  • Author(s): Klukowski Piotr, Riek Roland, Guentert Peter
  • Journal Title: Nature Communications Volume: 13 Issue: 1 Pages: 6151-6151
  • DOI: 10.1038/s41467-022-33879-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] PDBcor: An automated correlation extraction calculator for multi-state protein structures (2022)
  • Author(s): Ashkinadze Dzmitry, Klukowski Piotr, Kadavath Harindranath, Guentert Peter, Riek Roland
  • Journal Title: Structure Volume: 30 Issue: 4 Pages: 646-652
  • DOI: 10.1016/j.str.2021.12.002
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A B-factor for NOEs? (2022)
  • Author(s): Guentert Peter
  • Journal Title: Journal of Magnetic Resonance Volume: 338 Pages: 107189-107189
  • DOI: 10.1016/j.jmr.2022.107189
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Atomic resolution protein allostery from the multi-state structure of a PDZ domain (2022)
  • Author(s): Ashkinadze Dzmitry, Kadavath Harindranath, Pokharna Aditya, Chi Celestine N., Friedmann Michael, Strotz Dean, Kumari Pratibha, Minges Martina, Cadalbert Riccardo, Koenigl Stefan, Guentert Peter, Voegeli Beat, Riek Roland
  • Journal Title: Nature Communications Volume: 13 Issue: 1 Pages: 6232-6232
  • DOI: 10.1038/s41467-022-33687-x
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 1H, 13C, and 15N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis. (2022)
  • Author(s): Kuwasako K, Suzuki S, Nameki N, Takizawa M, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Guntert P, Shirouzu M, Yokoyama S, Muto Y
  • Journal Title: Biomol NMR Assign. Volume: 16 Issue: 2 Pages: 297-303
  • DOI: 10.1007/s12104-022-10094-3
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Atomic-resolution chemical characterization of (2x)72 kDa tryptophan synthase via 4D and 5D 1H-detected solid-state NMR (2022)
  • Author(s): Klein, A., Rovo, P., Sakhrani, V. V., Wang, Y., Holmes, J. B., Liu, V., Skowronek, P., Kukuk, L., Vasa, S. K., Guentert, P., Mueller, L. J., Linser, R.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 119 Issue: 4
  • DOI: 10.1073/pnas.2114690119
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 1 H, 13 C and 15 N resonance assignments and solution structures of the two RRM domains of Matrin-3 (2021)
  • Author(s): He F, Kuwasako K, Takizawa M, Takahashi M, Tsuda K, Nagata T, Watanabe S, Tanaka A, Kobayashi N, Kigawa T, Guntert P, Shirouzu M, Yokoyama S, Muto Y.
  • Journal Title: Biomol NMR Assign. Volume: Nov16 Issue: 1 Pages: 41-49
  • DOI: 10.1007/s12104-021-10057-0
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] An automated iterative approach for protein structure refinement using pseudocontact shifts (2021)
  • Author(s): Cucuzza, S., Guentert, P., Plueckthun, A., Zerbe, O.
  • Journal Title: Journal of Biomolecular NMR Volume: 75 Issue: 8-9 Pages: 319-334
  • DOI: 10.1007/s10858-021-00376-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Evaluation of multi-objective optimization algorithms for NMR chemical shift assignment (2021)
  • Author(s): Maden Yilmaz, E., Guentert, P., Etaner-Uyar, S.
  • Journal Title: Molecules Volume: 26 Issue: 12 Pages: 3699-3699
  • DOI: 10.3390/molecules26123699
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Paramagnetic solid-state NMR to localize the metal-ion cofactor in an oligomeric DnaB helicase (2021)
  • Author(s): Zehnder, J., Cadalbert, R., Terradot, L., Guentert, P., Boeckmann, A., Meier, B. H., Wiegand, T.
  • Journal Title: Chemistry Europe Volume: 27 Issue: 28 Pages: 7745-7755
  • DOI: 10.1002/chem.202100462
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] H, 13C and 15N resonance assignment of the YTH domain of YTHDC2. (2020)
  • Author(s): F. He, R. Endo, K. Kuwasako, M. Takahashi, K. Tsuda, T. Nagata, S. Watanabe, A. Tanaka, N. Kobayashi, T. Kigawa, P. Guentert, M. Shirouzu, S. Yokoyama and Y. Muto.
  • Journal Title: Biomol. NMR Assign. Volume: 15 Issue: 1 Pages: 1-7
  • DOI: 10.1007/s12104-020-09974-3
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Chapter 5. Protein Structure Determination in Living Cells from NOE-derived Distance Restraints (2020)
  • Author(s): Ikeya Teppei、Guentert Peter、Ito Yutaka
  • Journal Title: In-cell NMR (Eds. Ito, Y., Dotsch, V., Shirakawa, M.), Royal Society of Chemistry Volume: - Pages: 63-89
  • DOI: 10.1039/9781788013079-00063
  • ISBN: 9781788012171
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Automated assignment of methyl NMR spectra from large proteins (2020)
  • Author(s): Pritisanac, I., Alderson, T. R., Guentert, P.
  • Journal Title: Progress in NMR Spectroscopy Volume: 118-119 Pages: 54-73
  • DOI: 10.1016/j.pnmrs.2020.04.001
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Automated backbone NMR resonance assignment of large proteins using redundant linking from a single simultaneous acquisition (2020)
  • Author(s): Stanek, J., Schubeis, T., Paluch, P., Guentert, P., Andreas, L. B., Pintacuda, G.
  • Journal Title: Journal of the American Chemical Society Volume: 142 Issue: 12 Pages: 5793-5799
  • DOI: 10.1021/jacs.0c00251
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The three-dimensional structure of human β-endorphin amyloid fibrils (2020)
  • Author(s): Seuring Carolin、Verasdonck Joeri、Gath Julia、Ghosh Dhimam、Nespovitaya Nadezhda、W?lti Marielle Aulikki、Maji Samir K.、Cadalbert Riccardo、Guentert Peter、Meier Beat H.、Riek Roland
  • Journal Title: Nature Structural & Molecular Biology Volume: 27 Issue: 12 Pages: 1178-1184
  • DOI: 10.1038/s41594-020-00515-z
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Dynamics of Bacteriorhodopsin in the Dark‐Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy (2020)
  • Author(s): Kooijman Laurens、Schuster Matthias、Baumann Christian、Jurt Simon、Loehr Frank、Fuertig Boris、Guentert Peter、Zerbe Oliver
  • Journal Title: Angewandte Chemie International Edition Volume: 59 Issue: 47 Pages: 20965-20972
  • DOI: 10.1002/anie.202004393
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Protein Allostery at Atomic Resolution (2020)
  • Author(s): Strotz Dean、Orts Julien、Kadavath Harindranath、Friedmann Michael、Ghosh Dhiman、Olsson Simon、Chi Celestine N.、Pokharna Aditya、Guentert Peter、Voegeli Beat、Riek Roland
  • Journal Title: Angewandte Chemie International Edition Volume: 59 Issue: 49 Pages: 22132-22139
  • DOI: 10.1002/anie.202008734
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Automated biomolecular NMR spectra analysis, assignments, and structures with the deep learning technique ARTINA (2022)
  • Author(s): Peter Guentert
  • Organizer: Biomolecular NMR: Advanced Tools, Machine Learning. Advanced hands-on PhD course, University of Gothenburg, Sweden
  • Invited
• [Presentation] Automated biomolecular NMR spectra analysis, assignments, and structures with the deep learning technique ARTINA (2022)
  • Author(s): Peter Guentert
  • Organizer: 43rd FGMR Discussion Meeting of the German Chemical Society, Karlsruhe, Germany
  • Int'l Joint Research / Invited
• [Presentation] Automated biomolecular NMR spectra analysis, assignments, and structures with the deep learning technique ARTINA (2022)
  • Author(s): Peter Guentert
  • Organizer: EMBO Workshop When predictions meet experiments: the future of structure determination, Palermo, Italy
  • Int'l Joint Research / Invited
• [Presentation] NMRtist: an online platform for automated biomolecular NMR spectra analysis (2022)
  • Author(s): Peter Guentert
  • Organizer: 29th International Conference on Magnetic Resonance in Biological Systems (ICMRBS 2022), Boston, USA
  • Int'l Joint Research / Invited
• [Presentation] NMR structure calculation (2022)
  • Author(s): Peter Guentert
  • Organizer: EMBO Practical Course Structure, Dynamics and Function of Biological Macromolecules by NMR, Biozentrum Basel, Switzerland
  • Int'l Joint Research / Invited
• [Presentation] NMRtist: An online platform for automated biomolecular NMR spectra analysis (2022)
  • Author(s): Peter Guentert
  • Organizer: 16th NMR Retreat of Protein-RNA Interactions, Parpan, Switzerland
  • Invited
• [Presentation] Machine learning approach to fully automated protein structure determination directly from NMR spectra (2021)
  • Author(s): Peter Guentert
  • Organizer: 42nd FGMR Annual Discussion Meeting, Online, Germany
  • Int'l Joint Research / Invited
• [Presentation] Machine learning approach to fully automated protein structure determination directly from NMR spectra (2021)
  • Author(s): Piotr Klukowski, Peter Guentert
  • Organizer: Biomolecular NMR: Advanced Tools, Advanced hands-on PhD course, Gothenburg, Sweden
  • Invited
• [Remarks] NMRtist
  • URL: https://nmrtist.org
• [Remarks] NMRtist
  • URL: https://nmrtist.org/