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2022 Fiscal Year Annual Research Report

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

Research Project

Project/Area Number 20K06508
Research InstitutionTokyo Metropolitan University

Principal Investigator

PETER GUENTERT  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
Keywordsmachine learning / NMR / protein structure / automated assignment
Outline of Annual Research Achievements

In the last year of this project, we have been able to incorporate 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 multi-dimensional NMR spectra without any manual work. The AlphaFold2 structures can be used in ARTINA for the structure-based prediction of approximate chemical shifts, as well as for generating the cross peaks that are expected in NOESY-type spectra. We could show that, in these ways, the AlphaFold2 structures improve the quality of the chemical shift assignment. In particular, AlphaFold2 structures allow to obtain reliable assignments also from much smaller sets of input spectra than were used in the absence of input structures. Consequently, NMR measurement times can be significantly reduced and the NMR analysis of proteins becomes more efficient.
The ARTINA algorithm has been made available as a webserver, NMRtist (https://nmrtist.org), that allows scientists to obtain assignments and structures of proteins within a few hours of pure computation time rather than weeks or months of manual analysis.
We have published the ARTINA algorithm in Nature Communications (2022) and the NMRtist webserver in 2023 in Bioinformatics (2023), and we have prepared a manuscript on the use of ARTINA in conjunction with AlphaFold2 structures that will be submitted soon.

  • Research Products

    (13 results)

All 2023 2022 Other

All Journal Article (7 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 7 results,  Open Access: 5 results) Presentation (5 results) (of which Int'l Joint Research: 4 results,  Invited: 5 results) Remarks (1 results)

  • [Journal Article] NMRtist: an online platform for automated biomolecular NMR spectra analysis2023

    • Author(s)
      Klukowski Piotr, Riek Roland, Guentert Peter
    • Journal Title

      Bioinformatics

      Volume: 39 Pages: btad066

    • 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 ARTINA2022

    • Author(s)
      Klukowski Piotr, Riek Roland, Guentert Peter
    • Journal Title

      Nature Communications

      Volume: 13 Pages: 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 structures2022

    • Author(s)
      Ashkinadze Dzmitry, Klukowski Piotr, Kadavath Harindranath, Guentert Peter, Riek Roland
    • Journal Title

      Structure

      Volume: 30 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

    • 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 domain2022

    • 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 Pages: 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 biogenesis2022

    • Author(s)
      Kuwasako Kanako, Suzuki Sakura, Nameki Nobukazu, Takizawa Masayuki, Takahashi Mar, Tsuda Kengo, Nagata Takashi, Watanabe Satoru、Tanaka Akiko, Kobayashi Naohiro, Kigawa Takanori, Guentert Peter, Shirouzu Mikako, Yokoyama Shigeyuki, Muto Yutaka
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 16 Pages: 297-303

    • DOI

      10.1007/s12104-022-10094-3

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 1H, 13C and 15N resonance assignments and solution structures of the two RRM domains of Matrin-32022

    • Author(s)
      He Fahu, Kuwasako Kanako, Takizawa Masayuki, Takahashi Mari, Tsuda Kengo, Nagata Takashi, Watanabe Satoru, Tanaka Akiko, Kobayashi Naohiro, Kigawa Takanori, Guentert Peter, Shirouzu Mikako, Yokoyama Shigeyuki, Muto Yutaka
    • Journal Title

      Biomolecular NMR Assignments

      Volume: 16 Pages: 41-49

    • DOI

      10.1007/s12104-021-10057-0

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Automated biomolecular NMR spectra analysis, assignments, and structures with the deep learning technique ARTINA2022

    • 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 ARTINA2022

    • 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 ARTINA2022

    • 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 analysis2022

    • 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 calculation2022

    • 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
  • [Remarks] NMRtist

    • URL

      https://nmrtist.org

URL: 

Published: 2023-12-25  

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