2022 Fiscal Year Annual Research Report
Use of contact prediction-based restraints for protein structure determination from sparse NMR data
| Project/Area Number |
20K06508
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| Research Institution | Tokyo Metropolitan University |
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Principal Investigator |
PETER GUENTERT 東京都立大学, 理学研究科, 客員教授 (20392110)
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| 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)
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| Project Period (FY) |
2020-04-01 – 2023-03-31
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| Keywords | machine learning / NMR / protein structure / automated assignment |
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| 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.
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Research Products
(13 results)
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[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
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Journal Title
Nature Communications
Volume: 13
Pages: 6232
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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[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
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Journal Title
Biomolecular NMR Assignments
Volume: 16
Pages: 297-303
DOI
Peer Reviewed / Int'l Joint Research
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[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
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Journal Title
Biomolecular NMR Assignments
Volume: 16
Pages: 41-49
DOI
Peer Reviewed / Int'l Joint Research
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[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
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