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Guerry P, Duong VD, Herrmann T. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO. JOURNAL OF BIOMOLECULAR NMR 2015; 62:473-480. [PMID: 25917899 DOI: 10.1007/s10858-015-9934-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/18/2015] [Indexed: 06/04/2023]
Abstract
UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved--including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO-ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications.
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Affiliation(s)
- Paul Guerry
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France
| | - Viet Dung Duong
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à très Hauts Champs, Université de Lyon (UMR 5280 CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), 5 rue de la Doua, 69100, Villeurbanne, France.
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Dutta SK, Serrano P, Proudfoot A, Geralt M, Pedrini B, Herrmann T, Wüthrich K. APSY-NMR for protein backbone assignment in high-throughput structural biology. JOURNAL OF BIOMOLECULAR NMR 2015; 61:47-53. [PMID: 25428764 PMCID: PMC4305044 DOI: 10.1007/s10858-014-9881-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/18/2014] [Indexed: 05/12/2023]
Abstract
A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.
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Affiliation(s)
- Samit Kumar Dutta
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
| | - Bill Pedrini
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA, and Joint Center for Structural Genomics (http://www.jcsg.org.), La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Torsten Herrmann
- Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, Université de Lyon, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
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