Journal of Biomolecular NMR

, Volume 53, Issue 4, pp 341–354 | Cite as

The J-UNIO protocol for automated protein structure determination by NMR in solution

  • Pedro Serrano
  • Bill Pedrini
  • Biswaranjan Mohanty
  • Michael Geralt
  • Torsten Herrmann
  • Kurt WüthrichEmail author


The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6–10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.


APSY-NMR Automation 1H–1H-NOE Joint Center for Structural Genomics (JCSG) JCSG targets Protein structure initiative (PSI) UNIO software 



The following financial support is acknowledged: Swiss National Science Foundation and ETH Zürich through the NCCR Structural Biology; Swiss National Science Foundation for a Fellowship to BP (PA00A–104097/1); NIH, National Institute of General Medical Services, Protein Structure Initiative, Grants U54 GM094586 and U54 GM074898 (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Science or the National Institutes of Health). KW is the Cecil H. and Ida M. Green Professor of Structural Biology at The Scripps Research Institute.


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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Pedro Serrano
    • 1
    • 3
  • Bill Pedrini
    • 1
    • 4
    • 6
  • Biswaranjan Mohanty
    • 1
    • 3
    • 7
  • Michael Geralt
    • 1
    • 3
  • Torsten Herrmann
    • 5
  • Kurt Wüthrich
    • 1
    • 2
    • 3
    • 4
    Email author
  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaUSA
  2. 2.Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA
  3. 3.Joint Center for Structural GenomicsThe Scripps Research InstituteLa JollaUSA
  4. 4.Institute of Molecular Biology and BiophysicsETH ZürichZurichSwitzerland
  5. 5.Centre de RMN à Très Hauts ChampsUniversité de Lyon, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1VilleurbanneFrance
  6. 6.SwissFEL ProjectPaul Scherrer InstituteVilligenSwitzerland
  7. 7.Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleAustralia

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