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


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Article Info

DATE

2012-07-03

AUTHORS

Pedro Serrano, Bill Pedrini, Biswaranjan Mohanty, Michael Geralt, Torsten Herrmann, Kurt Wüthrich

ABSTRACT

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. More... »

PAGES

341-354

References to SciGraph publications

  • 2010-03-16. SAGA: rapid automatic mainchain NMR assignment for large proteins in JOURNAL OF BIOMOLECULAR NMR
  • 2002-11. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS in JOURNAL OF BIOMOLECULAR NMR
  • 2005-11-09. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS
  • 2008-10-08. APSY-NMR with proteins: practical aspects and backbone assignment in JOURNAL OF BIOMOLECULAR NMR
  • 1992-03. Assessment of protein models with three-dimensional profiles in NATURE
  • 2008-05-06. Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach in JOURNAL OF BIOMOLECULAR NMR
  • 2008-05-30. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH in JOURNAL OF BIOMOLECULAR NMR
  • 2008-11-26. Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm in JOURNAL OF BIOMOLECULAR NMR
  • 2008-09-06. Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach in JOURNAL OF BIOMOLECULAR NMR
  • 2000-06. A tracked approach for automated NMR assignments in proteins (TATAPRO) in JOURNAL OF BIOMOLECULAR NMR
  • 2011-03-30. Exclusively NOESY-based automated NMR assignment and structure determination of proteins in JOURNAL OF BIOMOLECULAR NMR
  • 2009-04-15. Highly automated protein backbone resonance assignment within a few hours: the «BATCH» strategy and software package in JOURNAL OF BIOMOLECULAR NMR
  • 1994-03. The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data in JOURNAL OF BIOMOLECULAR NMR
  • 2008-08-16. Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY in JOURNAL OF BIOMOLECULAR NMR
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10858-012-9645-2

    DOI

    http://dx.doi.org/10.1007/s10858-012-9645-2

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22752932


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    38 APSY-NMR spectroscopy
    39 JCSG target list
    40 JCSG targets
    41 NMR
    42 NMR data
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    46 Shewanella amazonensis
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