Journal of Biomolecular NMR

, Volume 61, Issue 1, pp 47–53 | Cite as

APSY-NMR for protein backbone assignment in high-throughput structural biology

  • Samit Kumar Dutta
  • Pedro Serrano
  • Andrew Proudfoot
  • Michael Geralt
  • Bill Pedrini
  • Torsten Herrmann
  • Kurt Wüthrich
Article

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 [1H,1H]-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.

Keywords

Automated projection spectroscopy Automated data analysis UNIO software J-UNIO protocol Protein structure determination 

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Samit Kumar Dutta
    • 1
    • 2
  • Pedro Serrano
    • 1
    • 2
  • Andrew Proudfoot
    • 1
    • 2
  • Michael Geralt
    • 1
    • 2
  • Bill Pedrini
    • 1
    • 2
    • 4
    • 6
  • Torsten Herrmann
    • 5
  • Kurt Wüthrich
    • 1
    • 2
    • 3
    • 4
  1. 1.Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaUSA
  2. 2.Joint Center for Structural GenomicsLa JollaUSA
  3. 3.Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA
  4. 4.Institute of Molecular Biology and BiophysicsETH ZürichZurichSwitzerland
  5. 5.Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1Université de LyonVilleurbanneFrance
  6. 6.SwissFEL ProjectPaul Scherrer Institute (PSI)VilligenSwitzerland

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