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 Wüthrich
Article

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.

Keywords

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

References

  1. Atreya HS, Sahu SC, Chary KVR, Govil G (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J Biomol NMR 17:125–136CrossRefGoogle Scholar
  2. Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT—a general algorithm for resonance assignment in multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149CrossRefGoogle Scholar
  3. Cavanagh J, Fairbrother WJ, Rance M, Palmer AG III, Skelton NJ (2007) Protein NMR spectroscopy: principles and practice, 2nd edn. Elsevier Academic Press, AmsterdamGoogle Scholar
  4. Crippen GM, Rousaki A, Revington M, Zhang Y, Zuiderweg ERP (2010) SAGA: rapid automatic mainchain NMR assignment for large proteins. J Biomol NMR 46:281–298CrossRefGoogle Scholar
  5. DeMarco A, Wüthrich K (1976) Digital filtering with a sinusoidal window function: an alternative technique for resolution enhancement in FT NMR. J Magn Reson 24:201–204Google Scholar
  6. Elsliger MA, Deacon A, Godzik A, Lesley S, Wooley J, Wüthrich K, Wilson IA (2010) The JCSG high-throughput structural biology pipeline. Acta Cryst F 66:1137–1142CrossRefGoogle Scholar
  7. Fiorito F, Herrmann T, Damberger FF, Wüthrich K (2008) Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved [1H,1H]-spectra. J Biomol NMR 42:23–33CrossRefGoogle Scholar
  8. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298CrossRefGoogle Scholar
  9. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227CrossRefGoogle Scholar
  10. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189CrossRefGoogle Scholar
  11. Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102(31):10876–10881ADSCrossRefGoogle Scholar
  12. Hiller S, Wider G, Wüthrich K (2008) APSY-NMR with proteins: practical aspects and backbone assignment. J Biomol NMR 42:179–195CrossRefGoogle Scholar
  13. Ikeya T, Jee J-G, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P (2011) Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J Biomol NMR 50:137–146CrossRefGoogle Scholar
  14. Jaudzems K, Geralt M, Serrano P, Mohanty B, Horst R, Pedrini B, Elsliger MA, Wilson IA, Wüthrich K (2010) NMR structure of the protein NP_247299.1: comparison with the crystal structure. Acta Cryst F 66:1367–1380CrossRefGoogle Scholar
  15. Keller R (2004) CARA: computer aided resonance assignment. http://cara.nmr.ch/
  16. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51–55CrossRefGoogle Scholar
  17. Kraulis PJ (1994) Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. J Mol Biol 243:696–728CrossRefGoogle Scholar
  18. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291CrossRefGoogle Scholar
  19. Lemak A, Steren CA, Arrowsmith CH, Llinas M (2008) Sequence specific resonance assignment via multicanonical Monte Carlo search using an ABACUS approach. J Biomol NMR 41:29–41CrossRefGoogle Scholar
  20. Lescop E, Brutscher B (2009) Highly automated protein backbone resonance assignment within a few hours: the «BATCH» strategy and software package. J Biomol NMR 44:43–57CrossRefGoogle Scholar
  21. Lesley S, Kuhn P, Godzik A, Deacon A, Mathews I, Kreusch A, Spraggon G, Klock H, McMullan D, Shin T, Vincent J, Robb A, Brinen L, Miller M, McPhillips T, Miller M, Scheibe D, Canaves J, Guda C, Jaroszewski L, Selby T, Elsliger MA, Wooley J, Taylor S, Hodgson K, Wilson IA, Schultz P, Stevens R (2002) Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 99:11664–11669ADSCrossRefGoogle Scholar
  22. Lüthy R, Bowie J, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85ADSCrossRefGoogle Scholar
  23. Metzler W, Constantine K, Friedrichs M, Bell A, Ernst E, Lavoie T, Mueller L (1993) Charecterization of the three-dimensional solution structure of human profilin: 1H, 13C, and 15N NMR assignments and global folding pattern. Biochemistry 32:13818–13829Google Scholar
  24. Mohanty B, Serrano P, Pedrini B, Jaudzems K, Geralt M, Horst R, Herrmann T, Elsliger ME, Wilson IA, Wüthrich K (2010) NMR structure of the protein NP_247299.1: comparison with the crystal structure. Acta Cryst F 66:1381–1392CrossRefGoogle Scholar
  25. Moseley HN, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Meth Enzym 399:91–108CrossRefGoogle Scholar
  26. Page R, Peti W, Wilson IA, Stevens RC, Wüthrich K (2005) NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc Natl Acad Sci USA 102(6):1901–1905ADSCrossRefGoogle Scholar
  27. Peti W, Page R, Moy K, O’Neil-Johnson M, Wilson IA, Stevens RC, Wüthrich K (2005) Towards miniaturization of a structural genomics pipeline using macro-expression and microcoil NMR. J Struct Funct Genomics 6:259–267CrossRefGoogle Scholar
  28. Schmucki R, Yokohama S, Güntert P (2008) Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm. J Biomol NMR 43:97–109CrossRefGoogle Scholar
  29. Serrano P, Pedrini B, Geralt M, Jaudzems K, Mohanty B, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K (2010) Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites. Acta Cryst F 66(10):1392–1405CrossRefGoogle Scholar
  30. Staykova DK, Fredriksson J, Bermel W, Billeter M (2008) Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach. J Biomol NMR 42:87–97CrossRefGoogle Scholar
  31. Volk J, Herrmann T, Wüthrich K (2008) Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR 41:127–138CrossRefGoogle Scholar
  32. Wishart D, Sykes B (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:135–140CrossRefGoogle Scholar
  33. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkGoogle Scholar
  34. Wüthrich K (2010) NMR in a crystallography-based high-throughput protein structure-determination environment. Acta Cryst F 66:1365–1366CrossRefGoogle Scholar
  35. Zimmermann DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610CrossRefGoogle Scholar

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
  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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