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Journal of Biomolecular NMR

, Volume 39, Issue 3, pp 223–227 | Cite as

CheckShift: automatic correction of inconsistent chemical shift referencing

  • Simon W. Ginzinger
  • Fabian Gerick
  • Murray Coles
  • Volker Heun
Article

Abstract

The construction of a consistent protein chemical shift database is an important step toward making more extensive use of this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated. Preprocessing of the data is therefore required to detect and correct referencing errors. We have developed a program for performing this task, based on the comparison of reported and expected chemical shift distributions. This program, named CheckShift, does not require additional data and is therefore applicable to data sets where structures are not available. Therefore CheckShift provides the possibility to re-reference chemical shifts prior to their use as structural constraints.

Keywords

Chemical shifts Re-referencing NMR 

References

  1. Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H (1999) The solution structure of VAT-N reveals a ‘missing link’ in the evolution of complex enzymes from a simple βαββ element. Curr Biol 9(20):1158–1168CrossRefGoogle Scholar
  2. Coles M, Hulko M, Djuranovic S, Truffault V, Koretke K, Martin J, Lupas AN (2006) Common evolutionary origin of swapped-hairpin and double-psi beta barrels. Structure 14(10):1489–1498CrossRefGoogle Scholar
  3. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13(3):289–302CrossRefGoogle Scholar
  4. Ginzinger SW, Fischer J (2006) SimShift: identifying structural similarities from NMR chemical shifts. Bioinformatics 22(4):460–465CrossRefGoogle Scholar
  5. Ginzinger SW, Gräupl T, Heun V (2007) SimShiftDB: Chemical-Shift-based homology modeling’. Proceedings of the first International Conference on Bioinformatics Research and Development, BIRD 2007, Springer LNBI 4414Google Scholar
  6. Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H (2006) The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode. J Biol Chem 281(14):9641–9649CrossRefGoogle Scholar
  7. Heinig M, Frishman D (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32(Web Server Issue):W500–W502CrossRefGoogle Scholar
  8. Heller M, John M, Coles M, Bosch G, Baumeister W, Kessler H (2004) NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region. J Mol Biol 336(3):717–729CrossRefGoogle Scholar
  9. Hulko M, Berndt F, Gruber M, Linder JU, Truffault V, Schultz A, Martin J, Schultz JE, Lupas AN, Coles M (2006) The HAMP domain structure implies helix rotation in transmembrane signaling. Cell 126(5):929–940CrossRefGoogle Scholar
  10. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195–202CrossRefGoogle Scholar
  11. Mao Y, Senic-Matuglia F, Fiore PPD, Polo S, Hodsdon ME, Camilli PD (2005) Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain. Proc Natl Acad Sci U.S.A. 102(36):12700–12705CrossRefADSGoogle Scholar
  12. Neal S, Berjanskii M, Zhang H, Wishart DS (2006) Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magn Reson Chem 44:S158–S167CrossRefGoogle Scholar
  13. Neal S, Nip AM, Zhang H, Wishart DS (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 26(3):215–240CrossRefGoogle Scholar
  14. Nicastro G, Menon RP, Masino L, Knowles PP, McDonald NQ, Pastore A (2005) The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition. Proc Natl Acad Sci U.S.A. 102(30):10493–10498CrossRefADSGoogle Scholar
  15. Oldfield E (1995) Chemical shifts and three-dimensional protein structures. J Biomol NMR 5(3):217–225CrossRefGoogle Scholar
  16. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160(1):65–73CrossRefADSGoogle Scholar
  17. Seavey B, Farr E, Westler W, Markley J (1991) A Relational Database for Sequence-Specific Protein NMR Data. J Biomol NMR 1:217–236CrossRefGoogle Scholar
  18. Wang L, Eghbalnia HR, Bahrami A, Markley JL (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR 32(1):13–22CrossRefGoogle Scholar
  19. Wang Y, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11(4):852–861CrossRefGoogle Scholar
  20. Wang Y, Wishart DS (2005) A simple method to adjust inconsistently ref- erenced 13C and 15N chemical shift assignments of proteins. J Biomol NMR 31(2):143–148zbMATHCrossRefGoogle Scholar
  21. Wishart DS, Sykes BD, Richards FM (1992) The Chemical Shift Index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31(6):1647–1651CrossRefGoogle Scholar
  22. Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25(3):173–195CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Simon W. Ginzinger
    • 1
  • Fabian Gerick
    • 1
    • 2
  • Murray Coles
    • 3
  • Volker Heun
    • 1
  1. 1.Institut für InformatikLudwig-Maximilians-Universität MünchenMünchenGermany
  2. 2.European Bioinformatics Institute, Wellcome Trust Genome CampusHinxtonUK
  3. 3.Lehrstuhl für Organische Chemie II, Department für ChemieTechnische Universität MünchenGarchingGermany

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