Journal of Biomolecular NMR

, Volume 54, Issue 1, pp 81–95 | Cite as

TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra

  • Anna Zawadzka-Kazimierczuk
  • Wiktor Koźmiński
  • Martin Billeter
Article

Abstract

While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space, combined with sparse multidimensional Fourier transform (SMFT), allows for efficient recording of very high dimensional spectra (≥4 dimensions) while maintaining high resolution. However, the nature of this data demands for automation of the assignment process. Here we present the program TSAR (Tool for SMFT-based Assignment of Resonances), which exploits all advantages of SMFT input. Moreover, its flexibility allows to process data from any type of experiments that provide sequential connectivities. The algorithm was tested on several protein samples, including a disordered 81-residue fragment of the δ subunit of RNA polymerase from Bacillus subtilis containing various repetitive sequences. For our test examples, TSAR achieves a high percentage of assigned residues without any erroneous assignments.

Keywords

Algorithm Automated resonance assignment High-dimensional fast NMR Intrinsically disordered protein 

Supplementary material

10858_2012_9652_MOESM1_ESM.pdf (365 kb)
Supplementary material 1 (PDF 364 kb)

References

  1. Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struct Biol 14:547–553CrossRefGoogle Scholar
  2. Baran MC, Huang YJ, Moseley HN, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3556CrossRefGoogle Scholar
  3. Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207–213CrossRefGoogle Scholar
  4. Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT—a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149CrossRefGoogle Scholar
  5. Bermel W, Bertini I, Felli IC, Piccioli M, Pierattelli R (2006) 13C-detected protonless NMR spectroscopy of proteins in solution. Prog Nucl Magn Reson Spectrosc 48:25–45CrossRefGoogle Scholar
  6. Bermel W, Bertini I, Csizmok V, Felli IC, Pierattelli R, Tompa P (2009) H-start for exclusively heteronuclear NMR spectroscopy: the case of intrinsically disordered proteins. J Magn Reson 198:275–281ADSCrossRefGoogle Scholar
  7. Borkar A, Kumar D, Hosur RV (2011) AUTOBA: automation of backbone assignment from HN(C)N suite of experiments. J Biomol NMR 50:285–297CrossRefGoogle Scholar
  8. Clubb RT, Thanabal V, Wagner G (1992) A constant-time three-dimensional triple-resonance pulse scheme to correlate intraresidue 1HN, 15 N, and 13C′ chemical shifts in 15 N,13C-labelled proteins. J Magn Reson 97:213–217Google Scholar
  9. Coggins BE, Venters RA, Zhou P (2010) Radial sampling for fast NMR: concepts and practices over three decades. Prog Nucl Magn Reson Spectrosc 57:381–419CrossRefGoogle Scholar
  10. Crippen GM, Rousaki A, Revington M, Zhang Y, Zuiderweg ER (2010) SAGA: rapid automatic mainchain NMR assignment for large proteins. J Biomol NMR 46:281–298CrossRefGoogle Scholar
  11. Forsen S, Drakenberg T, Johansson C, Linse S, Thulin E, Kordel J (1990) Protein engineering and structure/function relations in bovine calbindin D9 k. Adv Exp Med Biol 269:37–42CrossRefGoogle Scholar
  12. Freeman R, Kupče E (2012) Concepts in projection-reconstruction. Top Curr Chem 316:1–20CrossRefGoogle Scholar
  13. Goddard TD, Kneller DG (2002) SPARKY 3. University of California, San FranciscoGoogle Scholar
  14. Grzesiek S, Bax A (1992a) Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114:6291–6293CrossRefGoogle Scholar
  15. Grzesiek S, Bax A (1992b) An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins. J Magn Reson 99:201–207Google Scholar
  16. Hiller S, Wider G (2012) Automated projection spectroscopy and its applications. Top Curr Chem 316:21–47CrossRefGoogle Scholar
  17. Hyberts SG, Arthanari H, Wagner G (2012) Applications of non-uniform sampling and processing. Top Curr Chem 316:125–148CrossRefGoogle Scholar
  18. Jaremko L, Jaremko M, Elfaki I, Mueller JW, Ejchart A, Bayer P, Zhukov I (2011) Structure and dynamics of the first archaeal parvulin reveal a new functionally important loop in parvulin-type prolyl isomerases. J Biol Chem 286:6554–6565CrossRefGoogle Scholar
  19. Jung YS, Zweckstetter M (2004) Mars—robust automatic backbone assignment of proteins. J Biomol NMR 30:11–23CrossRefGoogle Scholar
  20. Kay LE, Ikura M, Tschudin R, Bax A (1990) Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins. J Magn Reson 89:496–514Google Scholar
  21. Kazimierczuk K, Zawadzka A, Koźmiński W (2009) Narrow peaks and high dimensionalities: exploiting the advantages of random sampling. J Magn Reson 197:219–228ADSCrossRefGoogle Scholar
  22. Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W (2010a) Random sampling in multidimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 57:420–434CrossRefGoogle Scholar
  23. Kazimierczuk K, Zawadzka-Kazimierczuk A, Koźmiński W (2010b) Non-uniform frequency domain for optimal exploitation of non-uniform sampling. J Magn Reson 205:286–292ADSCrossRefGoogle Scholar
  24. Kazimierczuk K, Misiak M, Stanek J, Zawadzka-Kazimierczuk A, Kozminski W (2012) Generalized fourier transform for non-uniform sampled data. Top Curr Chem 316:79–124CrossRefGoogle Scholar
  25. Lopez de Saro FJ, Woody AY, Helmann JD (1995) Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. J Mol Biol 252:189–202CrossRefGoogle Scholar
  26. Maciejewski MW, Mobli M, Schuyler AD, Stern AS, Hoch JC (2012) Data sampling in multidimensional NMR: fundamentals and strategies. Top Curr Chem 316:49–77CrossRefGoogle Scholar
  27. Motáčková V, Nováček J, Zawadzka-Kazimierczuk A, Kazimierczuk K, Žídek L, Šanderová H, Krásný L, Koźmiński W, Sklenář V (2010) Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR 48:169–177CrossRefGoogle Scholar
  28. Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Žídek L, Šanderová H, Krásný L, Koźmiński W, Sklenář V (2011) 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomol NMR 50:1–11CrossRefGoogle Scholar
  29. Orekhov VY, Jaravine VA (2011) Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. Prog Nucl Magn Reson Spectrosc 59:271–292CrossRefGoogle Scholar
  30. Parr SR, Barber D, Greenwood C (1976) A purification procedure for the soluble cytochrome oxidase and some other respiratory proteins from Pseudomonas aeruginosa. Biochem J 157:423–430Google Scholar
  31. Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Guntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM (2009) CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods 6:625–626CrossRefGoogle Scholar
  32. Skelton NJ, Kordel J, Chazin WJ (1995) Determination of the solution structure of Apo calbindin D9 k by NMR spectroscopy. J Mol Biol 249:441–462CrossRefGoogle Scholar
  33. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408CrossRefGoogle Scholar
  34. 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
  35. Xu Y, Wang X, Yang J, Vaynberg J, Qin J (2006) PASA–a program for automated protein NMR backbone signal assignment by pattern-filtering approach. J Biomol NMR 34:41–56CrossRefGoogle Scholar
  36. Zawadzka-Kazimierczuk A, Kazimierczuk K, Koźmiński W (2010) A set of 4D NMR experiments of enhanced resolution for easy resonance assignment in proteins. J Magn Reson 202:109–116ADSCrossRefGoogle Scholar
  37. Zawadzka-Kazimierczuk A, Koźmiński W, Šanderová H, Krásný L (2012) High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins. J Biomol NMR 52:329–337CrossRefGoogle Scholar
  38. Zimmerman 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

  • Anna Zawadzka-Kazimierczuk
    • 1
  • Wiktor Koźmiński
    • 1
  • Martin Billeter
    • 2
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Biophysics Group, Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden

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