Journal of Biomolecular NMR

, Volume 42, Issue 2, pp 77–86 | Cite as

Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data

  • Leo E. Wong
  • James E. Masse
  • Victor Jaravine
  • Vladislav Orekhov
  • Konstantin Pervushin
Article

Abstract

The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa 13C,15 N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.

Keywords

MDD Automatic resonance assignment Nonlinear data sampling Targeted NMR data acquisition 

Abbreviations

DSS

2,2-Dimethyl-2-silapentane-5-sulfonate, sodium salt

NMR

Nuclear magnetic resonance

RHP

Relative hypothesis prioritization

MDD

Multidimensional decomposition

NLS

Nonlinear sampling

TA

Targeted acquisition

Supplementary material

10858_2008_9269_MOESM1_ESM.pdf (881 kb)
MOESM1 (PDF 880 kb)

References

  1. Armstrong GS, Mandelshtam VA, Shaka AJ, Bendiak B (2005) Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides. J Magn Reson 173:160–168CrossRefADSGoogle Scholar
  2. 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
  3. Atreya HS, Chary KVR, Govil G (2002) Automated NMR assignments of proteins for high throughput structure determination: TATAPRO II. Curr Sci 83:1372–1376Google Scholar
  4. Atreya HS, Garcia E, Shen Y, Szyperski T (2007) J-GFT NMR for precise measurement of mutually correlated nuclear spin-spin couplings. J Am Chem Soc 129:680–692CrossRefGoogle Scholar
  5. Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The Program Xeasy for computer-supported nmr spectral-analysis of biological macromolecules. J Biomol NMR 6:1–10CrossRefGoogle Scholar
  6. Bohm M, Stadlthanner K, Tome AM, Gruber P, Teixeira AR, Theis FJ, Puntonet CG, Lang EW (2005) AutoAssign—an automatic assignment tool for independent components. In: Proceedings of pattern recognition and image analysis, Pt. 2, vol. 3523. Springer, Berlin, pp 75–82Google Scholar
  7. Coggins BE, Zhou P (2003) PACES: protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93–111CrossRefGoogle Scholar
  8. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) Nmrpipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  9. Eghbalnia HR, Bahrami A, Tonelli M, Hallenga K, Markley JL (2005a) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am Chem Soc 127:12528–12536CrossRefGoogle Scholar
  10. Eghbalnia HR, Bahrami A, Wang LY, Assadi A, Markley JL (2005b) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO). J Biomol NMR 32:219–233CrossRefGoogle Scholar
  11. Enggist E, Thony-Meyer L, Güntert P, Pervushin K (2002) NMR structure of the heme chaperone CcmE reveals a novel functional motif. Structure 10:1551–1557CrossRefGoogle Scholar
  12. Fiorito F, Hiller S, Wider G, Wüthrich K (2006) Automated resonance assignment of proteins: 6D APSY-NMR. J Biomol NMR 35:27–37CrossRefGoogle Scholar
  13. Frueh DP, Sun ZY, Vosburg DA, Walsh CT, Hoch JC, Wagner G (2006) Non-uniformly sampled double-TROSY hNcaNH experiments for NMR sequential assignments of large proteins. J Am Chem Soc 128:5757–5763CrossRefGoogle Scholar
  14. Frydman L, Lupulescu A, Scherf T (2003) Principles and features of single-scan two-dimensional NMR spectroscopy. J Am Chem Soc 125:9204–9217CrossRefGoogle Scholar
  15. Gal M, Schanda P, Brutscher B, Frydman L (2007) UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. J Am Chem Soc 129:1372–1377CrossRefGoogle Scholar
  16. Grishaev A, Llinas M (2004) BACUS: a Bayesian protocol for the identification of protein NOESY spectra via unassigned spin systems. J Biomol NMR 28:1–10CrossRefGoogle Scholar
  17. Grishaev A, Steren CA, Wu B, Pineda-Lucena A, Arrowsmith C, Llinas M (2005) ABACUS, a direct method for protein NMR structure computation via assembly of fragments. Proteins 61:36–43CrossRefGoogle Scholar
  18. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189CrossRefGoogle Scholar
  19. Herrmann T, Güntert P, Wüthrich K (2002b) 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
  20. Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876–10881CrossRefADSGoogle Scholar
  21. Hiller S, Wasmer C, Wider G, Wüthrich K (2007) Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR spectroscopy. J Am Chem Soc 129:10823–10828CrossRefGoogle Scholar
  22. Hitchens TK, Lukin JA, Zhan YP, McCallum SA, Rule GS (2003) MONTE: an automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 25:1–9CrossRefGoogle Scholar
  23. Jaravine V, Orekhov V (2006) Targeted acquisition for real-time NMR spectroscopy. J Am Chem Soc 128:13421–13426CrossRefGoogle Scholar
  24. Jaravine VA, Ibraghimov I, Orekhov VY (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 3:605–607CrossRefGoogle Scholar
  25. Jaravine VA, Zhuravleva AV, Permi P, Ibraghimov I, Orekhov VY (2008) Hyperdimensional NMR spectroscopy with nonlinear sampling. J Am Chem Soc 130:3927–3936CrossRefGoogle Scholar
  26. Jung YS, Zweckstetter M (2004) Mars—robust automatic backbone assignment of proteins. J Biomol NMR 30:11–23CrossRefGoogle Scholar
  27. Kazimierczuk K, Kozminski W, Zhukov I (2006a) Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. J Magn Reson 179:323–328CrossRefADSGoogle Scholar
  28. Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006b) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157–168CrossRefGoogle Scholar
  29. Kim S, Szyperski T (2003) GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc 125:1385–1393CrossRefGoogle Scholar
  30. Kupce E, Freeman R (2004) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126:6429–6440CrossRefGoogle Scholar
  31. Kupce E, Freeman R (2007) Fast multidimensional NMR by polarization sharing. Magn Reson Chem 45:2–4 CrossRefGoogle Scholar
  32. Langmead CJ, Donald BR (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J Biomol NMR 29:111–138CrossRefGoogle Scholar
  33. Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL (2005) GANA—a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res 33:4593–4601CrossRefGoogle Scholar
  34. Luan T, Jaravine V, Yee A, Arrowsmith CH, Orekhov VY (2005) Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition. J Biomol NMR 33:1–14CrossRefGoogle Scholar
  35. Mandelshtam VA (2000) The multidimensional filter diagonalization method. J Magn Reson 144:343–356CrossRefADSGoogle Scholar
  36. Mandelshtam VA, Taylor HS, Shaka AJ (1998) Application of the filter diagonalization method to one- and two-dimensional NMR spectra. J Magn Reson 133:304–312CrossRefADSGoogle Scholar
  37. Marion D (2005) Fast acquisition of NMR spectra using Fourier transform of non-equispaced data. J Biomol NMR 32:141–150CrossRefGoogle Scholar
  38. Masse JE, Keller R (2005) AutoLink: automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 174:133–151CrossRefADSGoogle Scholar
  39. Masse JE, Keller R, Pervushin K (2006) SideLink: automated side-chain assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 181:45–67CrossRefADSGoogle Scholar
  40. Mishkovsky M, Kupce E, Frydman L (2007) Ultrafast-based projection-reconstruction three-dimensional nuclear magnetic resonance spectroscopy. J Chem Phys 127:034507CrossRefADSGoogle Scholar
  41. Nilges M, Macias MJ, Odonoghue SI, Oschkinat H (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 269:408–422CrossRefGoogle Scholar
  42. Orekhov VY, Ibraghimov IV, Billeter M (2001) MUNIN: a new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR 20:49–60CrossRefGoogle Scholar
  43. Pervushin K, Vogeli B, Eletsky A (2002) Longitudinal H-1 relaxation optimization in TROSY NMR spectroscopy. J Am Chem Soc 124:12898–12902CrossRefGoogle Scholar
  44. Pristovsek P, Ruterjans H, Jerala R (2002) Semiautomatic sequence-specific assignment of proteins based on the tertiary structure—the program st2nmr. J Comput Chem 23:335–340CrossRefGoogle Scholar
  45. Rovnyak D, Frueh DP, Sastry M, Sun ZY, Stern AS, Hoch JC, Wagner G (2004) Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. J Magn Reson 170:15–21CrossRefADSGoogle Scholar
  46. Schanda P, Kupce E, Brutscher B (2005) SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33:199–211CrossRefGoogle Scholar
  47. Snyder DA, Xu Y, Yang D, Brüschweiler R (2007a) Resolution-enhanced 4D 15 N/13C NOESY protein NMR spectroscopy by application of the covariance transform. J Am Chem Soc 129:14126–14127CrossRefGoogle Scholar
  48. Snyder DA, Zhang F, Brüschweiler R (2007b) Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins. J Biomol NMR 39:165–175CrossRefGoogle Scholar
  49. Takeda M, Ikeya T, Güntert P, Kainosho M (2007) Automated structure determination of proteins with the SAIL-FLYA NMR method. Nat Protocol 2:2896–2902CrossRefGoogle Scholar
  50. Tian F, Valafar H, Prestegard JH (2001) A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J Am Chem Soc 123:11791–11796CrossRefGoogle Scholar
  51. Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY (2005) High-resolution four-dimensional H-1-C-13 NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J Am Chem Soc 127:2767–2775CrossRefGoogle Scholar
  52. Wu KP, Chang JM, Chen JB, Chang CF, Wu WJ, Huang TH, Sung TY, Hsu WL (2005) RIBRA—an error-tolerant algorithm for the NMR backbone assignment problem. In: Proceedings of research in computational molecular biology, vol. 3500. Springer, Berlin, pp 103–117Google Scholar
  53. Zhang F, Brüschweiler R (2004) Indirect covariance NMR spectroscopy. J Am Chem Soc 126:13180–13181CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Leo E. Wong
    • 1
  • James E. Masse
    • 2
    • 3
  • Victor Jaravine
    • 4
    • 5
  • Vladislav Orekhov
    • 4
  • Konstantin Pervushin
    • 1
    • 6
  1. 1.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
  2. 2.Laboratorium für Physikalische ChemieETH-HönggerbergZurichSwitzerland
  3. 3.National Institutes of HealthBethesdaUSA
  4. 4.Swedish NMR CentreGothenburg UniversityGothenburgSweden
  5. 5.Institute of Biophysical ChemistryJ. W. Goethe-University FrankfurtFrankfurt am MainGermany
  6. 6.Biozentrum of University BaselBaselSwitzerland

Personalised recommendations