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 PervushinEmail author


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.


MDD Automatic resonance assignment Nonlinear data sampling Targeted NMR data acquisition 



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


Nuclear magnetic resonance


Relative hypothesis prioritization


Multidimensional decomposition


Nonlinear sampling


Targeted acquisition



This work was funded by the Academic Research Fund Tier-2 grant of Ministry of Education of Singapore to Konstantin Pervushin and Bruker BioSpin Group AG, Germany, grant to James E. Masse.

Supplementary material

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


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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
    Email author
  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

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