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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

Notes

Acknowledgement

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
  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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