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SAGA: rapid automatic mainchain NMR assignment for large proteins

Journal of Biomolecular NMR volume 46, pages 281–298 (2010)Cite this article

Abstract

Here we describe a new algorithm for automatically determining the mainchain sequential assignment of NMR spectra for proteins. Using only the customary triple resonance experiments, assignments can be quickly found for not only small proteins having rather complete data, but also for large proteins, even when only half the residues can be assigned. The result of the calculation is not the single best assignment according to some criterion, but rather a large number of satisfactory assignments that are summarized in such a way as to help the user identify portions of the sequence that are assigned with confidence, vs. other portions where the assignment has some correlated alternatives. Thus very imperfect initial data can be used to suggest future experiments.

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Acknowledgments

E.R.P.Z. acknowledges support from NIH grants GM063027 and GM063027-08S1 (E.R.P.Z., PI) and NS059690 (J.E. Gestwicki, PI). We thank Drs. A.V. Kurochkin and D.S. Weaver for the preparation of the Hsc70 NMR samples.

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Author notes

  1. Matthew Revington

    Present address: Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada

  2. Yongbo Zhang

    Present address: Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL, 60208, USA

Affiliations

  1. College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA

    Gordon M. Crippen

  2. LSA Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA

    Aikaterini Rousaki, Matthew Revington & Yongbo Zhang

  3. Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA

    Erik R. P. Zuiderweg

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  1. Gordon M. Crippen
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  2. Aikaterini Rousaki
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  3. Matthew Revington
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  4. Yongbo Zhang
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  5. Erik R. P. Zuiderweg
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Corresponding authors

Correspondence to Gordon M. Crippen or Erik R. P. Zuiderweg.

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Crippen, G.M., Rousaki, A., Revington, M. et al. SAGA: rapid automatic mainchain NMR assignment for large proteins. J Biomol NMR 46, 281–298 (2010). https://doi.org/10.1007/s10858-010-9403-2

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  • DOI: https://doi.org/10.1007/s10858-010-9403-2

Keywords

  • Automatic assignment
  • Generic spin system
  • Triple resonance
  • Large proteins