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NMR: prediction of protein flexibility

Nature Protocols volume 1, pages 683–688 (2006)Cite this article

Abstract

We present a protocol for predicting protein flexibility from NMR chemical shifts. The protocol consists of (i) ensuring that the chemical shift assignments are correctly referenced or, if not, performing a reference correction using information derived from the chemical shift index, (ii) calculating the random coil index (RCI), and (iii) predicting the expected root mean square fluctuations (RMSFs) and order parameters (S2) of the protein from the RCI. The key advantages of this protocol over existing methods for studying protein dynamics are that (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments. When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1–2 h using a spreadsheet program.

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Figure 1: Correlation of RCI with model-free order parameters (S2) and RMSFs of MD and NMR ensembles.

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References

  1. Carugo, O. & Argos, P. Reliability of atomic displacement parameters in protein crystal structures. Acta Crystallogr. D Biol. Crystallogr. 55, 473–478 (1999).

    Article  CAS  Google Scholar 

  2. Petsko, G.A. & Ringe, D. Fluctuations in protein structure from X-ray diffraction. Annu. Rev. Biophys. Bioeng. 13, 331–371 (1984).

    Article  CAS  Google Scholar 

  3. Hansson, T., Oostenbrink, C. & van Gunsteren, W. Molecular dynamics simulations. Curr. Opin. Struct. Biol. 12, 190–196 (2002).

    Article  CAS  Google Scholar 

  4. Elofsson, A. & Nilsson, L. How consistent are molecular-dynamics simulations — comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. J. Mol. Biol. 233, 766–780 (1993).

    Article  CAS  Google Scholar 

  5. Kay, L.E. Protein dynamics from NMR. Nat. Struct. Biol. 5 (Suppl.): 513–517 (1998).

    Article  CAS  Google Scholar 

  6. Ishima, R. & Torchia, D.A. Protein dynamics from NMR. Nat. Struct. Biol. 7, 740–743 (2000).

    Article  CAS  Google Scholar 

  7. Palmer, A.G. NMR probes of molecular dynamics: overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30, 129–155 (2001).

    Article  CAS  Google Scholar 

  8. Lacroix, E., Bruix, M., Lopez-Hernandez, E., Serrano, L. & Rico, M. Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli. J. Mol. Biol. 271, 472–487 (1997).

    Article  CAS  Google Scholar 

  9. Korzhnev, D.M., Orekhov, V.Y. & Arseniev, A.S. Model-free approach beyond the borders of its applicability. J. Magn. Reson. 127, 184–191 (1997).

    Article  CAS  Google Scholar 

  10. Palmer, A.G., Kroenke, C.D. & Loria, J.P. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 339, 204–238 (2001).

    Article  CAS  Google Scholar 

  11. Fushman, D., Cahill, S. & Cowburn, D. The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution — analysis of N-15 relaxation with monomer/dimer equilibration. J. Mol. Biol. 266, 173–194 (1997).

    Article  CAS  Google Scholar 

  12. Berjanskii, M.V. & Wishart, D.S. A simple method to predict protein flexibility using secondary chemical shifts. J. Am. Chem. Soc. 127, 14970–14971 (2005).

    Article  CAS  Google Scholar 

  13. Wishart, D.S., Sykes, B.D. & Richards, F.M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31, 1647–1651 (1992).

    Article  CAS  Google Scholar 

  14. Wishart, D.S. & Sykes, B.D. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J. Biomol. NMR 4, 171–180 (1994).

    Article  CAS  Google Scholar 

  15. Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559 (1982).

    Article  CAS  Google Scholar 

  16. Clore, G.M. et al. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112, 4989–4991 (1990).

    Article  CAS  Google Scholar 

  17. Markley, J.L. et al. Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC–IUBMB–IUPAB inter-union task group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J. Biomol. NMR 12, 1–23 (1998).

    Article  CAS  Google Scholar 

  18. Wishart, D.S. et al. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR 6, 135–140 (1995).

    Article  CAS  Google Scholar 

  19. Zhang, H., Neal, S. & Wishart, D.S. RefDB: a database of uniformly referenced protein chemical shifts. J. Biomol. NMR 25, 173–195 (2003).

    Article  CAS  Google Scholar 

  20. Schwarzinger, S., Kroon, G.J., Foss, T.R., Wright, P.E. & Dyson, H.J. Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView. J. Biomol. NMR 18, 43–48 (2000).

    Article  CAS  Google Scholar 

  21. Schwarzinger, S. et al. Sequence-dependent correction of random coil NMR chemical shifts. J. Am. Chem. Soc. 123, 2970–2978 (2001).

    Article  CAS  Google Scholar 

  22. Wang, Y. & Jardetzky, O. Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci. 11, 852–861 (2002).

    Article  CAS  Google Scholar 

  23. Iwahara, J., Peterson, R.D. & Clubb, R.T. Compensating increases in protein backbone flexibility occur when the dead ringer AT-rich interaction domain (ARID) binds DNA: a nitrogen-15 relaxation study. Protein Sci. 14, 1140–1150 (2005).

    Article  CAS  Google Scholar 

  24. Zhang, F. & Bruschweiler, R. Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654–12655 (2002).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the Natural Sciences and Engineering Research Council, the National Research Council's National Institute for Nanotechnology and the Protein Engineering Network of Centers of Excellence.

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Authors and Affiliations

  1. Department of Computing Science, 2-21 Athabasca Hall, University of Alberta, Edmonton, T6G 2E8, Alberta, Canada

    Mark Berjanskii & David S Wishart

  2. NRC National Institute for Nanotechnology, Edmonton, Alberta, Canada

    David S Wishart

Authors
  1. Mark Berjanskii
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  2. David S Wishart
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Corresponding author

Correspondence to David S Wishart.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Random coil reference chemical shifts. (DOC 56 kb)

Supplementary Table 2

Neighboring residue chemical shift (in ppm) corrections. (DOC 132 kb)

Supplementary Table 3

Averaged chemical shifts (ppm) observed in β-strands and α-helices. (DOC 79 kb)

Supplementary Table 4

Weighting coefficients for RCI calculations (equation 1) with different sets of chemical shifts. (DOC 147 kb)

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Berjanskii, M., Wishart, D. NMR: prediction of protein flexibility. Nat Protoc 1, 683–688 (2006). https://doi.org/10.1038/nprot.2006.108

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