Journal of Biomolecular NMR

, Volume 37, Issue 3, pp 159–177 | Cite as

Unraveling protein dynamics through fast spectral density mapping

  • Virginie Ropars
  • Sabine Bouguet-Bonnet
  • Daniel Auguin
  • Philippe Barthe
  • Daniel Canet
  • Christian Roumestand


Spectral density mapping at multiple NMR field strengths is probably the best method to describe the dynamical behavior of a protein in solution through the analysis of 15N heteronuclear relaxation parameters. Nevertheless, such analyses are scarcely reported in the literature, probably because this method is excessively demanding in spectrometer measuring time. Indeed, when using n different magnetic fields and assuming the validity of the high frequency approximation, the discrete sampling of the spectral density function with 2n + 1 points needs the measurement of 3n 15N heteronuclear relaxation measurements (n R 1, n R 2, and n15N{1H}NOEs). Based on further approximations, we proposed a new strategy that allows us to describe the spectral density with n + 2 points, with the measurement of a total of n + 2 heteronuclear relaxation parameters. Applied to the dynamics analysis of the protein p13 MTCP1 at three different NMR fields, this approach allowed us to divide by nearly a factor of two the total measuring time, without altering further results obtained by the “model free” analysis of the resulting spectral densities. Furthermore, simulations have shown that this strategy remains applicable to any low isotropically tumbling protein (\(\uptau_{c} > 3\)  ns), and is valid for the types of motion generally envisaged for proteins.


protein dynamics 15N relaxation spectral density mapping 



heteronuclear 15N nuclear Overhauser enhancement

RN(Nz) (R1)

heteronuclear 15N longitudinalrelaxation rate

RN(Nxy) (R2)

heteronuclear 15N transverserelaxation rate

RN(Hz- > Nz) (\(\upsigma\))

cross-relaxation rate between15N and its attached amide proton.


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The authors are grateful to the “Association pour la Recherche sur le Cancer” for a research grant. V. Ropars is supported by the “Ligue Nationale contre le Cancer”.


  1. Abragam A. (1961) Principles of Nuclear Magnetism. Oxford Science Publication, Clarendon Press, OxfordGoogle Scholar
  2. Atkinson R.A., Kieffer B. (2004). Progress in Nuclear Magnetic Resonance Spectroscopy 44:141–187CrossRefGoogle Scholar
  3. Austin R.H., Beeson K.W., Eisenstein L., Frauenfelder H., Gunsalus I.C. (1975). Biochemistry 14:5355–5373CrossRefGoogle Scholar
  4. Barthe P., Chiche L., Declerck N., Delsuc M.-A., Lefèvre J.-F., Malliavin T., Mispelter J., Stern M.-H., Lhoste J.M., Roumestand C. (1999). J. Biomol. NMR 15:271–288CrossRefGoogle Scholar
  5. Barthe, P., Ropars, V. and Roumestand, C. (2006) C. R. Chimie 9, 503–513Google Scholar
  6. Bouguet-Bonnet S., Mutzenhardt P., Roumestand C., Canet D. (2005a). Concepts in Magnetic Resonance 24(1):1–9Google Scholar
  7. Bouguet-Bonnet S., Mutzenhardt P., Roumestand C., Canet D. (2005b). Concepts in Magnetic Resonance 24(1):10–16Google Scholar
  8. Canet D., Barthe P., Mutzenhardt P., Roumestand C. (2001). J. Am. Chem. Soc. 123(19):4567–4576CrossRefGoogle Scholar
  9. Carr H.Y., Purcell E.M. (1954). Phys. Rev. 94:630–632CrossRefADSGoogle Scholar
  10. Clore G.M., Szabo A., Bax A., Kay L.E., Driscoll P.C., Wingfield P.T., Gronenborn A.M. (1990a). J. Am. Chem. Soc. 112:4989–4991CrossRefGoogle Scholar
  11. Clore G.M., Driscoll P.C., Wingfield P.T., Gronenborn A.M. (1990b). Biochemistry 29:7387–7401CrossRefGoogle Scholar
  12. Cornilescu G., Bax A. (2000). J. Am. Chem. Soc. 122:10143–10154CrossRefGoogle Scholar
  13. Eisenmesser E.Z., Millet O., Labeikovsky W., Korzhnev D.M., Wolf-Watz M., Bosco D.A., Skalicky J.J, Kay L.E., Kern D. (2005). Nature 438:117–121CrossRefADSGoogle Scholar
  14. Farrow N.A., Zhang O., Szabo A., Torchia D.A., Kay L.E. (1995). J. Biomol. NMR 6:153–162CrossRefGoogle Scholar
  15. Fushman D., Tjandra N., Cowburn D. (1998). J. Am. Chem. Soc. 120:10947–10952CrossRefGoogle Scholar
  16. Fushman D., Tjandra N., Cowburn D. (1999). J. Am. Chem. Soc. 121:8577–8582CrossRefGoogle Scholar
  17. Fushman D., Cowburn D. (2001). Methods Enzymol. 339:109–126CrossRefGoogle Scholar
  18. Guignard L., Padilla A., Mispelter J., Yang Y.-S., Stern M.-H., Lhoste J.M., Roumestand C. (2000). J. Biomol. NMR 17:215–230CrossRefGoogle Scholar
  19. Habazettl J., Wagner G. (1995). J. Magn. Reson. B109:100–104Google Scholar
  20. Ishima R., Nagayama K. (1995a). Biochemistry 34:3162–3171CrossRefGoogle Scholar
  21. Ishima R., Nagayama K. (1995b) J. Magn. Reson. B108:73–76Google Scholar
  22. Kay L.E., Torchia D.A., Bax A. (1989). Biochemistry 28:8972–8979CrossRefGoogle Scholar
  23. Kay L.E., Nicholson L.K., Delaglio F., Bax A., Torchia D.A. (1992). J. Magn. Reson. 97:359–375Google Scholar
  24. Kitahara R., Royer C., Yamada H., Boyer M., Saldana J.-L., Akasaka K., Roumestand C. (2002). J. Mol Biol. 320:609–628CrossRefGoogle Scholar
  25. Lefèvre J.-F., Dayie K.T., Peng J.W., Wagner G. (1996). Biochemistry 35:2674–2686CrossRefGoogle Scholar
  26. Lienin S.F., Bremi T., Brutscher B., Brushweiler R., Ernst R.R. (1998). J. Am. Chem. Soc. 120:9870–9879CrossRefGoogle Scholar
  27. Lipari G., Szabo A. (1982). J. Am. Chem. Soc. 104:4546–4559CrossRefGoogle Scholar
  28. Marion D., Ikura M., Tschudin R., Bax A. (1989b) J. Magn. Reson. 85:393–399Google Scholar
  29. Meiboom S., Gill D. (1958). Rev. Sci. Instrum. 29:688–691CrossRefADSGoogle Scholar
  30. Mulder F.A.A., Mittermaier A., Hon B., Dahlquist F.W., Kay L.E. (2001). Nature Struct. Biol. 8:932–935CrossRefGoogle Scholar
  31. Palmer A.G. (2004). Chem. Rev. 104:3623–3640CrossRefGoogle Scholar
  32. Peng J.W., Wagner G. (1992a). Biochemistry 31:8571–8586CrossRefGoogle Scholar
  33. Peng J.W., Wagner G. (1992b). J. Magn. Reson. 98:308–332Google Scholar
  34. Peng J.W., Wagner G. (1995). Biochemistry 34:16733–16752CrossRefGoogle Scholar
  35. Piotto M., Saudek V., Sklenar V. (1992). J. Biomol. NMR 2:661–665CrossRefGoogle Scholar
  36. Press W.H., Flannery B.P., Teukolsky S.A., Vetterling W.T. (1986). Numerical Recipes. Cambridge University Press, CambridgeGoogle Scholar
  37. Skelton N.J., Palmer A.G., III, Akke M., Kördel J., Rance M., Chazin W.J. (1993). J. Magn. Reson. B102:253–264Google Scholar
  38. Sklenar V. (1995) J. Magn. Reson. A114:132–135Google Scholar
  39. Tjandra, N., Feller, S.E., Pastor, R.W. and Bax, A. (1995) J. Am. Chem. Soc., 117, 12562-12566.CrossRefGoogle Scholar
  40. Tjandra N., Szabo A., Bax A. (1996). J. Am. Chem. Soc. 118:6986–6991CrossRefGoogle Scholar
  41. Tollinger M., Skrynnikov N.R., Mulder F.A.A., Forman-Kay J.D., Kay L.E. (2001). J. Am. Chem. Soc. 123:11341–11352CrossRefGoogle Scholar
  42. Vis H., Vorgias C.E., Wison K.S., Kaptein R., Boelens R. (1998). J. Biomol. NMR 11:265–277CrossRefGoogle Scholar
  43. Wagner G., Wüthrich K. (1978). Nature 275:247–248CrossRefADSGoogle Scholar
  44. Yang Y.-S., Guignard L., Padilla A., Hoh F., Strub M.P., Stern M.-H., Lhoste J.M., Roumestand C (1998). J. Biomol. NMR 11(3):337–354CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Virginie Ropars
    • 1
  • Sabine Bouguet-Bonnet
    • 2
  • Daniel Auguin
    • 1
  • Philippe Barthe
    • 1
  • Daniel Canet
    • 2
  • Christian Roumestand
    • 1
  1. 1.Centre de Biochimie StructuraleUMR UM1/5048 CNRS/554 INSERMMontpellier CedexFrance
  2. 2.Méthodologie RMN (UMR 7565 CNRS-UHP, Nancy 1)Université H. Poincaré, Nancy 1Vandoeuvre-lès-Nancy CedexFrance

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