Journal of Biomolecular NMR

, Volume 20, Issue 4, pp 297–310

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

  • Christine Peter
  • Xavier Daura
  • Wilfred F. van Gunsteren


Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages (〈r−6−1/6 or 〈r−31/3) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of β-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.

internal dynamics molecular dynamics simulation NMR relaxation NOESY peptides relaxation matrix ROESY spectral density functions 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Boelens, R., Koning, T.M.G., van der Marel, G.A., van Boom, J.H. and Kaptein, R. (1989) J. Magn. Reson., 82, 290-308.Google Scholar
  2. Brüschweiler, R. and Case, D. (1994) Progr. NMR Spectrosc., 26, 27-58.Google Scholar
  3. Daura, X., Antes, I., van Gunsteren, W.F., Thiel, W. and Mark, A.E. (1999a) Proteins, 36, 542-555.Google Scholar
  4. Daura, X., Jaun, B., Seebach, D., van Gunsteren, W.F. and Mark, A.E. (1998) J. Mol. Biol., 280, 925-932.Google Scholar
  5. Daura, X., van Gunsteren, W.F. and Mark, A.E. (1999b) Proteins, 34, 269-280.Google Scholar
  6. Edmondson, S.P. (1992) J. Magn. Reson., 98, 283-298.Google Scholar
  7. Edmondson, S.P. (1994) J. Magn. Reson., B103, 222-233.Google Scholar
  8. Fischer, M.W.F., Majumdar, A. and Zuiderweg, E.R.P. (1998) Progr. NMR Spectrosc., 33, 207-272.Google Scholar
  9. Keepers, J.W. and James, T.L. (1984) J. Magn. Reson., 57, 404-426.Google Scholar
  10. Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546-4559.Google Scholar
  11. Macura, S. and Ernst, R.R. (1980) Mol. Phys., 41, 95-117.Google Scholar
  12. Neuhaus, D. and Williamson, M. (1989) The Nuclear Overhauser Effect in Structural and Conformational Analysis, VCH, New York, NY.Google Scholar
  13. Olejniczak, E.T. (1989) J. Magn. Reson., 81, 392-394.Google Scholar
  14. Seebach, D., Ciceri, P.E., Overhand, M., Jaun, B., Rigo, D., Oberer, L., Hommel, U., Amstutz, R. and Widmer, H. (1996) Helv. Chim. Acta, 79, 2043-2066.Google Scholar
  15. Tropp, J. (1980) J. Chem. Phys., 72, 6035-6043.Google Scholar
  16. Walser, R., Mark, A.E., van Gunsteren, W.F., Lauterbach, M. and Wipff, G. (2000) J. Chem. Phys., 112, 10450-10459.Google Scholar
  17. Woessner, D.E. (1962) J. Chem. Phys., 36, 1-4.Google Scholar

Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • Christine Peter
    • 1
  • Xavier Daura
    • 1
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ZürichETH-ZentrumZürichSwitzerland

Personalised recommendations