Biochemistry (Moscow)

, Volume 77, Issue 6, pp 616–623 | Cite as

Comparison of experimental and theoretical data on hydrogen-deuterium exchange for ten globular proteins

  • M. Yu. Suvorina
  • A. K. Surin
  • N. V. Dovidchenko
  • M. Yu. Lobanov
  • O. V. GalzitskayaEmail author


The number of protons available for hydrogen-deuterium exchange was predicted for ten globular proteins using a method described elsewhere by the authors. The average number of protons replaced by deuterium was also determined by mass spectrometry of the intact proteins in their native conformations. Based on these data, we find that two models proposed earlier agree with each other in estimation of the number of protons replaced by deuterium. Using a model with a probability scale for hydrogen bond formation, we estimated a number of protons replaced by deuterium that is close to the experimental data for long-term incubation in D2O (24 h). Using a model based on estimations with a scale of the expected number of contacts in globular proteins there is better agreement with the experimental data obtained for a short period of incubation in D2O (15 min). Therefore, the former model determines weakly fluctuating parts of a protein that are in contact with solvent only for a small fraction of the time. The latter model (based on the scale of expected number of contacts) predicts either flexible parts of a protein chain exposed to interactions with solvent or disordered parts of the protein.

Key words

hydrogen-deuterium exchange secondary structure hydrogen bond mass spectrometry 


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  1. 1.
    Hvidt, A., and Linderstrom-Lang, K. (1955) Biochim. Biophys. Acta, 16, 168–169.PubMedCrossRefGoogle Scholar
  2. 2.
    Goodman, J. L., Pagel, M. D., and Stone, M. J. (2000) J. Mol. Biol., 295, 963–978.PubMedCrossRefGoogle Scholar
  3. 3.
    Englander, S. W. (2006) J. Am. Soc. Spectrom., 17, 1481–1489.CrossRefGoogle Scholar
  4. 4.
    Zhang, Z., and Smith, D. L. (1993) Protein Sci., 2, 522–531.PubMedCrossRefGoogle Scholar
  5. 5.
    Johnson, R. S. (1996) J. Am. Soc. Mass Spectrom., 7, 515–521.CrossRefGoogle Scholar
  6. 6.
    Yan, X., Watson, J., Ho, P. S., and Deinzer, M. L. (2004) Molec. Cell. Proteom., 3, 10–23.CrossRefGoogle Scholar
  7. 7.
    Deng, Y., Zhang, Z., and Smith, D. L. (1999) J. Am. Soc. Mass. Spectrom., 10, 675–684.PubMedCrossRefGoogle Scholar
  8. 8.
    Sheinerman, F. B., and Brooks, C. L. (1998) Proc. Natl. Acad. Sci. USA, 95, 1562–1567.PubMedCrossRefGoogle Scholar
  9. 9.
    Bahar, I., Wallqvist, A., Covell, D. G., and Jernigan, R. L. (1998) Biochemistry, 37, 1067–1075.PubMedCrossRefGoogle Scholar
  10. 10.
    Vendruscolo, M., Paci, E., Dobson, C. M., and Karplus, M. (2003) J. Am. Chem. Soc., 125, 15686–15687.PubMedCrossRefGoogle Scholar
  11. 11.
    Best, R. B., and Vendruscolo, M. (2006) Structure, 14, 97–106.PubMedCrossRefGoogle Scholar
  12. 12.
    Tartaglia, G. G., Cavalli, A., and Vendruscolo, M. (2007) Structure, 15, 139–143.PubMedCrossRefGoogle Scholar
  13. 13.
    Dovidchenko, N. V., Lobanov, M. Yu., Garbuzynskiy, S. O., and Galzitskaya, O. V. (2009) Biochemistry (Moscow), 74, 888–897.PubMedGoogle Scholar
  14. 14.
    Galzitskaya, O. V., Garbuzynskiy, S. O., and Lobanov, M. Y. (2006) Mol. Biol. (Moscow), 40, 341–348.Google Scholar
  15. 15.
    Savitski, M. M., Kjeldsen, F., Nielsen, M. L., Garbuzynskiy, S. O., Galzitskaya, O. V., Surin, A. K., and Zubarev, R. A. (2007) Angew. Chem. Int. Ed. Engl., 46, 1481–1484.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2012

Authors and Affiliations

  • M. Yu. Suvorina
    • 1
  • A. K. Surin
    • 1
  • N. V. Dovidchenko
    • 1
  • M. Yu. Lobanov
    • 1
  • O. V. Galzitskaya
    • 1
    Email author
  1. 1.Institute of Protein ResearchRussian Academy of SciencesPushchino, Moscow RegionRussia

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