Skip to main content
SpringerLink
Log in

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

  • Short Communications
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Summary

The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  • Boelens, R., Koning, T.M.G. and Kaptein, R. (1988) J. Mol. Struct., 173, 299–311.

    Google Scholar 

  • Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1993) In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 2 (Eds, Van, Gunsteren, W.F., Weiner, P.K. and Wilkinson, A.J.), ESCOM, Leiden, pp. 407–440.

  • Bonvin, A.M.J.J. and Brünger, A.T. (1995) J. Mol. Biol., 250, 80–93.

    Google Scholar 

  • Borgias, B.A., Cochin, M., Kerwood, D.J. and James, T.L. (1990) Prog. NMR Spectrosc., 22, 83–100.

    Google Scholar 

  • Brünger, A.T. (1993) X-PLOR v. 3.1: A system for X-ray crystallography and NMR, Yale University Press, New Haven, CT.

    Google Scholar 

  • Brünger, A.T., Clore, M.G., Gronenborn, A.M., Saffrich, R. and Nilges, M. (1993) Science, 261, 328–331.

    Google Scholar 

  • Burling, F.T. and Brünger, A.T. (1994) Isr. J. Chem., 34, 165–175.

    Google Scholar 

  • Burling, F.T., Weis, W.I., Flaherty, K.M. and Brünger, A.T. (1996) Science, 271, 72–77.

    Google Scholar 

  • DeLano, W.L. and Brünger, A.T. (1994) Proteins, 20, 105–123.

    Google Scholar 

  • Edmonson, S. (1992) J. Magn. Reson. 98, 283–298.

    Google Scholar 

  • Fennen, J., Torda, A.E. and Van, Gunsteren, W.F. (1995) J. Biomol. NMR, 6, 163–170.

    Google Scholar 

  • Gerstein, M., Lesk, A.M. and Chothia, C. (1994) Biochemistry, 33, 6739–6749.

    Google Scholar 

  • Gros, P., Van, Gunsteren, W.F. and Hol, W.G.J. (1990), Science, 249, 1149–1152.

    Google Scholar 

  • Jeffrey, P.D., Russo, A.A., Polyak, K., Gibbs, E., Hurwitz, J., Massagé, J. and Pavletich, N.P. (1995) Nature, 376, 313–320.

    Google Scholar 

  • Keepers, J.W. and James, T.L. (1984) J. Magn. Reson., 57, 404–426.

    Google Scholar 

  • Kim, Y. and Prestegard, J.H. (1989) Biochemistry, 28, 8792–8797.

    Google Scholar 

  • Kim, Y. and Prestegard, J.H. (1990) Proteins, 8, 377–385.

    Google Scholar 

  • Koehl, P. and Lefèvre, J.-P. (1990) J. Magn. Reson., 86, 565–583.

    Google Scholar 

  • Kruse, L.I., DeBrosse, C.W. and Kruse, C.H. (1985) J. Am. Chem. Soc., 107, 5435–5442.

    Google Scholar 

  • Kuriyan, J., Ösapay, K., Burley, S.K., Brünger, A.T., Hendrickson, W.A. and Karplus, M. (1991) Protein Struct. Funct. Genet., 10, 340–358.

    Google Scholar 

  • Landis, C.R., Luck, L.L. and Wright, J.M. (1995) J. Magn. Reson. Ser. B, 109, 44–59.

    Google Scholar 

  • Leeflang, B.R. and Kroon-Batenburg, L.M.J. (1992) J. Biomol. NMR, 2, 495–518.

    Google Scholar 

  • Liu, H., Banville, D.L., Basus, V.J. and James, T.L. (1995) J. Magn. Reson. Ser. B, 107, 51–59.

    Google Scholar 

  • Madrid, M., Llinás, E. and Llinás, M. (1991) J. Magn. Reson., 93, 329–346.

    Google Scholar 

  • Metzler, W.J., Valentine, K., Roebber, M., Friedrichs, M.S., March, D.G. and Mueller, L. (1992) Biochemistry, 31, 5117–5127.

    Google Scholar 

  • Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1995) Science, 269, 656–663.

    Google Scholar 

  • Nicholson, L.K., Yamazaki, T., Torchia, D.A., Grzesiek, S., Bax, A., Stahl, S.J., Kaufman, J.D., Wingfield, P.T., Lam, P.Y.S., Jadhav, P.K., Hodge, N., Domaille, P.J. and Chang, C.-H. (1995) Nature Struct. Biol., 2, 274–280.

    Google Scholar 

  • Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988) FEBS Lett., 229, 317–324.

    Google Scholar 

  • Olejniczak, E.T., GampeJr., R.T. and Fesik, S.W. (1986) J. Magn. Reson., 67, 28–41.

    Google Scholar 

  • Post, C.B., Meadows, R.P. and Gorenstein, D.G. (1990) J. Am. Chem. Soc., 112, 6796–6803.

    Google Scholar 

  • Scheek, R.M., Torda, A.E., Kemmink, J. and Van, Gunsteren, W.F. (1991) In Computational Aspects of the Study of Biological Macromolecules by NMR (Eds, Hoch, J.C., Poulsen, F.M. and Redfield, C.), Plenum Press, New York, NY, pp. 209–217.

  • Schirmer, R.E., Davis, J.P., Noggle, J.H. and Hart, P.A. (1972) J. Am. Chem. Soc., 94, 2561–2572.

    Google Scholar 

  • Torda, A.E., Scheek, R.M. and Van, Gunsteren, W.F. (1989) Chem. Phys. Lett., 157, 289–294.

    Google Scholar 

  • Torda, A.E., Brunne, R.M., Huber, T., Kessler, H. and Van, Gunsteren, W.F. (1993) J. Biomol. NMR, 3, 55–66.

    Google Scholar 

  • Van de Ven, F.J.M., Blommers, M.J.J., Schouten, R.E. and Hilbers, C.W. (1991) J. Magn. Reson., 94, 140–151.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Howard Hughes Medical Institute, Yale University, P.O. Box 208114, 06520, New Haven, CT, USA

    Alexandre M. J. J. Bonvin & Axel T. Brünger

  2. Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, 06520, New Haven, CT, USA

    Alexandre M. J. J. Bonvin & Axel T. Brünger

Authors
  1. Alexandre M. J. J. Bonvin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Axel T. Brünger
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

To whom correspondence should be addressed.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bonvin, A.M.J.J., Brünger, A.T. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?. J Biomol NMR 7, 72–76 (1996). https://doi.org/10.1007/BF00190458

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00190458

Keywords

Search

Navigation