Summary
NMR data are collected as time- and ensemble-averaged quantities. Yet, in commonly used methods for structure determination of biomolecules, structures are required to satisfy simultaneously a large number of constrainsts. Recently, however, methods have been developed that allow a better fit of the experimental data by the use of time- or ensemble-averaged restraints. Thus far, these methods have been applied to structure refinement using distance and J-coupling restraints. In this paper, time and ensemble averaging is extended to the direct refinement with experimental NOE data. The implementation of time- and ensemble-averaged NOE restraints in DINOSAUR is described and illustrated with experimental NMR data for crambin, a 46-residue protein. Structure refinement with both time- and ensemble-averaged NOE restraints results in lower R-factors, indicating a better fit of the experimental NOE data.
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References
Baleja, J.D., Moult, J. and Sykes, B.D. (1990) J. Magn. Reson., 87, 375–384.
Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) J. Chem. Phys., 81, 3684–3690.
Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1991) J. Biomol. NMR, 1, 305–309.
Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1993a) 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., Rullmann, J.A.C., Lamerichs, R.M.J.N., Boelens, R. and Kaptein, R. (1993b) Biopolymers, 15, 385–400.
Bonvin, A.M.J.J., Boelens, R. and Kaptein, R. (1993c) Biopolymers, in press.
Bonvin, A.M.J.J., Vis, H., Breg, J.N., Burgering, M.J.M., Boelens, R. and Kaptein, R. (1993d) J. Mol. Biol., in press.
Brünger, A.T. and Krukowski, A. (1990) Acta Crystallogr., A46, 585–593.
Kemmink, J., Van Mierlo, C.P.M., Scheek, R.M. and Creighton, T.E. (1993) J. Mol. Biol., 230, 312–322.
Landy, S.B. and Rao, B.D.N. (1989) J. Magn. Reson., 81, 371–377.
Mertz, J.E., Güntert, P., Wüthrich, K. and Braun, W. (1991) J. Biomol. NMR, 1, 257–269.
Nilges, M., Habazettl, J., Brünger, A.T. and Holak, T.A. (1991) J. Mol. Biol., 219, 499–510.
Pearlman, D.A. and Kollman, P.A. (1991) J. Mol. Biol., 220, 457–479.
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.
Schmitz, U., Kumar, A. and James, T.L. (1992) J. Am. Chem. Soc., 114, 10654–10656.
Stawarz, B., Genest, M. and Genest, D. (1992) Biopolymers, 32, 633–642.
Torda, A.E., Scheek, R.M. and Van Gunsteren, W.F. (1989) Chem. Phys. Lett., 157, 289–294.
Torda, A.E., Scheek, R.M. and Van Gunsteren, W.F. (1990) J. Mol. Biol., 214, 223–235.
Torda, A.E., Brunne, R.M., Huber, T., Kessler, H. and Van Gunsteren, W.F. (1993) J. Biomol. NMR, 3, 55–66.
Van Gunsteren, W.F. and Berendsen, H.J.C. (1987) Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, University of Groningen, Groningen.
Yip, P. and Case, D.A. (1989) J. Magn. Reson., 83, 643–648.
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Bonvin, A.M.J.J., Boelens, R. & Kaptein, R. Time- and ensemble-averaged direct NOE restraints. J Biomol NMR 4, 143–149 (1994). https://doi.org/10.1007/BF00178343
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DOI: https://doi.org/10.1007/BF00178343