Abstract
We discuss a method for the refinement of NMR based solution structures which attempts to account for the effect of mobility on measured NMR data. Rather than regard the NOE as a measure of a static distance, we attempt to account for the fact that the measured quantity actually reflects a time averaged property of the molecule.
A penalty function, suitable for incorporation into molecular dynamics simulations, is described which perturbs a system only to the extent necessary to ensure that a trajectory average is consistent with measured interproton distances.
Finally, we present some results which suggest wide applicability for the method, while also noting the limitations and scope for improvement.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
B. A. Borgias and T. L. James, J. Mágn. Reson. 79, 493–512 (1988).
R. Boelens, T. M. G. Koning, and R. Kaptein, J. Mol. Struct. 173, 299–311 (1988).
P. Yip, and D. A. Case, J. Mag. Reson. 83, 643–648 (1989).
O. Jardetzky, Biochim. Biophys. Acta. 621, 227–232 (1980).
A. D. Kline, W. Braun, and K. Wüithrich, J. Mol. Biol. 204, 675–724 (1988).
W. F. van Gunsteren, R. Kaptein, and E. R. P. Zuiderweg, in “Proceedings of a NATO/CECAM Workshop on Nucleic Acid Conformation and Dynamics,” W. K. Olsen, ed., CECAM, Orsay, pp. 79–82, CECAM, Orsay (1984).
R. Kaptein, E. R. P. Zuiderweg, R. M. Scheek, R. Boelens, and W. F. van Gunsteren, J. Mol. Biol 182, 179–182 (1985).
J. Tropp, J. Chem. Phys. 72, 6035–6043 (1980).
A. E. Torda, R. M. Scheek, and W. F. van Gunsteren, Chem. Phys. Lett. 157, 289–294 (1989).
A. E. Torda, R. M. Scheek, and W. F. van Gunsteren, J. Mol Biol. 214, 223–235 (1990).
W. Braun, and N. Gō J. Mol. Biol. 186, 611–626 (1985).
K. Wüthrich, Science 243, 45–50 (1989).
W. F. van Gunsteren, and H. J. C. Berendsen, “Groningen Molecular Simulation (GROMOS) Library Manual”, Biomos, Groningen, (1987).
M. Billeter, A. D. Kline, W. Braun, R. Huber, and K. Wüthrich, J. Mol Biol 206, 677–687 (1989).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1991 Springer Science+Business Media New York
About this chapter
Cite this chapter
Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1991). Time Averaged Distance Restraints in NMR Based Structural Refinement. In: Hoch, J.C., Poulsen, F.M., Redfield, C. (eds) Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy. NATO ASI Series, vol 225. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-9794-7_16
Download citation
DOI: https://doi.org/10.1007/978-1-4757-9794-7_16
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4757-9796-1
Online ISBN: 978-1-4757-9794-7
eBook Packages: Springer Book Archive