How to Deal with Spin-Diffusion and Internal Mobility in Biomolecules. A Relaxation Matrix Approach
Errors in proton-proton distances derived from NOEs are mainly due to the effects of spin-diffusion and local mobility. Both can be treated in the frame-work of relaxation matrix theory. The iterative relaxation matrix approach (IRMA), by which errors due to spin-diffusion can be corrected, is reviewed. Symmetrical exchange processes in biomolecules such as aromatic ring flips and methyl group rotation can be easily treated. To account for fast local motions on a picosecond time-scale a method is proposed, in which generalized order parameters S 2 are calculated from a free molecular dynamics run of the molecule in H2O. The S 2 values are then used to correct NOE derived distances, which in turn are used for the final structure refinement.
KeywordsSpectral Density Function Nuclear Overhauser Effect Time Correlation Function Local Mobility Relaxation Matrix
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- 2.R. Boelens, T. M. G. Koning, G. A. van der Marel, J. H. van Boom, and R. Kaptein, J. Mágn. Res. 82, 290 (1989).Google Scholar
- 3.T. M. G. Koning, R. Boelens, and R. Kaptein, J.Magn. Res., 90, 111 (1990).Google Scholar
- 5.D. Neuhaus and M. Williamson, “The Nuclear Overhauser Effect in Structural and Cornformational Analysis”, VCH Publishers, Inc., New York (1989).Google Scholar
- 8.E. T. Olejniczak, R. T. Jr. Gaupe, and S. W. Fesic, J. Magn. Reson. 67, 28 (1986).Google Scholar
- 9.J. A. C. Rullmann, A. M. J. J. Bonvin, R. Boelens, and R. Kaptein, to be published.Google Scholar
- 10.S. B. Landy and N. Rao, J. Magn. Reson. 81, 371 (1989).Google Scholar
- 12.D. E. Woessner, J. Chem. Phys. 36, 1(1962).Google Scholar