Abstract
We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek, J. Biomol. NMR, 1999, 15, 77–82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anderson, E., Bai, Z., Bischof, C., Blackford, S., Demmel, J., Dongarra, J., Du Croz, J., Greenbaum, A., Hammarling, S., McKenney, A. and Sorenson, D. (1999) LAPACK Users' Guide, Society for Industrial and Applied Mathematics, Philadelphia.
Brünger, A. (1992) X-PLOR Version 3.1: A system for Crystallography and NMR, Yale University New Haven, CT, U.S.A.
Clore, G.M., Gronenborn, A.M. and Bax, A. (1988a) J. Magn. Reson., 133, 216-221.
Cordier, F., Dingley, A.J. and Grzesiek, S. (1999) J. Biomol. NMR, 13, 175-180.
Cornilescu, G., Marquart, J.L., Ottiger, M. and Bax, A. (1998) J. Am. Chem. Soc., 120, 6836-6837.
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer J. and Bax, A. (1995) J. Biomol. NMR, 6, 277-293.
Garrett, D.S., Powers, S., Gronenborn, A.M. and Clore, G.M. (1991) J. Magn. Reson., 95, 214-220.
Golub, G.H. and Pereyra, V. (1973) SIAM J. Nummer. Anal., 10, 413-432.
Grzesiek, S., Bax, A., Hu, J.S., Kaufman, J., Palmer, I., Stahl, S.J., Tjandra, N. and Wingfield, P.T. (1997) Protein Sci., 6, 1248-1263.
Hansen, M.R., Mueller, L. and Pardi, A. (1998) Nat. Struct. Biol., 5, 1065-74.
Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J. Biomol. NMR, 8, 477-86.
Losonczi, J.A., Andrec, M., Fischer, M.W.F. and Prestegard, J.H. (1999) J. Magn. Reson., 138, 334-342.
Moltke, S. and Grzesiek, S. (1999) J. Biomol. NMR, 15, 77-82.
Ottiger, M., Delaglio, F., Marquardt, J.L., Tjandra, N. and Bax, A. (1998) J. Magn. Reson., 134, 365-369.
Sass, H.-J., Musco, G., Stahl, S.J., Wingfield, P.T. and Grzesiek, S. (2000) J. Biomol. NMR, 18, 305-311.
Saupe, A. (1964) Z. Naturforsch., 19a, 161-171.
Tjandra, N. and Bax, A. (1997) Science, 278, 1111-1114.
Tjandra, N. and Bax, A. (1997) J. Magn. Reson., 124, 512-515.
Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. and Bax, A. (1997) Nat. Struct. Biol., 4, 732-738.
Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1995) Proc. Natl. Acad Sci. USA, 92, 9279-9283.
Tycko, R., Blanco, F.J. and Ishii, Y. (2000) J. Am. Chem. Soc., 122, 9340-9341.
Warren, J.J. and Moore, P.B. (2001) J. Magn. Reson., 149, 271-275.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Sass, HJ., Musco, G., Stahl, S.J. et al. An easy way to include weak alignment constraints into NMR structure calculations. J Biomol NMR 21, 275–280 (2001). https://doi.org/10.1023/A:1012998006281
Issue Date:
DOI: https://doi.org/10.1023/A:1012998006281