Abstract
One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assignment tool based onpattern recognition techniques. This tool employs user-specified ’templates‘to search for patterns of peaks in the original spectra; these patterns maycorrespond to side-chain or backbone fragments. Multiple spectra willnormally be searched simultaneously to reduce the impact of noise. Thesearch generates a preliminary list of putative assignments, which arefiltered by a set of heuristic algorithms to produce the final results list.Each result contains a set of chemical shift values plus information aboutthe peaks found. The results may be used as input for combinatorialroutines, such as sequential assignment procedures, in place of peak lists.Two examples are presented, in which (i) HCCH-COSY and -TOCSY spectra arescanned for side-chain spin systems; and (ii) backbone spin systems aredetected in a set of spectra comprising HNCA, HN(CO)CA, HNCO, HN(CA)CO,CBCANH and CBCA(CO)NH.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bartels, C., Xia, T., Billeter, M., Güntert, P. and Wüthrich, K. (1995) J. Biomol. NMR, 6, 1–10.
Bax, A., Clore, G.M. and Gronenborn, A.M. (1990) J. Magn. Reson., 88, 425–431.
Billeter, M. (1991) In Computational Aspects of the Study of Biological Macromolecules by NMR Spectroscopy(Eds., Hoch, J.C., Redfield, C. and Poulsen, F.M.), NATO ASI Series Vol. A225, Plenum Press, New York, NY, U.S.A., pp. 279–290.
Cieslar, C., Clore, G.M., Gronenborn, A.N. (1988) J. Magn. Reson., {vn80}, 119–127.
Denk, W., Wagner, G., Rance, M. and Wüthrich, K. (1985) J. Magn. Reson., 62, 350–366.
Dötsch, V., Oswald, R.E. and Wagner, G. (1996a) J. Magn. Reson., {vnB110}, 107–111.
Dötsch, V., Oswald, R.E. and Wagner, G. (1996b) J. Magn. Reson., {vnB110}, 304–308.
Eads, C.D. and Kuntz, I.D. (1989) J. Magn. Reson., 82, 467–482.
Eccles, C., Güntert, P., Billeter, M. and Wüthrich, K. (1991) J. Biomol. NMR, 1, 111–130.
Fesik, S.W. and Zuiderweg, E.R.P. (1988) J. Magn. Reson., 78, 588–593.
Groß, K.-H. and Kalbitzer, H.R. (1988) J. Magn. Reson., 76, 87–99.
Ikura, M., Kay, L.E. and Bax, A. (1991) J. Biomol. NMR, 1, 299–304.
Kay, L.E., Ikura, M. and Bax, A. (1990a) J. Am. Chem. Soc., 112, 888–889.
Kay, L.E., Ikura, M., Tschudin, R. and Bax, A. (1990b) J. Magn. Reson., 89, 496–514.
Kemmink, J., Darby, N.J., Dijkstra, K., Scheek, R.M. and Creighton, T.E. (1995) Protein Sci., 4, 2587–2593.
Kemmink, J., Darby, N.J., Dijkstra, K., Nilges, M. and Creighton, T.E. (1996) Biochemistry, 35, 7684–7691.
Kleywegt, G.J., Boelens, R., Cox, M., Llinás, M. and Kaptein, R. (1991) J. Biomol. NMR, 1, 23–47.
Kraulis, P.J. (1989) J. Magn. Reson., 84, 627–633.
Marion, D., Driscoll, P.C., Kay, L.E., Wingfield, P.T., Bax, A., Gronenborn, A.M. and Clore, G.M. (1989) Biochemistry, 28, 6150–6156.
Meadows, R.P., Olejniczak, E.T. and Fesik, S.W. (1994) J. Biomol. NMR, 4, 79–96.
Neidig, K.-P. (1992) AURELIA: Computer aided analysis of 2D and 3D NMR, User’s Guide, Bruker Analytik GmbH, Rheinstetten, Germany.
Nelson, S.J., Schneider, D.M., Di Stefano, D.L. and Wand, A.J. (1991) Bull. Magn. Reson., 13, 14–21.
Nietlispach, D., Clowes, R.T., Broadhurst, R.W., Yutaka, I., Keeler, J., Kelly, M., Ashurst, J., Oschkinat, O., Domaille, P.J. and Laue, E.D. (1996) J. Am. Chem. Soc., 118, 407–415.
Oschkinat, H., Holak, T.A. and Cieslar, C. (1991) Biopolymers, 31, 699–712.
Schalkoff, R.J. (1989) Digital Image Processing and Computer Vision, Wiley, New York, NY, U.S.A.
Shaw, G.L., Müller, T., Mott, H.R., Oschkinat, H., Campbell, I.D. and Mitschang, L. (1997) J. Magn. Reson., 124, 479–483.
Van de Ven, F.J.M. (1990) J. Magn. Reson., 86, 633–644.
Vuister, G.W., Boelens, R., Padilla, A., Kleywegt, G.J. and Kaptein, R. (1990) Biochemistry, 29, 1829–1839.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J. Mol. Biol., {vn222}, 311–333.
Wüthrich, K., Wider, G., Wagner, G. and Braun, W. (1982) J. Mol. Biol., 155, 311–319.
Xu, J., Straus, S.K., Sanctuary, B.C. and Trimbles, L. (1994) J. Magn. Reson., B103, 53–58.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Croft, D., Kemmink, J., Neidig, KP. et al. Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J Biomol NMR 10, 207–219 (1997). https://doi.org/10.1023/A:1018329420659
Issue Date:
DOI: https://doi.org/10.1023/A:1018329420659