Automated combined assignment of NOESY spectra and three-dimensional protein structure determination
Tóm tắt
A procedure for automated protein structure determination is presented that is based on an iterative procedure during which the NOESY peak list assignment and the structure calculation are performed simultaneously. The input consists of a list of NOESY peak positions and a list of chemical shifts as obtained from sequence-specific resonance assignment. For the present applications of this approach the previously introduced NOAH routine was implemented in the distance geometry program DIANA. As an illustration, experimental 2D and 3D NOESY cross-peak lists of six proteins have been analyzed, for which complete sequence-specific 1H assignments are available for the polypeptide backbone and the amino acid side chains. The automated method assigned 70–90% of all NOESY cross peaks, which is on average 10% less than with the interactive approach, and only between 0.8% and 2.4% of the automatically assigned peaks had a different assignment than in the corresponding manually assigned peak lists. The structures obtained with NOAH/DIANA are in close agreement with those from manually assigned peak lists, and with both approaches the residual constraint violations correspond to high-quality NMR structure determinations. Systematic comparisons of the bundles of conformers that represent corresponding automatically and interactively determined structures document the absence of significant bias in either approach, indicating that an important step has been made towards automation of structure determination from NMR spectra.
Tài liệu tham khảo
Antuch, W., Güntert, P. and Wüthrich, K. (1996) Nat.Struct.Biol., 3, 662–665.
Bartels, Ch., Billeter, M., Güntert, P. and Wüthrich, K. (1996) J. Biomol.NMR, 7, 207–213.
Bartels, Ch., Güntert, P., Billeter, M. and Wüthrich, K. (1997) J. Comput.Chem., 18, 139–149.
Braun, W. and Gō, N. (1985) J.Mol.Biol., 186, 611–626.
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz Jr., K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) J.Am.Chem.Soc., 117, 5179–5197.
Donoghue, S.I., King, G.F. and Nilges, M. (1996) J.Biomol.NMR, 8, 193–206.
Fernández, C., Szyperski, T., Bruyère, T., Ramage, P., Mössinger, E. and Wüthrich, K. (1997) J.Mol.Biol., 266, 576–593.
Güntert, P., Braun, W., Billeter, M. and Wüthrich, K. (1989) J.Am. Chem.Soc., 111, 3997–4004.
Güntert, P., Braun, W. and Wüthrich, K. (1991) J.Mol.Biol., 217, 517–530.
Güntert, P. and Wüthrich, K. (1991) J.Biomol.NMR, 1, 447–456.
Güntert, P., Berndt, K.D. and Wüthrich, K. (1993) J.Biomol.NMR, 3, 601–606.
Güntert, P., Mumenthaler, Ch. and Wüthrich, K. (1996) Abstracts XVIIth International Conference on Magnetic Resonance in Biological Systems, Keystone, CO, U.S.A., August 18–23, p. 175.
Hare, B.J. and Prestegard, J.H. (1994) J.Biomol.NMR, 4, 35–46.
Koradi, R., Billeter, M. and Wüthrich, K. (1996) J.Mol.Graph., 14, 51–55.
Kraulis, P.J. (1994) J.Mol.Biol., 243, 696–718.
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J.Biomol.NMR, 8, 477–486.
Luginbühl, P., Güntert, G., Billeter, M. and Wüthrich, K. (1996) J. Biomol.NMR, 8, 136–146.
Meadows, R.P., Olejniczak, E.T. and Fesik, S.W. (1994) J.Biomol. NMR, 4, 79–96.
Morelle, N., Brutscher, B., Simorre, J.-P. and Marion, D. (1995) J. Biomol.NMR, 5, 154–160.
Mumenthaler, Ch. and Braun, W. (1995) J.Mol.Biol., 254, 465–480.
Nilges, M. (1993) Proteins, 17, 297–309.
Nilges, M. (1995) J.Mol.Biol., 245, 645–660.
Olson Jr., J.B. and Markley, J.L. (1994) J.Biomol.NMR, 4, 385–410.
Oshiro, C.M. and Kuntz, I.D. (1993) Biopolymers, 33, 107–115.
Ottiger, M., Szyperski, T., Luginbühl, P., Ortenzi, C., Luporini, P., Bradshaw, R.A. and Wüthrich, K. (1994) Protein Sci., 3, 1515–1526.
Pellecchia, M., Szyperski, T., Wall, D., Georgopoulos, C. and Wüthrich, K. (1996) J.Mol.Biol., 260, 236–250.
Pervushin, K., Billeter, M., Siegal, G. and Wüthrich, K. (1996) J. Mol.Biol., 264, 1002–1012.
Stein, E.G., Rice, L.M. and Brünger, A.T. (1997) J.Magn.Reson., 124, 154–164.
Szyperski, T., Güntert, P., Stone, S.R. and Wüthrich, K. (1992) J. Mol.Biol., 228, 1193–1205.
Williamson, M.P., Havel, T.F. and Wüthrich, K. (1985) J.Mol.Biol., 182, 295–315.
Wüthrich, K., Billeter, M. and Braun, W. (1983) J.Mol.Biol., 169, 949–961.
Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY, U.S.A.
Xu, Y., Wu, J., Gorenstein, D. and Braun, W. (1997) Abstracts 38th Experimental Nuclear Magnetic Resonance Conference, Orlando, FL, U.S.A., March 23–27.
Zimmermann, D., Kulikowski, C., Wang, L., Lyons, B. and Montelione, G.T. (1994) J.Biomol.NMR, 4, 241–256.