Abstract
A reliable automated approach for assignment of NOESY spectra would allow more rapid determination of protein structures by NMR. In this paper we describe a semi-automated procedure for complete NOESY assignment (SANE, Structure Assisted NOE Evaluation), coupled to an iterative procedure for NMR structure determination where the user is directly involved. Our method is similar to ARIA [Nilges et al. (1997) J. Mol. Biol., 269, 408–422], but is compatible with the molecular dynamics suites AMBER and DYANA. The method is ideal for systems where an initial model or crystal structure is available, but has also been used successfully for ab initio structure determination. Use of this semi-automated iterative approach assists in the identification of errors in the NOE assignments to short-cut the path to an NMR solution structure.
Similar content being viewed by others
References
Breg, J.N., van Opheusden, J.H.J., Burgering, M.J.M., Boelens, R. and Kaptein, R. (1990) Nature, 346, 586-589.
Brünger, A.T. (1992) X-PLOR 3.1: A System for X-Ray Crystallography and NMR, Yale University Press, New Haven, CT.
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (1999) AMBER 6, University of California, San Francisco, CA.
Duggan, B.M., Dyson, H.J. and Wright, P.E. (1999) Eur. J. Biochem., 265, 539-548.
Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283-298.
Hare, B.J. and Wagner, G. (1999) J. Biomol. NMR, 15, 103-113.
Johnson, B.A. and Blevins, R.A. (1994) J. Chem. Phys., 29, 1012-1014.
Kriwacki, R.W., Legge, G.B., Hommel, U., Ramage, P., Chung, J., Tennant, L.L., Wright, P.E. and Dyson, H.J. (2000) J. Biomol. NMR, 16, 271-272.
Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J. Biomol. NMR, 8, 477-486.
Legge, G.B., Kriwacki, R.W., Chung, J., Hommel, U., Ramage, P., Case, D.A., Dyson, H.J. and Wright, P.E. (1999) J. Mol. Biol., 295, 1251-1264.
Mumenthaler, C. and Braun, W. (1995) J. Mol. Biol., 254, 465-480.
Nilges, M., Macias, M.J., O'Donoghue, S.I. and Oschkinat, H. (1997) J. Mol. Biol., 269, 408-422.
Nilges, M. and O'Donoghue, S.I. (1998) Prog. NMR Spectrosc., 32, 107-139.
Qu, A. and Leahy, D.J. (1995) Proc. Natl. Acad. Sci. USA, 92, 10277-10281.
Wüthrich, K., Billeter, M. and Braun, W. (1983) J. Mol. Biol., 169, 949-961.
Zhang, O., Forman-Kay, J.D., Shortle, D. and Kay, L.E. (1997) J. Biomol. NMR, 9, 181-200.
Zhang, O., Kay, L.E., Olivier, J.P. and Forman-Kay, J.D. (1994) J. Biomol. NMR, 4, 845-858.
Rights and permissions
About this article
Cite this article
Duggan, B.M., Legge, G.B., Dyson, H.J. et al. SANE (Structure Assisted NOE Evaluation): An automated model-based approach for NOE assignment. J Biomol NMR 19, 321–329 (2001). https://doi.org/10.1023/A:1011227824104
Issue Date:
DOI: https://doi.org/10.1023/A:1011227824104