Summary
A suite of computer programs (CLAIRE) is described which can be of assistance in the process of assigning 2D1H NMR spectra of proteins. The programs embody a software implementation of the sequential assignment approach first developed by Wüthrich and co-workers (K. Wüthrich. G. Wider, G. Wagner and W. Braun (1982)J. Mol. Biol. 155, 311). After data-abstraction (peakpicking), the software can be used to detect patterns (spin systems), to find cross peaks between patterns in 2D NOE data sets and to generate assignments that are consistent with all available data and which satisfy a number of constraints imposed by the user. An interactive graphics program calledCONPAT is used to control the entire assignment process as well as to provide the essential feedback from the experimental NMR spectra. The algorithms are described in detail and the approach is demonstrated on a set of spectra from the mistletoe protein phoratoxin B, a homolog of crambin. The results obtained compare well with those reported earlier based entirely on a manual assignment process.
Similar content being viewed by others
References
Bax, A. and Davis, D.G. (1985)J. Magn. Reson. 65, 355–360.
Billeter, M., Basus, V.J. and Kuntz, I.D. (1988)J. Magn. Reson.,76, 400–415.
Brown, S.C., Weber, P.L. and Mueller, L. (1988)J. Magn. Reson.,77, 166–169.
Catasti, P., Carrara, E. and Nicolini, C. (1990)J. Comput. Chem.,11, 805–818.
Cieslar, C., Clore, G.M. and Gronenborn, A.M. (1988)J. Magn. Reson.,80, 119–127.
Clore, G.M., Sukumaran, D.K., Nilges, M. and Gronenborn, A.M. (1987)Biochemistry,26, 1732–1745.
DiStefano, D.L. and Wand, A.J. (1987)Biochemistry,26, 7272–7281.
Eads, C.D. and Kuntz, I.D. (1989)J. Magn. Reson.,82, 467–482.
Englander, S.W. and Wand, A.J. (1987)Biochemistry,26, 5953–5958.
Feng, Y., Roder, H., Englander, S.W., Wand, A.J. and DiStefano, D.L. (1989)Biochemistry,28, 195–203.
Gross, K.H. and Kalbitzer, H.R. (1988).J. Magn. Reson. 76, 87–99.
Kaptein, R., Boelens, R., Scheek, R.M. and Van Gunsteren, W.F. (1988)Biochemistry,27, 5389–5395.
Kleywegt, G.J., Lamerichs, R.M.J.N., Boelens, R. and Kaptein, R. (1989)J. Magn. Reson.,85, 186–197.
Kleywegt, G.J., Boelens, R. and Kaptein, R. (1990)J. Magn. Reson.,88, 601–608.
Kraulis, P.J. (1989)J. Magn. Reson.,84, 627–633.
Lecomte, J.T.J., Kaplan, D., Llinás, M., Thunberg, E. and Samuelsson, G. (1987)Biochemistry,26, 1187–1194.
Marion, D. and Wüthrich, K. (1983)Biochem. Biophys. Res. Comm.,113, 967–974.
Meier, B.U., Bodenhausen, G. and Ernst, R.R. (1984)J. Magn. Reson.,60, 161–163.
Meier, B.U., Mádi, Z.L. and Ernst, R.R. (1987)J. Magn. Reson.,74, 565–573.
Mellstrand, S.T. and Samuelsson, G. (1974)Acta Pharm. Suec.,11, 347–360.
Neidig, K.P., Bodenmueller, H. and Kalbitzer, H.R. (1984)Biochem. Biophys. Res. Commun.,125, 1143–1150.
Pfändler, P., Bodenhausen, G., Meier, B.U. and Ernst, R.R. (1985)Anal. Chem.,57 2510–2516.
Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983)Biochem. Biophys. Res. Comm.,117, 479–485.
States, D.J., Haberkorn, R.A. and Ruben, D.J. (1982)J. Magn. Reson.,48, 286–292.
Thunberg, E. (1974)Acta Pharm. Suec.,20, 115–122.
Van de Ven, F.J.M. (1990)J. Magn. Reson.,86, 633–644.
Van de Ven, F.J.M., Lycksell, P.O., Van Kammen, A. and Hilbers, C.W. (1990)Eur. J. Biochem.,190, 583–591.
Vermeulen, J.A.W.H., Lamerichs, R.M.J.N., Berliner, L.J., DeMarco, A., Llinás, M., Boelens, R., Alleman, J. and Kaptein, R. (1987)FEBS Lett.,219, 426–430.
Wand, A.J. and Nelson, S.J. (1988)Trans. Amer. Cryst. Ass.,24, 131–144.
Wand, A.J., DiStefano, D.L., Feng, Y., Roder, H. and Englander, S.W. (1989)Biochemistry,28, 186–194.
Weber, P.L., Malikayil, J.A. and Mueller, L. (1989)J. Magn. Reson.,82, 419–426.
Wüthrich K., Wider, G., Wagner, G. and Braun, W. (1982)J. Mol. Biol.,155, 311–319.
Wüthrich, K. (1986)NMR of Proteins and Nucleic Acids, Wiley, New York.
Wüthrich, K. (1989)Science,243, 45–50.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Kleywegt, G.J., Boelens, R., Cox, M. et al. Computer-assisted assignment of 2D1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B. J Biomol NMR 1, 23–47 (1991). https://doi.org/10.1007/BF01874567
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF01874567