Journal of Biomolecular NMR

, Volume 1, Issue 1, pp 23–47

Computer-assisted assignment of 2D1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B

  • Gerard J. Kleywegt
  • Rolf Boelens
  • Michel Cox
  • Miguel Llinás
  • Robert Kaptein
Research Papers

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.

Keywords

2D NMR Proteins Semi-automatic assignment Software package 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bax, A. and Davis, D.G. (1985)J. Magn. Reson. 65, 355–360.Google Scholar
  2. Billeter, M., Basus, V.J. and Kuntz, I.D. (1988)J. Magn. Reson.,76, 400–415.Google Scholar
  3. Brown, S.C., Weber, P.L. and Mueller, L. (1988)J. Magn. Reson.,77, 166–169.Google Scholar
  4. Catasti, P., Carrara, E. and Nicolini, C. (1990)J. Comput. Chem.,11, 805–818.Google Scholar
  5. Cieslar, C., Clore, G.M. and Gronenborn, A.M. (1988)J. Magn. Reson.,80, 119–127.Google Scholar
  6. Clore, G.M., Sukumaran, D.K., Nilges, M. and Gronenborn, A.M. (1987)Biochemistry,26, 1732–1745.Google Scholar
  7. DiStefano, D.L. and Wand, A.J. (1987)Biochemistry,26, 7272–7281.Google Scholar
  8. Eads, C.D. and Kuntz, I.D. (1989)J. Magn. Reson.,82, 467–482.Google Scholar
  9. Englander, S.W. and Wand, A.J. (1987)Biochemistry,26, 5953–5958.Google Scholar
  10. Feng, Y., Roder, H., Englander, S.W., Wand, A.J. and DiStefano, D.L. (1989)Biochemistry,28, 195–203.Google Scholar
  11. Gross, K.H. and Kalbitzer, H.R. (1988).J. Magn. Reson. 76, 87–99.Google Scholar
  12. Kaptein, R., Boelens, R., Scheek, R.M. and Van Gunsteren, W.F. (1988)Biochemistry,27, 5389–5395.Google Scholar
  13. Kleywegt, G.J., Lamerichs, R.M.J.N., Boelens, R. and Kaptein, R. (1989)J. Magn. Reson.,85, 186–197.Google Scholar
  14. Kleywegt, G.J., Boelens, R. and Kaptein, R. (1990)J. Magn. Reson.,88, 601–608.Google Scholar
  15. Kraulis, P.J. (1989)J. Magn. Reson.,84, 627–633.Google Scholar
  16. Lecomte, J.T.J., Kaplan, D., Llinás, M., Thunberg, E. and Samuelsson, G. (1987)Biochemistry,26, 1187–1194.Google Scholar
  17. Marion, D. and Wüthrich, K. (1983)Biochem. Biophys. Res. Comm.,113, 967–974.Google Scholar
  18. Meier, B.U., Bodenhausen, G. and Ernst, R.R. (1984)J. Magn. Reson.,60, 161–163.Google Scholar
  19. Meier, B.U., Mádi, Z.L. and Ernst, R.R. (1987)J. Magn. Reson.,74, 565–573.Google Scholar
  20. Mellstrand, S.T. and Samuelsson, G. (1974)Acta Pharm. Suec.,11, 347–360.Google Scholar
  21. Neidig, K.P., Bodenmueller, H. and Kalbitzer, H.R. (1984)Biochem. Biophys. Res. Commun.,125, 1143–1150.Google Scholar
  22. Pfändler, P., Bodenhausen, G., Meier, B.U. and Ernst, R.R. (1985)Anal. Chem.,57 2510–2516.Google Scholar
  23. Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983)Biochem. Biophys. Res. Comm.,117, 479–485.Google Scholar
  24. States, D.J., Haberkorn, R.A. and Ruben, D.J. (1982)J. Magn. Reson.,48, 286–292.Google Scholar
  25. Thunberg, E. (1974)Acta Pharm. Suec.,20, 115–122.Google Scholar
  26. Van de Ven, F.J.M. (1990)J. Magn. Reson.,86, 633–644.Google Scholar
  27. Van de Ven, F.J.M., Lycksell, P.O., Van Kammen, A. and Hilbers, C.W. (1990)Eur. J. Biochem.,190, 583–591.Google Scholar
  28. 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.Google Scholar
  29. Wand, A.J. and Nelson, S.J. (1988)Trans. Amer. Cryst. Ass.,24, 131–144.Google Scholar
  30. Wand, A.J., DiStefano, D.L., Feng, Y., Roder, H. and Englander, S.W. (1989)Biochemistry,28, 186–194.Google Scholar
  31. Weber, P.L., Malikayil, J.A. and Mueller, L. (1989)J. Magn. Reson.,82, 419–426.Google Scholar
  32. Wüthrich K., Wider, G., Wagner, G. and Braun, W. (1982)J. Mol. Biol.,155, 311–319.Google Scholar
  33. Wüthrich, K. (1986)NMR of Proteins and Nucleic Acids, Wiley, New York.Google Scholar
  34. Wüthrich, K. (1989)Science,243, 45–50.Google Scholar

Copyright information

© ESCOM Science Publishers B.V. 1991

Authors and Affiliations

  • Gerard J. Kleywegt
    • 1
  • Rolf Boelens
    • 1
  • Michel Cox
    • 1
  • Miguel Llinás
    • 1
  • Robert Kaptein
    • 1
  1. 1.Department of ChemistryUniversity of UtrechtUtrechtThe Netherlands
  2. 2.Department of ChemistryCarnegie Mellon UniversityPittsburghU. S. A.

Personalised recommendations