Journal of Biomolecular NMR

, Volume 24, Issue 3, pp 191–201 | Cite as

Three-way decomposition of a complete 3D 15N-NOESY-HSQC

  • Aleksandras Gutmanas
  • Patrik Jarvoll
  • Vladislav Yu. Orekhov
  • Martin Billeter

Abstract

Three-way decomposition is applied for the structural analysis of a complete three-dimensional 15N-NOESY-HSQC of the 128 residues long protein azurin. The procedure presented includes decomposition using the software MUNIN, providing an initial characterization of the complete spectrum by 355 components. This is followed by post-processing yielding a final list of 149 components, 123 of which characterize 1859 NOE peaks from backbone N-H groups. Components from three-way decomposition are defined as direct products of one-dimensional shapes along the three dimensions. Thus, a complete set of distance constraints from this spectrum is obtained by one-dimensional peak picking of the shapes along the NOE dimension. Correctness and completeness of this set of NOEs are tested for all backbone amide groups against both an independent peak picking algorithm and the three-dimensional crystal structure of azurin, and a coincidence of about 95% is observed. Automated `demixing' of components that are `mixed' in a complex manner due to overlap of the HN and/or 15N frequencies is illustrated.

automated spectral analysis azurin demixing MUNIN 15N-NOESY-HSQC PARAFAC peak-picking 

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References

  1. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L. (1998) Acta Crystallogr., D54, 905–921.Google Scholar
  2. Caroll, J.D. and Chang, J. (1970) Psychometrica, 35, 283–319.Google Scholar
  3. Damberg, C.S., Orekhov, V.Y. and Billeter, M. (2002) J. Med. Chem., in press.Google Scholar
  4. Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A. (1995) J. Biomol. NMR, 6, 277–293.PubMedGoogle Scholar
  5. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997)J. Mol. Biol., 273, 283–298.PubMedGoogle Scholar
  6. Hajduk, P.J., Meadows, R.P. and Fesik, S.W. (1999) Q. Rev. Biophys., 32,211–240.PubMedGoogle Scholar
  7. Harshman, R.A. (1970) UCLA Working Papers in Phonetics, 16, 1–84.Google Scholar
  8. Jarvoll, P. (2002)Automatic Peak Picking, Diploma Thesis, Göteborg University, Göteborg.Google Scholar
  9. Karlsson, B.G., Pascher, T., Nordling, M., Arvidsson, R.H. and Lundberg, L.G. (1989) FEBS Lett., 246, 211–217.PubMedGoogle Scholar
  10. Koradi, R., Billeter, M., Engeli, M., Güntert, P. and Wüthrich, K. (1998) J. Magn. Reson., 135, 288–297.PubMedGoogle Scholar
  11. Koradi, R., Billeter, M. and Wüthrich, K.(1996) J. Mol. Graph., 14, 51–55, 29–32.PubMedGoogle Scholar
  12. Korzhnev, D.M., Ibraghimov, I.V., Billeter, M. and Orekhov, V.Y.(2001) J. Biomol. NMR, 21, 263–268.PubMedGoogle Scholar
  13. Kruskal, J.B. (1977) Linear Algebra Appl., 18, 95–138.Google Scholar
  14. Kruskal, J.B. (1989) In Multiway Data Analysis, Coppi, R. and Bolasco, S. (Eds.), North-Holland Elsevier Science Publishers, Amsterdam.Google Scholar
  15. Nar, H., Messerschmidt, A., Huber, R., van de Kamp, M. and Canters, G.W. (1991) J. Mol. Biol.,221, 765–772.PubMedGoogle Scholar
  16. Nilges, M., Macias, M.J., O'Donoghue, S.I. and Oschkinat, H. (1997) J. Mol. Biol., 269,408–422.PubMedGoogle Scholar
  17. Orekhov, V.Y., Ibraghimov, I.V. and Billeter, M. (2001) J. Biomol. NMR, 20, 49–60.PubMedGoogle Scholar
  18. Press, W.H., Teukolsky, S.A., Vetterling, W.T. and Flannery, B.P. (1992) Numerical Recipes in C, Cambridge University Press, Cambridge.Google Scholar
  19. Zhang, O., Kay, L.E., Olivier, J.P. and Forman-Kay, J.D. (1994) J. Biomol. NMR, 4, 845–858.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Aleksandras Gutmanas
    • 1
  • Patrik Jarvoll
    • 2
  • Vladislav Yu. Orekhov
    • 2
  • Martin Billeter
    • 1
  1. 1.Biochemistry and BiophysicsGöteborg UniversityGöteborgSweden
  2. 2.Swedish NMR CentreGöteborg UniversityGöteborgSweden

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