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Journal of Biomolecular NMR

, Volume 14, Issue 3, pp 223–230 | Cite as

Recognition of protein folds via dipolar couplings

  • Arto Annila
  • Helena Aitio
  • Eva Thulin
  • Torbjörn Drakenberg
Article

Abstract

Alignment of proteins in dilute liquid crystalline medium gives rise to residual dipolar couplings which provide orientational information of vectors connecting the interacting nuclei. Considering that proteins are mainly composed of regular secondary structures in a finite number of different mutual orientations, main chain dipolar couplings appear sufficient to reveal structural resemblance. Similarity between dipolar couplings measured from a protein and corresponding values computed from a known structure imply homologous structures. For dissimilar structures the agreement between experimental and calculated dipolar couplings remains poor. In this way protein folds can be readily recognized prior to a comprehensive structure determination. This approach has been demonstrated by showing the similarity in fold between the hitherto unknown structure of calerythrin and sarcoplasmic calcium-binding proteins from Nereis diversicolor and Branchiostoma lanceolatum with known crystal structures.

alignment bicelle calcium-binding proteins calerythrin dipolar coupling protein fold 

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References

  1. Andersson, P., Annila, A. and Otting, G. (1998) J. Magn. Reson., 13, 364–367.Google Scholar
  2. Babu, Y.S., Bugg, C.E. and Cook, W.J. (1988) J. Mol. Biol., 204, 191–204.Google Scholar
  3. Bax, A. and Tjandra, N. (1997) J. Biomol. NMR, 10, 289–292.Google Scholar
  4. Chattopadhyaya, R., Meador, W.E., Means, A.R. and Quiocho, F.A. (1992) J. Mol. Biol., 228, 1177–1192.Google Scholar
  5. Clore, G.M., Gronenborn, A.M. and Bax, A. (1998a) J. Magn. Reson., 133, 216–221.Google Scholar
  6. Clore, G.M., Starich, M.R. and Gronenborn, A.M. (1998b) J. Am. Chem. Soc., 120, 10571–10572.Google Scholar
  7. Clore, G.M., Gronenborn, A.M. and Tjandra, N. (1998c) J. Magn. Reson., 131, 159–162.Google Scholar
  8. Cook, W.J., Jeffrey, L.C., Cox, J.A. and Vijay-Kumar, S. (1993) J. Mol. Biol., 229, 461–471.Google Scholar
  9. Cordier, F., Dingley, A.J. and Grzesiek S. (1999) J. Biomol. NMR, 13, 175–180.Google Scholar
  10. Czisch, M. and Boelens, R. (1998) J. Magn. Reson., 134, 158–160.Google Scholar
  11. Flaherty, K.M., Zozulya, S., Stryer, L. and McKay, D.B. (1993) Cell, 75, 709–716.Google Scholar
  12. Griffith, J.P., Kim, J.L., Kim, E.E., Sintchak, M.D., Thomson, J.A., Fitzgibbon, M.J., Fleming, M.A., Caron, P.R., Hsiao, K. and Navia, M.A. (1995) Cell, 82, 507–522.Google Scholar
  13. Hansen, M.R., Mueller, L. and Pardi, A. (1998) Nat. Struct. Biol., 12, 1065–1074.Google Scholar
  14. Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. (1992) Science, 256, 632–638.Google Scholar
  15. Losonczi, J.A. and Prestegard, J.H. (1998) J. Biomol. NMR, 12, 447–451.Google Scholar
  16. Lounila, J. and Jokisaari, J. (1982) Progr. NMR Spectrosc., 15, 249–290.Google Scholar
  17. Muhandiram, D.R. and Kay, L.E. (1994) J. Magn. Reson., B103, 203–216.Google Scholar
  18. Ottiger, M., Delaglio, F. and Bax, A. (1998) J. Magn. Reson., 131, 373–378.Google Scholar
  19. Ottiger, M. and Bax, A. (1998) J. Biomol. NMR, 12, 361–372.Google Scholar
  20. Pervushin, K., Riek, R., Wider, G. and Wüthrich, K. (1997) Proc. Natl. Acad. Sci. USA, 94, 12366–12371.Google Scholar
  21. Pervushin, K., Wider, G. and Wüthrich, K. (1998) J. Biomol. NMR, 12, 345–348.Google Scholar
  22. Piotto, M., Saudek, V. and Sklenár, V. (1992) J. Biomol. NMR, 2, 661–665.Google Scholar
  23. Ramirez, B. and Bax, A. (1998) International Conference of NMR on Biological Systems, Tokyo.Google Scholar
  24. Sanchez, R. and Sali, A. (1997) Curr. Opin. Struct. Biol., 7, 206–214.Google Scholar
  25. Sanchez, R. and Sali, A. (1998) Proc. Natl. Acad. Sci. USA, 95, 13597–13602.Google Scholar
  26. Sanders II, C.R. and Prestegard, J.H. (1990) Biophys. J., 58, 447–460.Google Scholar
  27. Sanders II, C.R. and Schwonek, J.P. (1992) Biochemistry, 31, 8898–8905.Google Scholar
  28. Swan, D.G., Hale, R.S., Dhillon, N. and Leadlay, P.F. (1987) Nature, 329, 84–85.Google Scholar
  29. Tjandra, N. and Bax, A. (1997) Science, 278, 1111–1114.Google Scholar
  30. Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. and Bax, A. (1997) Nat. Struct. Biol., 4, 732–738.Google Scholar
  31. Vijay-Kumar, S. and Cook, W.J. (1992) J. Mol. Biol., 224, 413–426.Google Scholar
  32. Wang, H., Eberstadt, M., Olejniczak, E.T., Meadows, R.P. and Fesik, S.W. (1998) J. Biomol. NMR, 12, 443–446.Google Scholar
  33. Weigelt, J. (1998) J. Am. Chem. Soc., 120, 10778–10779.Google Scholar
  34. Wishart, D. and Sykes, B.D. (1994) Methods Enzymol., 239, 363–392.Google Scholar
  35. Yamazaki, D., Lee, W., Arrowsmith, C.H., Muhandiram, D.R. and Kay, L.E. (1994) J. Am. Chem. Soc., 16, 11655–11666.Google Scholar
  36. Yang, D., Tolman, J.R., Goto, N.K. and Kay, L.E. (1998) J. Biomol. NMR, 12, 325–332.Google Scholar

Copyright information

© Kluwer Academic Publishers 1999

Authors and Affiliations

  • Arto Annila
    • 1
  • Helena Aitio
    • 2
  • Eva Thulin
    • 3
  • Torbjörn Drakenberg
    • 1
  1. 1.VTT Chemical TechnologyVTTFinland
  2. 2.Institute of BiotechnologyUniversity of HelsinkiFinland
  3. 3.Department of Physical Chemistry 2University of LundLundSweden

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