Advertisement

Journal of Biomolecular NMR

, Volume 18, Issue 3, pp 217–227 | Cite as

Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings

  • James J. Chou
  • Shipeng Li
  • Ad Bax
Article

Abstract

For an increasing fraction of proteins whose structures are being studied, sequence homology to known structures permits building of low resolution structural models. It is demonstrated that dipolar couplings, measured in a liquid crystalline medium, not only can validate such structural models, but also refine them. Here, experimental 1H-15N, 1Hα-13Cα, and 13C′-13Cα dipolar couplings are shown to decrease the backbone rmsd between various homology models of calmodulin (CaM) and its crystal structure. Starting from a model of the Ca2+-saturated C-terminal domain of CaM, built from the structure of Ca2+-free recoverin on the basis of remote sequence homology, dipolar couplings are used to decrease the rmsd between the model and the crystal structure from 5.0 to 1.25 Å. A better starting model, built from the crystal structure of Ca2+-saturated parvalbumin, decreases in rmsd from 1.25 to 0.93 Å. Similarly, starting from the structure of the Ca2+-ligated CaM N-terminal domain, experimental dipolar couplings measured for the Ca2+-free form decrease the backbone rmsd relative to the refined solution structure of apo-CaM from 4.2 to 1.0 Å.

calmodulin dipolar coupling heteronuclear NMR homology model liquid crystal refinement 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aitio, H., Annila, A., Heikkinen, S., Thulin, E., Drakenberg, T. and Kilpelainen, I. (1999) Protein Sci., 8, 2580–2588.Google Scholar
  2. Annila, A., Aitio, H., Thulin, E. and Drakenberg, T. (1999) J. Biomol. NMR, 14, 223–230.Google Scholar
  3. Babu, Y.S., Bugg, C.E. and Cook, W.J. (1988) J. Mol. Biol., 204, 191–204.Google Scholar
  4. Ban, C., Ramakrishnan, B., Ling, K.Y., Kung, C. and Sundaralingam, M. (1994) Acta Crystallogr., D50, 50–63.Google Scholar
  5. Brünger, A.T. (1993) XPLOR: A System for X-ray Crystallography and NMR, v. 3.1, Yale University Press, New Haven, CT.Google Scholar
  6. Chothia, C. (1992) Nature, 357, 543–544.Google Scholar
  7. Clore, G.M., Gronenborn, A.M. and Bax, A. (1998) J. Magn. Reson., 133, 216–221.Google Scholar
  8. Cordier, F. and Grzesiek, S. (1999) J. Am. Chem. Soc., 121, 1601–1602.Google Scholar
  9. Cornilescu, G., Delaglio, F. and Bax, A. (1999) J. Biomol. NMR, 13, 289–302.Google Scholar
  10. Delaglio, F., Kontaxis, G. and Bax, A. (2000) J. Am. Chem. Soc., 122, 2142–2143.Google Scholar
  11. Eisenstein, E., Gilliland, G.L., Herzberg, O., Moult, J., Orban, J., Poljak, R.J., Banerjei, L., Richardson, D. and Howard, A.J. (2000) Curr. Opin. Biotechnol., 11, 25–30.Google Scholar
  12. Elshorst, B., Hennig, M., Forsterling, H., Diener, A., Maurer, M., Schulte, P., Schwalbe, H., Griesinger, C., Krebs, J., Schmid, H., Vorherr, T. and Carafoli, E. (1999) Biochemistry, 38, 12320–12332.Google Scholar
  13. Finn, B.E., Evenas, J., Drakenberg, T., Waltho, J.P., Thulin, E. and Forsen, S. (1995) Nat. Struct. Biol., 2, 777–783.Google Scholar
  14. Grzesiek, S. and Bax, A. (1992) J. Magn. Reson., 96, 432–440.Google Scholar
  15. Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. (1992) Science, 256, 632–638.Google Scholar
  16. Ikura, M., Kay, L.E. and Bax, A. (1990) Biochemistry, 29, 4659–4667.Google Scholar
  17. Klee, C.B. (1988) In Molecular Aspects of Cellular Regulation (Cohen, P. and Klee, C.B., Eds.), Elsevier, Amsterdam, pp. 35–56.Google Scholar
  18. Kontaxis, G., Clore, G.M. and Bax, A. (2000) J. Magn. Reson., 143, 184–196.Google Scholar
  19. Kretsinger, R.H. and Nockolds, C.E. (1973) J. Biol. Chem., 248, 3313–3326.Google Scholar
  20. Kuboniwa, H., Tjandra, N., Grzesiek, S., Ren, H., Klee, C.B. and Bax, A. (1995) Nat. Struct. Biol., 2, 768–776.Google Scholar
  21. Kuszewski, J., Gronenborn, A.M. and Clore, G.M. (1997) J. Magn. Reson., 125, 171–177.Google Scholar
  22. Kuszewski, J., Gronenborn, A.M. and Clore, G.M. (1999) J. Am. Chem. Soc., 121, 2337–2338.Google Scholar
  23. Levitt, M. (1992) J. Mol. Biol., 226, 507–533.Google Scholar
  24. Losonczi, J.A., Andrec, M., Fischer, M.W.F. and Prestegard, J.H. (1999) J. Magn. Reson., 138, 334–342.Google Scholar
  25. Marassi, F.M. and Opella, S.J. (2000) J. Magn. Reson., 144, 150–155.Google Scholar
  26. Maune, J.F., Beckingham, K., Martin, S.R. and Bayley, P.M. (1992) Biochemistry, 31, 7779–7786.Google Scholar
  27. Meador, W.E., Means, A.R. and Quiocho, F.A. (1992) Science, 257, 1251–1255.Google Scholar
  28. Meador, W.E., Means, A.R. and Quiocho, F.A. (1993) Science, 262, 1718–1721.Google Scholar
  29. Meiler, J., Peti, W. and Griesinger, C. (2000) J. Biomol. NMR, 17, 283–294.Google Scholar
  30. Ottiger, M. and Bax, A. (1998) J. Am. Chem. Soc., 120, 12334–12341.Google Scholar
  31. Ottiger, M., Delaglio, F. and Bax, A. (1998) J. Magn. Reson., 131, 373–378.Google Scholar
  32. Tanaka, T., Ames, J.B., Harvey, T.S., Stryer, L. and Ikura, M. (1995) Nature, 376, 444–447.Google Scholar
  33. Tjandra, N. and Bax, A. (1997a) Science, 278, 1111–1114.Google Scholar
  34. Tjandra, N. and Bax, A. (1997b) J. Am. Chem. Soc., 119, 9576–9577.Google Scholar
  35. Tjandra, N., Garrett, D.S., Gronenborn, A.M., Bax, A. and Clore, G.M. (1997) Nat. Struct. Biol., 4, 443–449.Google Scholar
  36. Tjandra, N., Kuboniwa, H., Ren, H. and Bax, A. (1995) Eur. J. Biochem., 230, 1014–1024.Google Scholar
  37. Tufty, R.M. and Kretsinger, R.H. (1975) Science, 187, 167–169.Google Scholar
  38. Wang, J., Denny, J., Tian, C., Kim, S., Mo, Y., Kovacs, F., Song, Z., Nishimura, K., Gan, Z., Fu, R., Quine, J.R. and Cross, T.A. (2000) J. Magn. Reson., 144, 162–167.Google Scholar
  39. Zhang, M., Tanaka, T. and Ikura, M. (1995) Nat. Struct. Biol., 2, 758–767.Google Scholar
  40. Zweckstetter, M. and Bax, A. (2000) J. Am. Chem. Soc., 122, 3791–3792.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • James J. Chou
    • 1
  • Shipeng Li
    • 2
  • Ad Bax
    • 1
  1. 1.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Cancer InstituteNational Institutes of HealthBethesdaU.S.A.
  2. 2.Laboratory of Biochemistry, National Cancer InstituteNational Institutes of HealthBethesdaU.S.A.

Personalised recommendations