Journal of Biomolecular NMR

, Volume 30, Issue 1, pp 25–35 | Cite as

Backbone assignment of proteins with known structure using residual dipolar couplings

Abstract

A prerequisite for NMR studies of protein-ligand interactions or protein dynamics is the assignment of backbone resonances. Here we demonstrate that protein assignment can significantly be enhanced when experimental dipolar couplings (RDCs) are matched to values back-calculated from a known three-dimensional structure. In case of small proteins, the program MARS allows assignment of more than 90% of backbone resonances without the need for sequential connectivity information. For bigger proteins, we show that the combination of sequential connectivity information with RDC-matching enables more residues to be assigned reliably and backbone assignment to be more robust against missing data. Structural or dynamic deviations from the employed 3D coordinates do not lead to an increased error rate in RDC-supported assignment. RDC-enhanced assignment is particularly useful when chemical shifts and sequential connectivity only provide a few reliable assignments.

assignment maltose-binding protein Mars NMR protein-ligand binding RDC software structural genomics 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Al-Hashimi, H.M., Gorin, A., Majumdar, A., Gosser, Y. and Patel, D.J. (2002) J. Mol. Biol., 318, 637-649.Google Scholar
  2. Amor, J.C., Seidel, R.D., Tian, F., Kahn, R.A. and Prestegard, J.H. (2002) J. Biomol. NMR, 23, 253-254.Google Scholar
  3. Bartels, C., Billeter, M., Güntert, P. and Wüthrich, K. (1996) J. Biomol. NMR, 7, 207-213.Google Scholar
  4. Bax, A. and Grzesiek, S. (1993) Accounts Chem. Res., 26, 131-138.Google Scholar
  5. Bax, A., Kontaxis, G. and Tjandra, N. (2001) Meth. Enzymol., 339, 127-174.Google Scholar
  6. Bernstein, R., Cieslar, C., Ross, A., Oschkinat, H., Freund, J. and Holak, T.A. (1993) J. Biomol. NMR, 3, 245-251.Google Scholar
  7. Clore, G.M., Gronenborn, A.M. and Bax, A. (1998) J. Magn. Reson., 133, 216-221.Google Scholar
  8. Cook, W.J., Jeffrey, L.C., Carson, M., Chen, Z.J. and Pickart, C.M. (1992) J. Biol. Chem., 267, 16467-16471.Google Scholar
  9. Cornilescu, G., Delaglio, F. and Bax, A. (1999) J. Biomol. NMR, 13, 289-302.Google Scholar
  10. Cornilescu, G., Marquardt, J.L., Ottiger, M. and Bax, A. (1998) J. Am. Chem. Soc., 120, 6836-6837.Google Scholar
  11. Doreleijers, J.F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J.L. and Ulrich, E.L. (2003) J. Biomol. NMR, 26, 139-146.Google Scholar
  12. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C. and Scharf, M. (1995) J. Comput. Chem., 16, 273-284.Google Scholar
  13. Evenas, J., Tugarinov, V., Skrynnikov, N.R., Goto, N.K., Muhandiram, R. and Kay, L.E. (2001) J. Mol. Biol., 309, 961-974.Google Scholar
  14. Gardner, K.H., Zhang, X.C., Gehring, K. and Kay, L.E. (1998) J. Am. Chem. Soc., 120, 11738-11748.Google Scholar
  15. Garrett, D.S., Seok, Y.J., Liao, D.I., Peterkofsky, A., Gronenborn, A.M. and Clore, G.M. (1997) Biochemistry, 36, 2517-2530.Google Scholar
  16. Garrett, D.S., Seok, Y.J., Peterkofsky, A., Gronenborn, A.M. and Clore, G.M. (1999) Nat. Struct. Biol., 6, 166-173.Google Scholar
  17. Grzesiek, S. and Bax, A. (1993) J. Biomol. NMR, 3, 185-204.Google Scholar
  18. Hansen, M.R., Mueller, L. and Pardi, A. (1998) Nat. Struct. Biol., 5, 1065-1074.Google Scholar
  19. Hus, J.C., Prompers, J.J. and Bruschweiler, R. (2002) J. Magn. Reson., 157, 119-123.Google Scholar
  20. Jain, N.U., Noble, S. and Prestegard, J.H. (2003) J. Mol. Biol., 328, 451-462.Google Scholar
  21. Jung, Y.S. and Zweckstetter, M. (2004) J. Biomol. NMR, 30, 11-23.Google Scholar
  22. Koradi, R., Billeter, M. and Wuthrich, K. (1996) J. Mol. Graph., 14, 51-&.Google Scholar
  23. Liao, D.I., Silverton, E., Seok, Y.J., Lee, B.R., Peterkofsky, A. and Davies, D.R. (1996) Structure, 4, 861-872.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. Moseley, H.N.B. and Montelione, G.T. (1999) Curr. Opin. Struct. Biol., 9, 635-642.Google Scholar
  26. Mueller, G.A., Choy, W.Y., Yang, D.W., Forman-Kay, J.D., Venters, R.A. and Kay, L.E. (2000) J. Mol. Biol., 300, 197-212.Google Scholar
  27. Prestegard, J.H. and Kishore, A.I. (2001) Curr. Opin. Chem. Biol., 5, 584-590.Google Scholar
  28. Pristovsek, P., Ruterjans, H. and Jerala, R. (2002) J. Comput. Chem., 23, 335-340.Google Scholar
  29. Sharff, A.J., Rodseth, L.E. and Quiocho, F.A. (1993) Biochemistry, 32, 10553-10559.Google Scholar
  30. Skrynnikov, N.R. and Kay, L.E. (2000) J. Biomol. NMR, 18, 239-252.Google Scholar
  31. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490-5492.Google Scholar
  32. Tian, F., Valafar, H. and Prestegard, J.H. (2001) J. Am. Chem. Soc., 123, 11791-11796.Google Scholar
  33. Vijaykumar, S., Bugg, C.E. and Cook, W.J. (1987) J. Mol. Biol., 194, 531-544.Google Scholar
  34. Warren, J.J. and Moore, P.B. (2001) J. Magn. Reson., 149, 271-275.Google Scholar
  35. Wüthrich, K. (2003) Angew. Chem.-Int. Edit., 42, 3340-3363.Google Scholar
  36. Xu, X.P. and Case, D.A. (2001) J. Biomol. NMR, 21, 321-333.Google Scholar
  37. Xu, X.P. and Case, D.A. (2002) Biopolymers, 65, 408-423.Google Scholar
  38. Yang, D.W., Venters, R.A., Mueller, G.A., Choy, W.Y. and Kay, L.E. (1999) J. Biomol. NMR, 14, 333-343.Google Scholar
  39. Zhang, F.L. and Bruschweiler, R. (2002) J. Am. Chem. Soc., 124, 12654-12655.Google Scholar
  40. Zweckstetter, M. (2003) J. Biomol. NMR, 27, 41-56.Google Scholar
  41. Zweckstetter, M. and Bax, A. (2000) J. Am. Chem. Soc., 122, 3791-3792.Google Scholar
  42. Zweckstetter, M. and Bax, A. (2001) J. Am. Chem. Soc., 123, 9490-9491.Google Scholar
  43. Zweckstetter, M. and Bax, A. (2002) J. Biomol. NMR, 23, 127-137.Google Scholar
  44. Zweckstetter, M., Hummer, G. and Bax, A. (2004) Biophys. J., 86, 3444-3460.Google Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  1. 1.Max Planck Institute for Biophysical ChemistryGöttingenGermany

Personalised recommendations