Journal of Biomolecular NMR

, Volume 26, Issue 4, pp 355–366

A use of Ramachandran potentials in protein solution structure determinations

  • Ivano Bertini
  • Gabriele Cavallaro
  • Claudio Luchinat
  • Irene Poli
Article

Abstract

A strategy is developed to use database-derived φ-ψ constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived φ-ψ constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the φ-ψ values for each residue are examined. In the second and final run, the database-derived φ-ψ constraints are enforced only for those residues which in the first run have ended in one and the same favored φ-ψ region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.

backbone conformation protein structure Ramachandran plot structure calculation structure databases 

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References

  1. Allen, F.H. and Johnson, O. (1991) Acta Cryst. B, 47, 62–67.Google Scholar
  2. Arnesano, F., Banci, L., Bertini, I., Huffman, D.L. and O'Halloran, T.V. (2001) Biochemistry, 40, 1528–1539.Google Scholar
  3. Arnesano, F., Banci, L., Bertini, I. and Thompsett, A.R. (2002) Structure, 10, 1337–1347.Google Scholar
  4. Assfalg, M., Banci, L., Bertini, I., Bruschi, M., Giudici-Orticoni, M.T. and Turano, P. (1999) Eur. J. Biochem., 266, 634–643.Google Scholar
  5. Assfalg, M., Bertini, I., Turano, P., Bruschi, M., Durand, M.C., Giudici-Orticoni, M.T. and Dolla, A. (2002) J. Biomol. NMR, 22, 107–122.Google Scholar
  6. Banci, L., Bertini, I., Cantini, F., D'Onofrio, M. and Viezzoli, M.S. (2002a) Protein Sci., 11, 2479–2492.Google Scholar
  7. Banci, L., Bertini, I., Ciofi-Baffoni, S., D'Onofrio, M., Gonnelli, L., Marhuenda-Egea, F.C. and Ruiz-Dueñas, F.J. (2002b) J. Mol. Biol., 317, 415–429.Google Scholar
  8. Banci, L., Bertini, I., Ciofi-Baffoni, S., Huffman, D.L. and O'Halloran, T.V. (2001) J. Biol. Chem., 276, 8415–8426.Google Scholar
  9. Banci, L., Bertini, I., Eltis, L.D., Felli, I.C., Kastrau, D.H.W., Luchinat, C., Piccioli, M., Pierattelli, R. and Smith, M. (1994) Eur. J. Biochem., 225, 715–725.Google Scholar
  10. Bartalesi, I., Bertini, I., Hajieva, P., Rosato, A. and Vasos, P. (2002) Biochemistry, 41, 5112–5119.Google Scholar
  11. Bertini, I., Donaire, A., Jimenez, B., Luchinat, C., Parigi, G., Piccioli, M. and Poggi, L. (2001) J. Biomol. NMR, 21, 85–98.Google Scholar
  12. Breiter, D.R., Meyer, T.E., Rayment, I. and Holden, H.M. (1991) J. Biol. Chem., 266, 18660–18667.Google Scholar
  13. Clore, G.M. and Gronenborn, A.M. (1998) Proc. Natl. Acad Sci. USA, 95, 5891–5898.Google Scholar
  14. Czjzek, M., Arnoux, P., Haser, R. and Shepard, W. (2001) Acta Cryst. D, 57, 670–678.Google Scholar
  15. Doreleijers, J.F., Rullmann, J.A.C. and Kaptein, R. (1998) J. Mol. Biol., 281, 149–164.Google Scholar
  16. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283–298.Google Scholar
  17. Herrmann, T., Güntert, P. and Wüthrich, K. (2002) J. Mol. Biol., 319, 209–227.Google Scholar
  18. Kleywegt, G.J. and Jones, T.A. (1996) Structure, 4, 1395–1400.Google Scholar
  19. Kleywegt, G.J. and Jones, T.A. (2002) Structure, 10, 465–472.Google Scholar
  20. Kuszewski, J., Gronenborn, A.M. and Clore, G.M. (1996) Protein Sci., 5, 1067–1080.Google Scholar
  21. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) J. Appl. Crystallogr., 26, 283–291.Google Scholar
  22. Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J. Biomol. NMR, 8, 477–486.Google Scholar
  23. Louie, G.V. and Brayer, G.D. (1990) J. Mol. Biol., 214, 527–555.Google Scholar
  24. MacArthur, M.W. and Thornton, J.M. (1993) Proteins Struct. Funct. Genet., 17, 232–251.Google Scholar
  25. MacArthur, M.W., Laskowski, R.A. and Thornton, J.M. (1994) Curr. Opin. Struct. Biol., 4, 731–737.Google Scholar
  26. Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K. (1998) J. Biomol. NMR, 12, 1–23.Google Scholar
  27. Morris, A.L., MacArthur, M.W., Hutchinson, E.G. and Thornton, J.M. (1992) Proteins Struct. Funct. Genet., 12, 345–364.Google Scholar
  28. Ramachandran, G.N., Ramakrishnan, C. and Sasisekharan, V. (1963) J. Mol. Biol., 7, 95–99.Google Scholar
  29. Rosenzweig, A.C., Huffman, D.L., Hou, M.Y., Wernimont, A.K., Pufahl, R.A. and O'Halloran, T.V. (1999) Struct. Fold Des., 7, 605–617.Google Scholar
  30. Schwieters, C.D., Kuszewski, J., Tjandra, N. and Clore, G.M. (2003) J. Magn. Reson., 160, 65–73.Google Scholar
  31. Sprangers, R., Bottomley, M.J., Linge, J.P., Schultz, J., Nilges, M. and Sattler, M. (2000) J. Biomol. NMR, 16, 47–58.Google Scholar
  32. Spronk, C.A.E.M., Linge, J.P., Hilbers, C.W. and Vuister, G.W. (2002) J. Biomol. NMR, 22, 281–289.Google Scholar
  33. Svensson, L.A., Thulin, E. and Forsén, S. (1992) J. Mol. Biol., 223, 601–606.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Ivano Bertini
    • 1
  • Gabriele Cavallaro
    • 1
  • Claudio Luchinat
    • 2
  • Irene Poli
    • 1
  1. 1.Magnetic Resonance Center and Department of ChemistryUniversity of FlorenceSesto FiorentinoItaly
  2. 2.Magnetic Resonance Center and Department of Agricultural BiotechnologyUniversity of FlorenceSesto FiorentinoItaly

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