Density Modification Methods

  • A. D. Podjarny
Part of the NATO ASI Series book series (NSSA, volume 126)

Abstract

Macromolecular crystallography is growing rapidly as a tool to image the structure of proteins, nucleic acids and their interactions . In many of these projects, however, MIR (Multiple Isomorphous Replacement) phasing methods have not been successful in imaging macromolecules within their crystals. These problems have motivated efforts to supplement or replace MIR as a phasing technique. Various approaches have been tried, both in real and reciprocal space, and among them DM (density modification) methods have proven to be quite succesful in improving phases using real-space constraints.

Keywords

Entropy Attenuation Recombination Assure Macromolecule 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Argos, P., Ford, G.C. and Rossmann, M.G., (1974) Acta Crvst.. A31, 499–506.Google Scholar
  2. Auslander, L., Feig, E. and Winograd, S. (1981) In Computational Crystallography ,edited by D.Sayre, pp. 451–469. Ottawa: Clarendon Press.Google Scholar
  3. Bantz, D. and Zwck, M. (1974). Acta Crvst, A30. 257–260.Google Scholar
  4. Barrett, A. N., and Zwick, M. (1971). Acta Cryst. A27, 6–11.Google Scholar
  5. Bentley, G. A., Lewit-Bentley, A., Finch, J.T., Podjarny, A.D and Roth, M. (1984). J. Mol.Biol. 176,55–75.PubMedCrossRefGoogle Scholar
  6. Bhat, T.N. and Blow, D.M. (1982). Acta Cryst., A38, 21–29.Google Scholar
  7. Bhat, T.N. (1984). Annual Meeting of the ACA, Lexington, Kentucky, Section Q.Google Scholar
  8. Bhat, T.N. (1985). Annual Meeting of the ACA. Stanford, California. Section H.Google Scholar
  9. Bricogne, G. (1974). Acta Crvst., A 30, 395–405.CrossRefGoogle Scholar
  10. Bhcogne, G. (1976). Acta Cryst., A 32, 832–847.CrossRefGoogle Scholar
  11. Buehner, M., Ford, G.C., Olsen, K.W., Moras, D., Rossmann, M.G. (1974). J. Mol. Biol.. 90(1), 25–49.PubMedCrossRefGoogle Scholar
  12. Cannillo, E., Oberti, R and Ungaretti, L. (1983). Acta Cryst., A39, 68–74.Google Scholar
  13. Collins, D. M., Cotton, F. A., Hazen, E.E. Jr., Meyer, E.F., and Morimoto, C.N. (1975)Science, Vol 190, 1047–1053.PubMedCrossRefGoogle Scholar
  14. Collins, D.M., Brice, M.D., La Cour, T.F. M. and Legg, M. J. (1976) In Crystallographic Computing Techniques, edited by F. R. Ahmed, K. Huml and B. Sedlacek, pp. 330–335.Copenhagen:Munskgaard.Google Scholar
  15. Hendrickson, W. A. (1981). In Structural Aspects of Biomolecules, edited by R.Shnivasan and V. Pattabhi, pp. 31–80. New Delhi:Macmillan.Google Scholar
  16. Hendrickson, W. A., Klippenstein, G. L., and Ward, K. B. (1975)PNAS. USA, 72, 2160–2164.PubMedCrossRefGoogle Scholar
  17. Hendrickson, W. A. and Lattman, E.E. (1970) Acta Cryst., B26, 136–143.Google Scholar
  18. Hoppe, W., and Gassman, J. (1968). Acta Cryst. B24, 97–107.Google Scholar
  19. Keith, C., Feldman, D., Deganello, S., Glick, J., Ward, K., Oliver Jones,E. and Sigler, P.B. (1981). JBC, 256, 8602–8607.Google Scholar
  20. Main, P. (1979). Acta Cryst., A35, 779–785.Google Scholar
  21. Nixon, P. E., and North, A.C.T. (1976) Acta Cryst., A32, 325.Google Scholar
  22. Otwinowski, Z. (1985). Personal communication.Google Scholar
  23. Podjarny, A. D., and Yonath, A., Acta Cryst. (1977) A33.655–661.Google Scholar
  24. Podjarny, A.D., Thierry, J.C., Cavarelli, J., Rees, B., Lewit-Bentley, A., Roth, M., Lorver, B.,Romby, P., Ebel, J.P, Giege, R. and Moras, D. (1985). PNAS. sent for publication.Google Scholar
  25. Podjarny, A. D., Sussman, J. L., Bhat, T. N., Westbrook, E. M., Harel, M.,Yonath, A., and Shoham, M. (1984). Acta Crvst. A35s, Abstract 01.4–2.Google Scholar
  26. Raghavan, N. V and Tulinsky, A. (1979) Acta Cryst., B35, 1776–1785.Google Scholar
  27. Rees, B. (1984). Personnal Communication.Google Scholar
  28. Rice, D.W. (1981). Acta Cryst., A37, 491–500.Google Scholar
  29. Rossman, M. G. and Blow, D. M. (1961). Acta Cryst., 14, 641–647.CrossRefGoogle Scholar
  30. Sayre, D. (1952). Acta Cryst., 5, 60–65.CrossRefGoogle Scholar
  31. Schevitz, R. W., Podjarny, A. D., Zwick, M., Hughes, J.J. and Sigler, P. B. (1981). Acta Cryst., A37, 669–677.Google Scholar
  32. Sim, G. A. (1959). Acta Cryst.. 12, 813–815.CrossRefGoogle Scholar
  33. Stuart, D. and Artymiuk, P. (1985). Acta Cryst., A40, 713–716.Google Scholar
  34. Ten Eyck, L.F. (1977) Acta Cryst., A33, 486–492.Google Scholar
  35. Wang, B.C. In Notes of the School on Direct Methods and Macromolecular Crystallography, 1983. Edited by H. Hauptman. Buffalo.Google Scholar
  36. Westbrook, E. (1984).Personnal Communication.Google Scholar
  37. Westbrook, E., Piro, O. and Sigler, P. B. (1984). JBC, 259, 9096–9103.Google Scholar
  38. Zwick, M., Bantz, D. and Hughes, J. (1976). Ultramicroscopy. 275–277.Google Scholar

Copyright information

© Springer Science+Business Media New York 1987

Authors and Affiliations

  • A. D. Podjarny
    • 1
  1. 1.Dept. of Biochemistry and Molecular BiologyU. of ChicagoChicagoUSA

Personalised recommendations