Biochemistry (Moscow)

, Volume 75, Issue 2, pp 249–256 | Cite as

A novel structural motif and structural trees for proteins containing it

  • A. M. Kargatov
  • A. V. EfimovEmail author


In the present study, a novel structural motif that can be represented as a combination of the known βαβ-unit and ψ-motif is described and analyzed. In theory, there are four possible combinations of the motifs since each of them can exist in two forms, left-handed and right-handed. For this study, we have selected 140 nonhomologous proteins in which 158 combinations of such types have been found. The combination of the right-handed ψ-motif and the right-handed βαβ-unit has been shown to occur most often (87 cases out of 158) and the combination of the left-handed βαβ-unit and the left-handed ψ-motif does not occur at all. Three novel structural trees in which the commonly occurring combinations are taken as the root structures have been constructed.

Key words

βαβ-unit modeling ψ-motif protein folding structural classification 


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  1. 1.
    Efimov, A. V. (1994) Structure, 2, 999–1002.CrossRefPubMedGoogle Scholar
  2. 2.
    Efimov, A. V. (1994) FEBS Lett., 355, 213–219.CrossRefPubMedGoogle Scholar
  3. 3.
    Efimov, A. V. (1997) Proteins, 28, 241–260.CrossRefPubMedGoogle Scholar
  4. 4.
    Efimov, A. V. (2004) Uspekhi Biol. Khim., 44, 109–132.Google Scholar
  5. 5.
    Levitt, M., and Chothia, C. (1976) Nature, 261, 552–558.CrossRefPubMedGoogle Scholar
  6. 6.
    Rao, S. T., and Rossmann, M. G. (1973) J. Mol. Biol., 76, 241–256.CrossRefPubMedGoogle Scholar
  7. 7.
    Sternberg, M. J. E., and Thornton, J. M. (1976) J. Mol. Biol., 105, 367–382.CrossRefPubMedGoogle Scholar
  8. 8.
    Suguna, K., Bott, R. R., Padlan, E. A., Subramanian, E., Sheriff, S., Cohen, G. H., and Davies, D. R. (1987) J. Mol. Biol., 196, 877–900.CrossRefPubMedGoogle Scholar
  9. 9.
    Castillo, R. M., Mizuguchi, K., Dhanaray, V., Albert, A., Blundell, T. L., and Murzin, A. G. (1999) Structure, 7, 227–236.CrossRefPubMedGoogle Scholar
  10. 10.
    Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissing, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res., 28, 235–242.CrossRefPubMedGoogle Scholar
  11. 11.
    Tatusova, T. A., and Madden, T. L. (1999) FEMS Microbiol. Lett., 174, 247–250.CrossRefPubMedGoogle Scholar
  12. 12.
    Efimov, A. V. (1995) J. Mol. Biol., 245, 402–415.CrossRefPubMedGoogle Scholar
  13. 13.
    Lim, V. I., Mazanov, A. L., and Efimov, A. V. (1978) Mol. Biol. (Moscow), 12, 206–213.Google Scholar
  14. 14.
    Richardson, J. S. (1977) Nature, 268, 495–500.CrossRefPubMedGoogle Scholar
  15. 15.
    Efimov, A. V. (2008) Biochemistry (Moscow), 73, 23–28.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2010

Authors and Affiliations

  1. 1.Institute of Protein ResearchRussian Academy of SciencesPushchino, Moscow RegionRussia

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