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A novel structural motif and structural trees for proteins containing it

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Abstract

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.

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References

  1. Efimov, A. V. (1994) Structure, 2, 999–1002.

    Article  CAS  PubMed  Google Scholar 

  2. Efimov, A. V. (1994) FEBS Lett., 355, 213–219.

    Article  CAS  PubMed  Google Scholar 

  3. Efimov, A. V. (1997) Proteins, 28, 241–260.

    Article  CAS  PubMed  Google Scholar 

  4. Efimov, A. V. (2004) Uspekhi Biol. Khim., 44, 109–132.

    CAS  Google Scholar 

  5. Levitt, M., and Chothia, C. (1976) Nature, 261, 552–558.

    Article  CAS  PubMed  Google Scholar 

  6. Rao, S. T., and Rossmann, M. G. (1973) J. Mol. Biol., 76, 241–256.

    Article  CAS  PubMed  Google Scholar 

  7. Sternberg, M. J. E., and Thornton, J. M. (1976) J. Mol. Biol., 105, 367–382.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  9. Castillo, R. M., Mizuguchi, K., Dhanaray, V., Albert, A., Blundell, T. L., and Murzin, A. G. (1999) Structure, 7, 227–236.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  11. Tatusova, T. A., and Madden, T. L. (1999) FEMS Microbiol. Lett., 174, 247–250.

    Article  CAS  PubMed  Google Scholar 

  12. Efimov, A. V. (1995) J. Mol. Biol., 245, 402–415.

    Article  CAS  PubMed  Google Scholar 

  13. Lim, V. I., Mazanov, A. L., and Efimov, A. V. (1978) Mol. Biol. (Moscow), 12, 206–213.

    CAS  Google Scholar 

  14. Richardson, J. S. (1977) Nature, 268, 495–500.

    Article  CAS  PubMed  Google Scholar 

  15. Efimov, A. V. (2008) Biochemistry (Moscow), 73, 23–28.

    CAS  Google Scholar 

Download references

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Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia

    A. M. Kargatov & A. V. Efimov

Authors
  1. A. M. Kargatov
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  2. A. V. Efimov
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Correspondence to A. V. Efimov.

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Published in Russian in Biokhimiya, 2010, Vol. 75, No. 2, pp. 305–312.

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Kargatov, A.M., Efimov, A.V. A novel structural motif and structural trees for proteins containing it. Biochemistry Moscow 75, 249–256 (2010). https://doi.org/10.1134/S0006297910020161

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  • DOI: https://doi.org/10.1134/S0006297910020161

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