Molecular Biology

, Volume 52, Issue 1, pp 36–41 | Cite as

Unique Combinations of βαβ-Units and Π-Like Modules in Proteins and Specific Features of Their Amino Acid Sequences

  • A. M. Kargatov
  • A. V. EfimovEmail author
Structural Functional Analysis of Biopolymers and Their Complexes


Possible combinations of βαβ-units and Π-like modules in proteins in both right- and left-handed forms have been analyzed in detail. The correlation between the mutual arrangement of the structural elements in the polypeptide chain and their handedness has been shown. In the βαβΠ combinations, which is encountered most frequently in proteins, the Π-module follows the βαβ unit along the chain and both elements are right-handed. In the Πβαβ combinations, where the Π-module is located at the N end and the βαβ-unit follows it, the former is left-handed and the latter is right-handed. In relatively rare combinations of the left-handed βαβ-units and right-handed Π-modules, the βαβ-unit follows Π-module in the chain. The combinations of left-handed Π-modules and the left-handed βαβ-units are unobservable in proteins. It has also been shown that the Π-modules with a β-strand—α-helix—arch—β-strand structure are observed in proteins only in a right-handed form and half of them (51%) contains cis-prolines in their arches. These arches of nonhomologous proteins, as well as the positions of cis-prolines, nearly coincide when superimposed. The superimposed Π-modules also demonstrate that their overall folds are very similar. Structural alignment of their amino acid sequences has shown that the Π-modules have very similar sequence patterns of the key hydrophobic, hydrophilic, glycine, and cis-proline residues.


α-helix β-strand crossover loop arch structural motif cis-proline 


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  1. 1.
    Efimov A.V. 1994. Favoured structural motifs in globular proteins. Structure. 2, 999–1002.CrossRefPubMedGoogle Scholar
  2. 2.
    Rao S.T., Rossmann M.G. 1973. Comparison of supersecondary structures in proteins. J. Mol. Biol. 76, 241–256.CrossRefPubMedGoogle Scholar
  3. 3.
    Sternberg M.J., Thornton J.M. 1976. On the conformation of proteins: The handedness of the beta-strand-alpha-helix-beta-strand unit. J. Mol. Biol. 105, 367–382.CrossRefPubMedGoogle Scholar
  4. 4.
    Levitt M., Chothia C. 1976. Structural patterns in globular proteins. Nature. 261, 552–558.CrossRefPubMedGoogle Scholar
  5. 5.
    Efimov A.V. 1995. Structural similarity between twolayer α/β- and β-proteins. J. Mol. Biol. 245, 402–415.CrossRefPubMedGoogle Scholar
  6. 6.
    Gordeev A.B., Efimov A.V. 2013. Modeling of folds and folding pathways for some protein families of (α + β)- and α/β-classes. J. Biomol. Struct. Dyn. 31, 4–16.Google Scholar
  7. 7.
    Kargatov A.M., Efimov A.V. 2010. A novel structural motif and structural trees for proteins containing it. Biochemistry (Moscow). 75, 249–256.CrossRefGoogle Scholar
  8. 8.
    Suguna K., Bott R.R., Padlan E.A., et al. 1987. Structure and refinement at 1.8 Å resolution of the aspartic proteinase from Rhizopus chinensis. J. Mol. Biol. 196, 877–900.CrossRefPubMedGoogle Scholar
  9. 9.
    Castillo R.M., Mizuguchi K., Dhanaraj V., et al. 1999. A six-stranded double-psi beta barrel is shared by several protein superfamilies. Structure. 7, 227–236.CrossRefPubMedGoogle Scholar
  10. 10.
    Efimov A.V. 2008. Structural trees for proteins containing ϕ-motifs. Biochemistry (Moscow). 73, 23–28.CrossRefGoogle Scholar
  11. 11.
    Efimov A.V. (2017) Structural motifs in which β-strands are clipped together with the Π-like module, PROTEINS: Structure, Functions and Bioinformatics, doi 10.1002/prot.25346Google Scholar
  12. 12.
    Gordeev A.B., Kargatov A.M., Efimov A.V. 2010. PCBOST: Protein classification based on structural trees. Biochem. Biophys. Res. Commun. 397, 470–471.CrossRefPubMedGoogle Scholar
  13. 13.
    Tatusova T.A., Madden T.L. 1999. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 177, 187–188.Google Scholar
  14. 14.
    Sayle R.A., Milner-White E.J. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20, 374–376.CrossRefPubMedGoogle Scholar
  15. 15.
    Koradi R., Billeter M., Wuthrich K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55.CrossRefPubMedGoogle Scholar
  16. 16.
    Efimov A.V. 1993. Standard structures in proteins. Prog. Biophys. Mol. Biol. 60, 201–239.CrossRefPubMedGoogle Scholar
  17. 17.
    Guex N., Peitsch M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis. 18, 2714–2723.CrossRefPubMedGoogle Scholar
  18. 18.
    Efimov A.V. 2010. Structural motifs are closed into cycles in proteins. Biochem. Biophys. Res. Commun. 399, 412–415.CrossRefPubMedGoogle Scholar
  19. 19.
    Lim V.I. 1974. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure}. J. Mol. Biol. 88, 857–872.CrossRefPubMedGoogle Scholar
  20. 20.
    MacArthur M.W., Thornton J.M. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218, 397–412.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

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

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