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Molecular Biology

, Volume 52, Issue 6, pp 929–936 | Cite as

Structure and Features of Amino Acid Sequences of L-Modules in SH3-Like Folds

  • A. M. Kargatov
  • E. V. Brazhnikov
  • A. V. EfimovEmail author
STRUCTURAL-FUNCTIONAL ANALYSIS OF BIOPOLYMERS AND THEIR COMPLEXES
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Abstract

A novel L-shaped repeat module whose structure can be represented as β-strand–loop–β-strand has been identified in a stereochemical analysis of nonhomologous SH3-like folds. β-Strands of the L-module are positioned at a ~90° angle to each other in different orthogonally packed β-layers. Together with a crossover loop, they form a half-turn of a right-handed superhelix. A database of 60 nonhomologous SH3-like domains has been compiled using the Protein Data Bank to study structural similarities and differences of L-modules. Occurrence frequencies of L-modules have been determined depending on the length of their loops. It has been shown that L-modules with βmαααβn- and βmαααβαβn-conformations, where m and n are numbers of β-residues in the first and second β-strands, occur most often (57 and 8%, respectively). Spatial structures of L-modules of the same type are very similar, demonstrated through superimposing them using computer programs. Structural alignment of the amino acid sequences encoding L-modules has been performed, making it possible to identify key positions for hydrophobic, hydrophilic, and proline residues.

Keywords:

α-helix β-strand structural motif structural similarity 

Notes

REFERENCES

  1. 1.
    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
  2. 2.
    Efimov A.V. 1997. A structural tree for proteins containing 3β-corners. FEBS Lett. 407, 37‒41.CrossRefGoogle Scholar
  3. 3.
    Efimov A.V. 1998. A structural tree for proteins containing S-like β-sheets. FEBS Lett. 437, 246‒250.CrossRefGoogle Scholar
  4. 4.
    Efimov A.V. 2010. Structural motifs are closed into cycles in proteins. Biochem. Biophys. Res. Commun. 399, 412‒415.CrossRefGoogle Scholar
  5. 5.
    Boshkova E.A., Brazhnikov E.V., Efimov A.V. 2016. Relationship between structure and amino acid sequence of strongly twisted and coiled β-hairpins in globular proteins. Mol. Biol. (Moscow). 50 (5), 777‒782.CrossRefGoogle Scholar
  6. 6.
    Gordeev A.B., Kargatov A.M., Efimov A.V. 2010. PCBOST: Protein classification based on structural trees. Biochem. Biophys. Res. Commun. 397, 470‒471.CrossRefGoogle Scholar
  7. 7.
    Sayle R.A., Milner-White E.J. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20, 374‒376.CrossRefGoogle Scholar
  8. 8.
    Koradi R., Billeter M., Wüthrich K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51‒55.CrossRefGoogle Scholar
  9. 9.
    Efimov A.V. 1986. Standard polypeptide chain conformations in irregular protein regions. Mol. Biol. (Moscow). 20, 250‒260.Google Scholar
  10. 10.
    Guex N., Peitsch M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis. 18, 2714‒2723.CrossRefGoogle Scholar
  11. 11.
    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.CrossRefGoogle Scholar
  12. 12.
    Efimov A.V. 1984. A novel supersecondary structural motif in proteins: αα-corner. Mol. Biol. (Moscow). 18, 1524‒1537.Google Scholar
  13. 13.
    Rao S.T., Rossmann M.G. 1973. Comparison of supersecondary structures in proteins. J. Mol. Biol. 76, 241‒256.CrossRefGoogle Scholar
  14. 14.
    Levitt M., Chothia C. 1976. Structural patterns in globular proteins. Nature. 261, 552‒558.CrossRefGoogle Scholar
  15. 15.
    Efimov A.V. 1994. Favoured structural motifs in globular proteins. Structure. 2, 999‒1002.CrossRefGoogle Scholar
  16. 16.
    Efimov A.V. 2018. Chirality and handedness of protein structures. Biochemistry (Moscow). 83 (Suppl. 1), 103‒110.Google Scholar
  17. 17.
    Efimov A.V. 1997. Structural trees for protein superfamilies. Proteins. 28, 241‒261.CrossRefGoogle Scholar
  18. 18.
    Efimov A.V. 2017. Structural motifs in which β-strands are clipped together with the П-like module. Proteins. 85, 1925‒1930.CrossRefGoogle Scholar
  19. 19.
    Kargatov A.M., Efimov A.V. 2018. Unique combinations of βαβ-units and Π-like modules in proteins and specific features of their amino acid sequences. Mol. Biol. (Moscow). 52 (1), 36‒41.CrossRefGoogle Scholar
  20. 20.
    Kutyshenko V.P., Gushchina L.V., Khristoforov V.S., Prokhorov D.A., Timchenko M.A., Kudrevatykh Yu.A., Fedyukina D.V., Filimonov V.V. 2010. NMR structure and dynamics of the chimeric protein SH3-F2. Mol. Biol. (Moscow). 44 (6), 948−957.CrossRefGoogle Scholar
  21. 21.
    Chothia C., Janin J. 1982. Orthogonal packing of beta-pleated sheets in proteins. Biochemistry. 21, 3955‒3965.CrossRefGoogle Scholar
  22. 22.
    Efimov A.V. 1991. Structure of coiled β-β-hairpins and β-β-corners. FEBS Lett. 284, 288‒292.CrossRefGoogle Scholar
  23. 23.
    Efimov A.V. 1992. A novel super-secondary structure of β-proteins: A triple-strand corner. FEBS Lett. 298, 261‒265.CrossRefGoogle Scholar
  24. 24.
    Efimov A.V., Boshkova E.A. 2014. Two mechanisms of protein folding: A theoretical analysis (review article). Russ. J. Bioorg. Chem. 40 (6), 612–619.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • A. M. Kargatov
    • 1
  • E. V. Brazhnikov
    • 1
  • A. V. Efimov
    • 1
    Email author
  1. 1.Institute of Protein Research, Russian Academy of SciencesPushchinoRussia

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