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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 
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Notes

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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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