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Vol 52(2018) N 6 p. 929-936; DOI 10.1134/S0026893318060092 Full Text

A.M. Kargatov1, E.V. Brazhnikov1, A.V. Efimov1*

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

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

*efimov@protres.ru
Received - 2018-04-17; Accepted - 2018-05-29

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.

α-helix, β-strand, structural motif, structural similarity



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