Structure and Features of Amino Acid Sequences of L-Modules in SH3-Like Folds
- 9 Downloads
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
- 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
- 9.Efimov A.V. 1986. Standard polypeptide chain conformations in irregular protein regions. Mol. Biol. (Moscow). 20, 250‒260.Google Scholar
- 12.Efimov A.V. 1984. A novel supersecondary structural motif in proteins: αα-corner. Mol. Biol. (Moscow). 18, 1524‒1537.Google Scholar
- 16.Efimov A.V. 2018. Chirality and handedness of protein structures. Biochemistry (Moscow). 83 (Suppl. 1), 103‒110.Google Scholar