Structure and Features of Amino Acid Sequences of L-Modules in SH3-Like Folds
- 16 Downloads
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 similarityNotes
REFERENCES
- 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.Efimov A.V. 1997. A structural tree for proteins containing 3β-corners. FEBS Lett. 407, 37‒41.CrossRefGoogle Scholar
- 3.Efimov A.V. 1998. A structural tree for proteins containing S-like β-sheets. FEBS Lett. 437, 246‒250.CrossRefGoogle Scholar
- 4.Efimov A.V. 2010. Structural motifs are closed into cycles in proteins. Biochem. Biophys. Res. Commun. 399, 412‒415.CrossRefGoogle Scholar
- 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.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.Sayle R.A., Milner-White E.J. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20, 374‒376.CrossRefGoogle Scholar
- 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.Efimov A.V. 1986. Standard polypeptide chain conformations in irregular protein regions. Mol. Biol. (Moscow). 20, 250‒260.Google Scholar
- 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.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.Efimov A.V. 1984. A novel supersecondary structural motif in proteins: αα-corner. Mol. Biol. (Moscow). 18, 1524‒1537.Google Scholar
- 13.Rao S.T., Rossmann M.G. 1973. Comparison of supersecondary structures in proteins. J. Mol. Biol. 76, 241‒256.CrossRefGoogle Scholar
- 14.Levitt M., Chothia C. 1976. Structural patterns in globular proteins. Nature. 261, 552‒558.CrossRefGoogle Scholar
- 15.Efimov A.V. 1994. Favoured structural motifs in globular proteins. Structure. 2, 999‒1002.CrossRefGoogle Scholar
- 16.Efimov A.V. 2018. Chirality and handedness of protein structures. Biochemistry (Moscow). 83 (Suppl. 1), 103‒110.Google Scholar
- 17.Efimov A.V. 1997. Structural trees for protein superfamilies. Proteins. 28, 241‒261.CrossRefGoogle Scholar
- 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.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.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.Chothia C., Janin J. 1982. Orthogonal packing of beta-pleated sheets in proteins. Biochemistry. 21, 3955‒3965.CrossRefGoogle Scholar
- 22.Efimov A.V. 1991. Structure of coiled β-β-hairpins and β-β-corners. FEBS Lett. 284, 288‒292.CrossRefGoogle Scholar
- 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.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