Analysis of the Conformations Corresponding to Hexapeptide and Large Sequences Characterized by Continuous Single Amino Acid Repeats in Proteins

Mannava      Gayatri; Kunchur      Guruprasad

doi:10.2174/0929866511009011459

Abstract

The analysis of conformations corresponding to continuous amino acid repeat peptides (CARPs) comprising six or more residues in proteins of known three-dimensional structure revealed that alanine, glycine, glutamic acid, proline, valine, histidine, aspartic acid, glutamine and lysine were associated as repeating amino acid residues. Alanine, glycine and histidine CARPs were most common, although the histidine hexapeptide and large CARPs mainly correspond to affinity tags and are not part of the native protein sequence. The Ala and Glu CARPs were observed either as part of helix, or coil or a combination of these conformations. The octapeptide Ala CARP in six-hairpin glycosidases was observed as part of strand and coil conformation. The Gly and Pro CARPs were mainly associated with coil conformation. Majority of the coil regions in CARPs contained beta and gamma-turn structural motifs. The conformations of the Asp, Glu and Lys hexapeptide or larger CARPs were not defined in the corresponding protein three-dimensional structures analyzed. The longest CARP of known conformation was observed for alanine as a decapeptide in a lysozyme-like protein that corresponds to helix. A feature of CARPs is that a majority are exposed to solvent with accessible surface area greater than 200 Å² units in the protein three-dimensional structure.

Keywords: Amyloid peptides, chameleon sequences, continuous amino acid repeats, inherited-diseases, peptide design, protein data bank, protein sequence-structure analysis, secondary structure conformations, Amino Acid Repeats, Proteins, CARPs, alanine, glycine, glutamic acid, proline, valine, histidine, aspartic acid, glutamine, lysine, six-hairpin glycosidases, homopolymeric amino acid, polyalanine, polyglutamine related-diseases, Polyalanine tracts, Protein Sequence Structure Analysis Relational Database, X-ray crystallography, NMR, Dictionary of Secondary Structure in Proteins, C-alpha atom, Structural Classification of Proteins (SCOP) database, histidine CARPs, Ala CARPs, methyl-accepting chemotaxis protein and lysozyme-like proteins, Bacillus megaterium, S-adenosyl-L-homocysteine, mid-gut procarboxypeptidase, Helicoverpa armigera, docking domain, Gly CARPs, glutathione transferases, Glu CARPs, bovine mitochondrial cytochrome bc1 complex, Val CARP, Pro CARP, His CARPs