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

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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 Ų units in the protein three-dimensional structure.





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

Document Type: Research Article

Publication date: 2010-12-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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