Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences

Abstract

Helices, strands and coils in proteins of known three-dimensional structure, corresponding to heptapeptide and large sequences (‘probe’ peptides), were scanned against peptide sequences of variable length, comprising seven or more residues that correspond to a different conformation (‘target’ peptides) in protein crystal structures available from the Protein Data Bank (PDB). Where the ‘probe’ and ‘target’ peptide sequences exactly match, they correspond to ‘chameleon’ sequences in protein structures. We observed ∼548 heptapeptide and large chameleon sequences that included peptides in the coil conformation from 53,794 PDB files that were analyzed. However, after excluding several chameleon peptides based on the quality of protein structure data, redundancy and peptides associated with cloning artifacts, such as, histidine-tags, we observed only ten chameleon peptides in structurally different proteins and the maximum length comprised seven amino acid residues. Our analysis suggests that the quality of protein structure data is important for identifying possibly, the ‘true chameleons’ in PDB. Majority of the chameleon sequences correspond to an entire strand in one protein that is observed as part of helix sequence in another protein. The heptapeptide chameleons are characterized with a high propensity of alanine, leucine and valine amino acid residues. The total hydropathy values range between −11.2 and 22.9, the difference in solvent accessibility between 2.0 Å 2 and 373 Å 2 units and the difference in total number of residue neighbor contacts between 0 and 7 residues. Our work identifies for the first time heptapeptide and large sequences that correspond to a single complete helix, strand or coil, which adopt entirely different secondary structures in another protein.