Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements

Abstract

The influence of flanking structures (alpha helices and beta strands in the primary sequence) on amino acid content of the elements of secondary structure has been analyzed in seven sets of nonhomologous proteins. Elevated usage of beta structural amino acid residues and pentapeptides in beta strands between two alpha helices can be explained by the stabilization of secondary structure of those beta strands by natural selection. High usage of alpha helical amino acids and pentapeptides in beta strands situated between two other beta strands is an evidence of the relaxation of natural selection: "passive" beta strands in these fragments of polypeptide chains are frequently formed due to the influence of flanking "active" beta strands. Alpha helices situated between alpha helix and beta strand are enriched by alpha helical pentapeptides and have lower usage of beta structural pentapeptides than those situated between beta strand and alpha helix, their N-termini are more frequently protected from helix to beta transitions by Glu residues. Alpha helices between two beta strands are stabilized by Ala residues and pentapeptides specific to alpha helices. Dipeptide content of the most stable alpha helices and beta strands was used for the creation of the PentaFOLD 2.0 algorithm (http://chemres.bsmu.by) that finds stable fragments of these elements of secondary structure in PDB files.

Keywords: Computer algorithm; Propensity scale; Protein; Secondary structure; Stability.