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Bioinformatics
Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins
E. V. Brazhnikov,
A. M. Kargatov,
A. V. Efimov Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moskovskaya obl.
Abstract:
Conformations of about 600 looped regions (loops) in
$\beta-\alpha$- and
$\alpha-\beta$-arches of a structural motif occurring in the abCd-unit of proteins were analyzed. On the whole, 258 abCd-units with a reverse turn of the polypeptide chain (236 PDB files) and 69 abCd-units with a direct turn (65 PDB files) were selected in non-homologous proteins. Four types of arches were studied:
$\beta-\alpha$- and
$\alpha-\beta$-ones at a direct turn of the chain;
$\beta-\alpha$- and
$\alpha-\beta$-ones at a reverse turn of the chain. For each type of arches, frequencies of loops occurrence of different lengths were determined and corresponding histograms were plotted. It was found that abCd-units with loops up to three amino acid residues long occur most frequently (57%). In
$\beta-\alpha$-arches with a direct turn of the chain, loops consisting of two amino acid residues occur most often (44%) and in 86% cases they have the
$\beta_m\alpha\beta\alpha_n$-conformation. They have no Gly and Pro residues, and in position
$\beta$ there is an Asn residue. In such type of arches, the loops of one residue (
$\beta_m\varepsilon\alpha_n$- or
$\beta_m\alpha_L\alpha_n$-conformation) contain the Gly residue most frequently.
$\alpha-\beta$-Arches with a direct turn of the chain have most commonly (18%) loops of four amino acid residues. In this case, there is no predominant conformation of the loops. In
$\beta-\alpha$-arches with a reverse turn of the chain, most common are loops of seven amino acid residues (17%), and most part of them (88%) have the $\beta_m\alpha_L\beta\beta\alpha\alpha\beta\beta\alpha_n$-conformation.
$\alpha-\beta$-Arches with a reverse turn of the chain contain most frequently (32%) loops of one amino acid residue (all Gly ones) with arch conformations
$\alpha_m\varepsilon\beta_n$ or
$\alpha_n\alpha_L\beta_n$. The above structural analysis of the abCd-unit has useful information for prediction of the three-dimensional structure of proteins and for molecular simulation of the
de novo design of protein structures.
Key words:
protein structure, conformational analysis, $\beta-\alpha$- and $\alpha-\beta$-arches, abCd-unit, glycine, proline. Received 06.06.2016,
Published 18.07.2016
DOI:
10.17537/2016.11.159