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

Matematičeskaâ biologiâ i bioinformatika, Tome 11 (2016) no. 2, pp. 159-169.

Résumé

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.

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