Abstract:
Conformations of about 600 looped regions (loops) in β−α- and α−β-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: β−α- and α−β-ones at a direct turn of the chain; β−α- and α−β-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 β−α-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 βmαβαn-conformation. They have no Gly and Pro residues, and in position β there is an Asn residue. In such type of arches, the loops of one residue (βmεαn- or βmαLαn-conformation) contain the Gly residue most frequently. α−β-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 β−α-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 βmαLββααββαn-conformation. α−β-Arches with a reverse turn of the chain contain most frequently (32%) loops of one amino acid residue (all Gly ones) with arch conformations αmεβn or αnαLβn. 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, β−α- and α−β-arches, abCd-unit, glycine, proline.
Citation:
E. V. Brazhnikov, A. M. Kargatov, A. V. Efimov, “Structure of looped regions in β−α- and α−β-arches in abcd-units of globular proteins”, Mat. Biolog. Bioinform., 11:2 (2016), 159–169
\Bibitem{BraKarEfi16}
\by E.~V.~Brazhnikov, A.~M.~Kargatov, A.~V.~Efimov
\paper Structure of looped regions in $\beta-\alpha$- and $\alpha-\beta$-arches in abcd-units of globular proteins
\jour Mat. Biolog. Bioinform.
\yr 2016
\vol 11
\issue 2
\pages 159--169
\mathnet{http://mi.mathnet.ru/mbb260}
\crossref{https://doi.org/10.17537/2016.11.159}
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This publication is cited in the following 1 articles:
E. V. Brazhnikov, A. V. Efimov, “Structure and features of amino acid sequences of Π-modules in OB-folds”, Mat. Biolog. Bioinform., 17:2 (2022), 441–451