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Volume 11   Issue 2   Year 2016
Structure of Looped Regions in β-α- and α-β-Arches in Abcd-Units of Globular Proteins

Brazhnikov E.V., Kargatov A.M., Efimov A.V.

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region

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 αmαLβn. 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, α-β- and β-α-arches, abCd-unit, glycine, proline.

Table of Contents Original Article
Math. Biol. Bioinf.
2016;11(2):159-169
doi: 10.17537/2016.11.159
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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