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Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures

Narayanan, Eswar and Ramakrishnan, C (1999) Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures. In: Protein Engineering, 12 (6). pp. 447-455.

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Abstract

Backbone mimicry by the formation of closed-loop $C_7,C_{10}$ and $C_{13}$ (mimics of $\gamma-, \beta-$ and $\alpha$-turns) conformations through side chain–main chain hydrogen bonds by polar groups is a frequent observation in protein structures. A data set of 250 non-homologous and high-resolution protein crystal structures was used to analyze these conformations for their characteristic features. Seven out of the nine polar residues (Ser, Thr, Asn, Asp, Gln, Glu and His) have hydrogen bonding groups in their side chains which can participate in such mimicry and as many as 15% of all these polar residues engage in such conformations. The distributions of dihedral angles of these mimics indicate that only certain combinations of the dihedral angles involved aid the formation of these mimics. The observed examples were categorized into various classes based on these combinations, resulting in well defined motifs. Asn and Asp residues show a very high capability to perform such backbone secondary structural mimicry. The most highly mimicked backbone structure is of the$C_{10}$ conformation by the Asx residues. The mimics formed by His, Ser, Thr and Glx residues are also discussed. The role of such conformations in initiating the formation of regular secondary structures during the course of protein folding seems significant.

Item Type: Journal Article
Additional Information: copyright of this article belongs to Oxford University Press
Keywords: backbone mimicry;conformations;hydrogen bonds;polar residues
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 08 Oct 2007
Last Modified: 19 Sep 2010 04:40
URI: http://eprints.iisc.ernet.in/id/eprint/12087

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