Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Vasudev, Prema G and Banerjee, Mousumi and Ramakrishnan, C and Balaram, P (2012) Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins. In: Proteins: Structure, Function, and Genetics, 80 (4). pp. 991-1002.

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Abstract

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

Item Type:	Journal Article
Publication:	Proteins: Structure, Function, and Genetics
Publisher:	John Wiley and Sons
Additional Information:	Copyright of this article belongs to John Wiley and Sons.
Keywords:	side chain-backbone hydrogen bonds;neutral polar residues; asparagine residue;glutamine residue;protein structures
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	13 Apr 2012 10:45
Last Modified:	13 Apr 2012 10:45
URI:	http://eprints.iisc.ac.in/id/eprint/44245

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