Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure

Lakshmi, Balasubramanian and Sinduja, Chandrasekaran and Archunan, Govind and Srinivasan, Narayanaswamy (2014) Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure. In: PROTEIN SCIENCE, 23 (6). pp. 843-850.

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Abstract

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (phi, ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (phi, ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (phi, ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins.

Item Type:	Journal Article
Publication:	PROTEIN SCIENCE
Publisher:	WILEY-BLACKWELL
Additional Information:	Copyright for this article belongs to the WILEY-BLACKWELL, USA.
Keywords:	glycyl conformation; homologous proteins; Ramachandran map; steric hindrance
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	16 Jul 2014 09:04
Last Modified:	16 Jul 2014 09:04
URI:	http://eprints.iisc.ac.in/id/eprint/49429

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