Influence of Solvent Molecules on the Stereochemical Code of Glycyl Residues in Proteins

Eswar, Narayanan and Nagarajaram, HA and Ramakrishnan, C and Srinivasan, N (2002) Influence of Solvent Molecules on the Stereochemical Code of Glycyl Residues in Proteins. In: Proteins: Structure, Function, and Genetics, 49 (3). pp. 326-334.

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Abstract

The Ramachandranstericmap and energy diagrams of the glycyl residue are symmetric. A plot of (\phi,\psi) angles of glycyl residues in 250 nonhomologous and high-resolution protein structures is also largely symmetric. However, there is a clear aberration in the symmetry. Although there is a cluster of points corresponding to the righthanded helical region, the "equivalent" cluster is clearly shifted to in and around the (\phi,\psi) values of $(90^o, 0^o)$ instead of being centered at the left-handed-helical region of $(60^o, 40^o)$. This lack of symmetry exists eveninthe (\phi,\psi) distributionof residues from non- \alpha -helical regions in proteins. Here we provide an explanation for this observation. An analysis of glycyl conformations in small peptide structures and in "coil" proteins, which are largely devoid of helical andsheet regions, shows that glycyl residues prefer to adopt conformations around $(\pm 90^o, 0^o)$ instead of right- and left-handed \alpha helical regions. By using theoretical calculations, such conformations are shown to have highest solvent accessibility in a system of two-linked peptide units with glycyl residue at the central $C^\alpha$ atom. This finding is consistent with the observations from 250 nonhomologous protein structures where glycyl residues with conformations close to $(\pm 90^o, 0^o)$ are seen to have high solvent accessibility. Analysis of a subset of nonhomologous structures with very high resolution (1.5 $\AA$ or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to $(\pm 90^o, 0^o)$. It is suggested that water molecules play a key role in determining and stabilizing these conformations of glycyl residues and explain the aberration in the symmetry of glycyl conformations inproteins.

Item Type: Journal Article The copyright belongs to Wiley-Liss, Inc. glycyl residues;protein structures;ramachandran map;solvation Division of Biological Sciences > Molecular Biophysics Unit 31 Dec 2007 19 Sep 2010 04:23 http://eprints.iisc.ernet.in/id/eprint/5599