Influence of solvent molecules on the stereochemical code of glycyl residues in proteins

Abstract

The Ramachandran steric map and energy diagrams of the glycyl residue are symmetric. A plot of (ϕ, ψ) 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 right-handed α-helical region, the "equivalent" cluster is clearly shifted to in and around the (ϕ, ψ) values of (90°, 0°) instead of being centered at the left-handed α-helical region of (60°, 40°). This lack of symmetry exists even in the (ϕ, ψ) distribution of residues from non-α-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 and sheet regions, shows that glycyl residues prefer to adopt conformations around (±90°, 0°) instead of right- and left-handed α-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^α atom. This finding is consistent with the observations from 250 nonhomologous protein structures where glycyl residues with conformations close to (±90°, 0°) are seen to have high solvent accessibility. Analysis of a subset of nonhomologous structures with very high resolution (1.5 Å or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to (±90°, 0°). 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 in proteins.