The nature of the turn in omega loops of proteins

Abstract

An analysis of Omega loops in a nonredundant set of protein structures from the Protein Data Bank has been carried out to determine the nature of the "turn elements" present. Because Omega loops essentially reverse their direction in three-dimensional space, this analysis was made with respect to four turn elements identified as (1) Gly; (2) Pro; (3) a residue with alpha-helical phi,psi angles, termed a helical residue; and (4) a cis peptide. A set of 1079 Omega loops from a set of 680 proteins were used for the analysis. Apart from other criteria that define Omega loops, the selection of an Omega loop from a cluster of loops is based on an exposure index. In this study, analyses have been made with two sets of data: (1) Omega loops arising from a minimum exposure index indicative of a less exposed loop (xmin set) and (2) Omega loops with a maximum exposure index indicative of a relatively exposed loop (xmax set). Overall residue preferences and positional preferences have been examined. Positions of the turn elements for Omega loops of varying length have also been studied. Specific positional preferences are observed for particular turn elements with regard to the length of Omega loops. Analysis in terms of the turn elements can provide guidelines for modeling of loops in proteins. Apart from Pro, which has the natural tendency to form cis peptide bonds, a higher occurrence of non-Pro cis peptide bonds is observed. Torsion angles in Omega loops also indicate the occurrence of a large number of residues with helical phi,psi angles, necessary for the turn in the loop structures.