Role of cation–π interactions in single chain ‘all-alpha’ proteins

Abstract

Cation–π interactions are known to be important contributors to protein stability and ligand–protein interactions. In this study, we have analyzed the influence of cation–π interactions in single chain ‘all-alpha’ proteins. We observed 135 cation–π interactions in a data set of 75 proteins. No significant correlation was observed between the total number of amino acid residues and number of cation–π interactions. These interactions are mainly formed by long-range contacts and there is preference of Arg over Lys in these interactions. Arg–Phe interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp–cation interactions, was quite high. This information implies that the cation–π interactions involving Trp, maybe of high relevance to the proteins. Secondary structure analysis reveals that cation–π interactions are formed preferrably between residues, in which at least one of them, is in the secondary structure of alpha-helical segments. Among the various types of folds of ‘all-alpha’ proteins considered for the analysis, proteins belonging to alpha–alpha superhelix fold have the highest number of cation–π interaction forming residues.