title: Role of cation-pi interactions in single chain 'all-alpha' proteins.
abstract: Cation-pi interactions are known to be important contributors to protein stability and ligand-protein interactions. In this study, we have analyzed the influence of cation-pi interactions in single chain 'all-alpha' proteins. We observed 135 cation-pi 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-pi 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-pi interactions involving Trp, maybe of high relevance to the proteins. Secondary structure analysis reveals that cation-pi interactions are formed preferably 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-pi interaction forming residues.
authors: Centre for Laser Spectroscopy, Manipal Life Sciences Centre, Manipal University, Manipal 576104, India.
authors: Remila L
authors: RL
authors: Martis
authors: Sameer Kumar
authors: SK
authors: Singh
authors: M Michael
authors: MM
authors: Gromiha
authors: C
authors: C
authors: Santhosh
mesh_terms: D000818:Animals; D002412:Cations / Q000378:metabolism; D019295:Computational Biology; D030562:Databases, Protein; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D055672:Static Electricity; D014364:Tryptophan / Q000378:metabolism
chemical_list: D002412:Cations; D014364:Tryptophan