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Nature of Cation–π Interactions and Their Role in Structural Stability of Immunoglobulin Proteins

I. A. Tayubi and R. Sethumadhavan*

Bioinformatics Division, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India; fax: 0416-224-3092; E-mail: rsethumadhavan@vit.ac.in; sethurao_2005@yahoo.com; iftikharaslamtayubi@vit.ac.in

* To whom correspondence should be addressed.

Received December 8, 2009; Revision received February 8, 2010
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 immunoglobulin proteins. We observed 87 cation–π interactions in a data set of 33 proteins. These interactions are mainly formed by long-range contacts, and there is preference of Arg over Lys in these interactions. Arg–Tyr interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp–cation interactions is quite high. This information suggests that the cation–π interactions involving Trp might be of high relevance to the proteins. Secondary structure analysis reveals that cation–π interactions are formed preferably between residues in which at least one is in β-strand. Proteins having β-strand regions have the highest number of cation–π interaction-forming residues.
KEY WORDS: cation–π, secondary structure, long-range interactions, accessible surface area, stabilization centers, immunoglobulin proteins, structural stability

DOI: 10.1134/S000629791007014X