Mapping mouse IL‐13 binding regions using structure modeling, molecular docking, and high‐density peptide microarray analysis

Abstract Interleukin‐13 is a Th2‐associated cytokine responsible for many pathological responses in allergic asthma including mucus production, inflammation, and extracellular matrix remodeling. In addition, IL‐13 is required for immunity to many helminth infections. IL‐13 signals via the type‐II IL‐4 receptor, a heterodimeric receptor of IL‐13Rα1 and IL‐4Rα, which is also used by IL‐4. IL‐13 also binds to IL‐13Rα2, but with much higher affinity than the type‐II IL‐4 receptor. Binding of IL‐13 to IL‐13Rα2 has been shown to attenuate IL‐13 signaling through the type‐II IL‐4 receptor. However, molecular determinants that dictate the specificity and affinity of mouse IL‐13 for the different receptors are largely unknown. Here, we used high‐density overlapping peptide arrays, structural modeling, and molecular docking methods to map IL‐13 binding sequences on its receptors. Predicted binding sequences on mouse IL‐13Rα1 and IL‐13Rα2 were in agreement with the reported human IL‐13 receptor complex structures and site‐directed mutational analysis. Novel structural differences were identified between IL‐13 receptors, particularly at the IL‐13 binding interface. Notably, additional binding sites were observed for IL‐13 on IL‐13Rα2. In addition, the identification of peptide sequences that are unique to IL‐13Rα1 allowed us to generate a monoclonal antibody that selectively binds IL‐13Rα1. Thus, high‐density peptide arrays combined with molecular docking studies provide a novel, rapid, and reliable method to map cytokine‐receptor interactions that may be used to generate signaling and decoy receptor‐specific antagonists. Proteins 2010. © 2010 Wiley‐Liss, Inc.