Identifying the multiple binding sites between arrestin-3 and JNK3

Abstract

Arrestin is a small family of multi-functional adaptor proteins. In additional to its colonial function as negative regulators to hundreds of G protein-coupled Receptors (GPCRs), arrestins also mediate a complex second wave G protein-independent signaling network by recruiting several kinases to construct signaling cascades, but the major interaction sites of this process remain largely unknown. In this study, several computational methods are employed in an attempt to accurately predict major interaction sites between arrestin-3 and one of its binding partners, c-Jun N-terminal Kinase 3 (JNK-3). These methods utilize the Protein Frustratometer to survey the energy landscape of the protein in question to identify residues that exist in a high energy conformation, as well as the Evolutionary Trace method to identify residues that are highly conserved down the phylogenetic tree, signifying evolutionary importance. Crystal structures of both proteins are subsequently submitted to ClusPro in order to sample possible docked conformations of the two structures. Our gathered data suggests that JNK-3 favors binding on its kinase domain, with seventy-four to eighty-two percent of all docked conformations depicting binding in this location, as well as having minor sites of interaction located on the C-terminal. Arrestin-3 is shown to favor binding on a hydrophobic proline hinge region located near the N-terminal, with thirty-nine to fifty-eight percent of all docked conformations depicting binding in this area. The methods developed here can be employed to predict the binding interfaces between arrestins and other partners.