Residue Interaction Network Reveals Allosteric Pathways Linking Orthosteric and Intracellular Sites in Class A GPCRs

Abstract

Understanding how allosteric modulators influence protein dynamics is essential for guiding drug design. This work analyses a total of 45 μs of classical molecular dynamics simulations for four class A G-protein-coupled receptors (GPCRs), namely the Complement C5a receptor (C5AR1), the Purinergic Receptor P2Y (P2RY1), and the Cannabinoid Receptors 1 and 2 (CNR1/CNR2). Protein dynamics is essential to detect the shallow extrahelical binding sites, such as the one found in P2RY1. Current methods for computing Allosteric Communication Networks (ACNs) produce complex outputs requiring expert interpretation. To address this, we focus on the shortest paths of information transfer between the orthosteric and G-protein binding sites in Class A GPCRs. Our retrospective analysis reveals state- and bias ligand-dependent residue interactions along these communication pathways. Furthermore, focusing on the predicted binding site of allosteric modulator EC21a at cannabinoid receptors, the ACN framework was used to prioritize two residues for mutational analysis that may contribute to allosteric communication.