Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein coupling.

Abstract

Biological receptors respond to environmental changes through allosteric regulation. In G-protein coupled receptors (GPCRs), the binding of ligands establishes chemical and dynamic communication networks resulting in key structural changes of a transmembrane helix that promotes the coupling and activation of G-proteins. The activation pathways and allosteric mechanisms of GPCRs present system-specific profiles among subtypes. Hence, the development of novel allosteric drugs clearly benefits from a complete characterization of the structural dynamics of the target receptor. In this work, we focus on the adenosine A1 receptor (A1R), for which regardless the progress made in understanding its allosteric modulation though experimental and computational studies, essential knowledge of the allosteric mechanism and communication networks that activates the receptor remains unknown. In particular, we have developed a computational strategy that combines molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection in order to decipher the interplay between the activation pathway of A1R, the allosteric networks and the transient pockets. Our simulations reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers together with the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of the transient pockets detected and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. This complete dynamic picture provides essential information to ease the design of efficient allosteric modulators for A1R. Our computational workflow can be also applied to other GPCRs and related receptors.