Agonist Binding Reshapes the Kinetic Landscape and Allosteric Communication of APLNR Toward Activation-Competent States

Abstract

APLNR is a therapeutically important G protein-coupled receptor (GPCR) implicated in cardiovascular and metabolic regulation; however, how agonist binding reorganizes receptor dynamics to promote signaling competence remains poorly understood. Here, we used the small-molecule agonist CMF-019 as a representative ligand and integrated Gaussian accelerated molecular dynamics (GaMD), Markov state models (MSMs), and neural relational inference (NRI) to characterize the conformational dynamics, kinetic organization, and allosteric communication of APLNR in apo and CMF-019-bound states. We found that CMF-019 binding altered structural flexibility in extracellular and intracellular regions while modifying collective motions within the transmembrane core, indicating a transition toward a more signaling-permissive dynamic state. MSM analyses further revealed that CMF-019 binding redistributed APLNR toward activation-related intermediate conformations and accelerated transitions among metastable states. Mechanistically, NRI uncovered extensive rewiring of the receptor communication network, in which CMF-019 binding strengthened transmembrane coupling and redirected signal propagation toward more convergent signaling routes linked to intracellular functional regions. Together, these findings suggest that CMF-019 promotes APLNR signaling competence through integrated kinetic and allosteric remodeling, revealing a dynamic mechanism by which an agonist can reorganize receptor communication prior to downstream coupling.