State-Dependent Dynamic Communication Networks in a Pentameric Ligand-Gated Ion Channel

Pentameric ligand-gated ion channels control synaptic neurotransmission via an allosteric mechanism, whereby agonist binding induces global protein conformational changes that open an ion-conducting pore. For the proton-activated bacterial (Gloeobacter) ligand-gated ion channel (GLIC), high-resolution structures are available in multiple conformational states. We used a library of atomistic molecular dynamics (MD) simulations to study conformational changes and to perform dynamic network analysis to elucidate the communication pathways underlying the gating process. We describe state- and pH-dependent communication between the agonist-binding extracellular domain (ECD) and the ion-conducting transmembrane domain (TMD), revealing variation in pathways associated with conformational changes. We identify five main signal pathway families that connect the TMD and ECD via intra- and intersubunit communication. These pathway families implicate the Cys loop, the β1-β2 loop, and loop F in the ECD, along with the pre-M1 covalent connection and the M2-M3 loop in the TMD, each of which has previously been suggested to be important for gating. The β1-β2 loop and loop F pathway families exhibit stark dependence on the functional state, in contrast to the more constant Cys-loop and pre-M1 pathway families, suggesting that the channel may communicate differently during its transitions between open, closed, and intermediate states of its activity cycle. We interpret the state dependence in terms of the conformational changes that affect ECD-TMD alignment and, in particular, the breakage of the D32-R192 salt bridge, which is crucial in regulating the communication pathway. These communication networks are expected to be conserved within the superfamily of pentameric ligand-gated channels, with potential applications in improved anesthetics, neuromodulatory drugs, antiparasitics, and pesticides.