String method solution of the gating pathways for a pentameric ligand-gated ion channel

Significance

High-resolution structures of pentameric ligand-gated ion channels have created an opportunity to discover the mechanisms of rapid synaptic transduction in the brain. This study describes the mechanisms of allosteric channel gating using string method simulations, applied to a complete atomistic ion channel, combined with a transition analysis approach to extract free-energy surfaces from swarms of trajectories. We reproduce pH-modulated activity of the channel, identify the molecular interactions associated with interdomain communication, and quantify the energetics of the gating process. These results provide general mechanistic understanding of the function of pentameric ligand-gated channels, with potential applications in the design of improved anesthetics, neuromodulatory drugs, antiparasitics, and pesticides.

Abstract

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.