Ionotropic glutamate receptors (iGluRs) are ion channels activated by the neurotransmitter glutamate and are essential to learning and memory formation. Despite intense structural and functional studies, significant gaps in knowledge remain about how agonist binding leads to channel activation. I will present our work in characterizing conformational states along the gating pathway. iGluR subunits have a highly modular architecture, in which the ligand-binding domain and the transmembrane domain are well separated and connected by flexible linkers. The ligand-binding domain in turn is composed of two lobes. Our molecular dynamics simulations illustrated that closure of the lower lobe, induced by agonist binding, forces the outward pulling of a linker tethered to the extracellular terminus of the major pore-lining helix of the transmembrane domain, thereby opening the channel. A critical test of these putative gating motions was made through introducing glycine insertions in the linker. Molecular dynamics simulations showed that, with lengthening by glycine insertions, the linker became less effective in pulling the pore-lining helix, leading to weaker stabilization of the channel-open state. In full agreement, single-channel recordings showed that the channel open probability decreased progressively as the linker was lengthened by glycine insertions. Crystal structures of ligand-binding domains showing different degrees of cleft closure between full and partial agonists suggested a simple mechanism for AMPA receptors, but mysteries surrounded NMDA receptors, where the ligand-binding domains open to similar degrees when bound with either full or partial agonists. Our free energy simulations suggest that broadening of the free energy basin for cleft closure is a plausible solution. Based on close integration between computation and electrophysiology, we propose conformations of kinetic states along the gating pathway and mechanisms of disease-associated mutations.

Conformational states along the gating pathway of ionotropic glutamate receptors: computation meets electrophysiology

2019 Spring National Meeting

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