D-Serine Potently Drives Ligand-Binding Domain Closure in the Ionotropic Glutamate Receptor GluD2

Structure. 2020 Oct 6;28(10):1168-1178.e2. doi: 10.1016/j.str.2020.07.005. Epub 2020 Jul 30.


Despite their classification as ionotropic glutamate receptors, GluD receptors are not functional ligand-gated ion channels and do not bind glutamate. GluD2 receptors bind D-serine and coordinate transsynaptic complexes that regulate synaptic plasticity. Instead of opening the ion channel pore, mechanical tension produced from closure of GluD2 ligand-binding domains (LBDs) drives conformational rearrangements for non-ionotropic signaling. We report computed conformational free energy landscapes for the GluD2 LBD in apo and D-serine-bound states. Unexpectedly, the conformational free energy associated with GluD2 LBD closure upon D-serine binding is greater than that for AMPA, NMDA, and kainate receptor LBDs upon agonist binding. This excludes insufficient force generation as an explanation for lack of ion channel activity in GluD2 receptors and suggests that non-ionotropic conformational rearrangements do more work than pore opening. We also report free energy landscapes for GluD2 LBD harboring a neurodegenerative mutation and demonstrate selective stabilization of closed conformations in the apo state.

Keywords: GRID2 gene; delta receptor; free energy calculations; glutamate receptors; ligand-gated receptors; molecular dynamics simulations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Ligands
  • Molecular Dynamics Simulation
  • Mutation
  • Protein Domains
  • Receptors, Glutamate / chemistry*
  • Receptors, Glutamate / genetics
  • Receptors, Glutamate / metabolism*
  • Serine / chemistry
  • Serine / metabolism*
  • Thermodynamics


  • Ligands
  • Receptors, Glutamate
  • glutamate receptor delta 2
  • Serine