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

Abstract

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 trans-synaptic 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 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.

Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels

“…Finally, the GluD1 and GluD2 receptors encoded by GRID1 and GRID2 do not mediate a conventional ligand-gated current response (Araki et al, 1993;Lomeli et al, 1993). Although GluD2 harbors a D-serine binding site, and the occupancy of this site can close the bilobed ABD clamshell (Naur et al, 2007;Tapken et al, 2017;Chin et al, 2020), D-serine does not open the ion channel in GluD1 or GluD2 receptors expressed in heterologous systems. However, transplantation of the ABD of kainate and AMPA receptors onto GluD2 (Schmid et al, 2009) or removal of a disulfide bond in the GluD2 ABD (Hansen et al, 2009) enables opening the ion channel in response to agonist binding, demonstrating that the gating machinery and pore within GluD2 is intact (Yuzaki and Aricescu, 2017;Gantz et al, 2020).…”

“…Receptor Activation, Deactivation, and Desensitization). Molecular dynamics simulations show that the free energy associated with D-serine binding to the GluD2 ABD is greater than that for other iGluR ABDs, suggesting that conformational rearrangements, such as desensitization, may occur in response to agonist binding to GluD2 and preclude channel gating (Chin et al, 2020), potentially explaining the lack of ion channel activity. Besides D-serine and glycine, b-fluoro-DL-alanine, L-and D-alanine, Dcysteine, and L-aspartate reduced responses at spontaneously active GluD2-A654T receptors by more than 25% (Naur et al, 2007;Kristensen et al, 2016a).…”

“…Isolated GluD2 ABDs in the apo form crystallize as homodimers in the presence of Ca 21 ions, which bind to and stabilize the ABD dimer interface (Naur et al, 2007;Chaudhry et al, 2009a;Hansen et al, 2009). GluD2 receptors may "predesensitize" in response to agonist binding, thereby precluding a current response, in part due to weak ABD dimer interactions (Chaudhry et al, 2009a;Hansen et al, 2009), but see Tapken et al (2017) and Chin et al (2020). Binding of Ca 21 to GluD2 cannot stabilize the ABD dimer interface enough to prevent this "predesensitization," but extracellular Ca 21 ions can potentiate spontaneously activated currents mediated by GluD2 receptors carrying the lurcher mutation GluD2-A654T (Wollmuth et al, 2000;Hansen et al, 2009).…”

Excitatory and inhibitory D-serine binding to the NMDA receptor

“…Blocks for which the window is not sampled were omitted from the error calculation; this was only necessary for high glycan distances >20 Å. A 1D projection of the (𝜉 " , 𝜉 # ) order parameter, 𝜉 "# , which averages 𝜉 " and 𝜉 # , was used as a single measure of LBD closure for computing glycan PMFs [16][54] [55]. Umbrella sampling molecular dynamics simulations were used to compute the potential of mean force (PMF) along the (𝜉 $ , 𝜉 % ) order parameter for (A) D-serine bound to GluN2A, (B) glycine bound to GluN2A, (C) apo GluN2A previously computed in [16], (D) glutamate bound to GluN2A in its crystallographic pose previously computed in [16], (E) glutamate bound to GluN2A in the inverted pose identified in [18], (F) D-serine bound to GluN1, (G) glycine bound to GluN1 previously computed in [16], (H) apo GluN1 previously computed in [16].…”

“…Blocks for which the window is not sampled were omitted from the error calculation; this was only necessary for high glycan distances >20 Å. A 1D projection of the (𝜉 " , 𝜉 # ) order parameter, 𝜉 "# , which averages 𝜉 " and 𝜉 # , was used as a single measure of LBD closure for computing glycan PMFs [16][54] [55]. 44 obtained by computing the minimum distance between all glycan heavy atoms and D2 lobe residues and binning the distribution from all glycosylated simulation systems.…”