Mechanism of Partial Agonism at NMDA Receptors for a Conformationally Restricted Glutamate Analog

Abstract

The NMDA ionotropic glutamate receptor is ubiquitous in mammalian central neurons. Because partial agonists bind to the same site as glutamate but induce less channel activation, these compounds provide an opportunity to probe the mechanism of activation of NMDAtype glutamate receptors. Molecular dynamics simulations and site-directed mutagenesis demonstrate that the partial agonist homoquinolinate interacts differently with binding pocket residues than glutamate. Homoquinolinate and glutamate induce distinct changes in the binding pocket, and the binding pocket exhibits significantly more motion with homoquinolinate bound than with glutamate. Patch-clamp recording demonstrates that single-channel activity induced by glutamate or by homoquinolinate has identical singlechannel current amplitude and mean open-channel duration but that homoquinolinate slows activation of channel opening relative to glutamate. We hypothesize that agonist-induced conformational changes in the binding pocket control the efficacy of a subunit-specific activation step that precedes the concerted global change in the receptor-channel complex associated with ion channel opening.

Disruption of Interdomain Interactions in the Glutamate Binding Pocket Affects Differentially Agonist Affinity and Efficacy of N-methyl-d-aspartate Receptor Activation

“…In contrast, the likelihood of reopening would be determined by the network of interactions between D1 and D2. In agreement with this model, partial agonists of either NR1 or NR2 have been reported to shift components of single channel shut time (35,37) but not open time histograms (i.e. to cause slower channel opening), whereas, complementarily, we find that a mutation, N668D, at the D1D2 interface of NR2A has no effect on channel opening but dramatically slows channel closing.…”

Zinc reverses glycine-dependent inactivation of NMDARs in cultured rat hippocampal neurons

“…The molecular determinants of high affinity zinc binding have been demonstrated to lie in the amino terminal domain of the NR2A subunit [24]. Studies of Gielen et al [25] and Erreger et al [26] suggest an allosteric interaction between Zn 2+ and glutamate binding domains on NR2A. In other words, the affinity of zinc for its binding site is regulated by glutamate binding, thus causing desensitization or allosteric inhibition of NMDARs.…”

Glutamate Receptor Ion Channels: Structure, Regulation, and Function

“…Because Tyr535 is complexed at the protomer interface in a manner analogous to that of aniracetam, it may similarly modulate deactivation of NMDA receptors, assuming the two receptors share similar mechanisms underlying deactivation . The time course of deactivation of virtually all GluN1/GluN2 receptors can be described by multiple exponential components, which for GluN2A may reflect complex channel behavior (e.g., Erreger et al, 2005b;Zhang et al, 2008b). Heterologously expressed recombinant kainate receptors, like AMPA receptors, can show relatively fast gating kinetics and strong desensitization (Table 16).…”

“…Such studies have provided hints about permissible intraprotein motions within the LBD during the cleft closure transition as well as interactions at the domain interface (Arinaminpathy et al, 2002;Kaye et al, 2006;Lau and Roux, 2007;Dravid et al, 2010). MD simulations can provide estimates of the stability of the ligand-protein interactions in the binding pocket, adding further detail to our understanding of ligand selectivity and efficacy (Mendieta et al, 2001(Mendieta et al, , 2005Erreger et al, 2005b;Kaye et al, 2006;Pentikä inen et al, 2006;Erreger et al, 2007). Additional experimental techniques that can test predictions obtained from MD simulations or crystal structures include NMR, ultraviolet or infrared spectroscopy, and fluorescence resonance energy transfer Oswald, 2002, 2004;Cheng et al, 2005;Du et al, 2005;Madden et al, 2005;Valentine and Palmer, 2005).…”