Comparative Dynamics of NMDA- and AMPA-Glutamate Receptor N-Terminal Domains

Abstract

SummaryIonotropic glutamate receptors (iGluRs) harbor two extracellular domains: the membrane-proximal ligand-binding domain (LBD) and the distal N-terminal domain (NTD). These are involved in signal sensing: the LBD binds L-glutamate, which activates the receptor channel. Ligand binding to the NTD modulates channel function in the NMDA receptor subfamily of iGluRs, which has not been observed for the AMPAR subfamily to date. Structural data suggest that AMPAR NTDs are packed into tight dimers and have lost their signaling potential. Here, we assess NTD dynamics from both subfamilies, using a variety of computational tools. We describe the conformational motions that underly NMDAR NTD allosteric signaling. Unexpectedly, AMPAR NTDs are capable of undergoing similar dynamics; although dimerization imposes restrictions, the two subfamilies sample similar, interconvertible conformational subspaces. Finally, we solve the crystal structure of AMPAR GluA4 NTD, and combined with molecular dynamics simulations, we characterize regions pivotal for an as-yet-unexplored dynamic spectrum of AMPAR NTDs.

Conformational Transitions in the Glycine-Bound GluN1 NMDA Receptor LBD via Single-Molecule FRET

“…First, the resulting smFRET distribution for the NMDAR LBD correlates well to the derived energy landscape seen in simulation studies of the glycine-bound NMDAR LBD (38,49), which, along with another recent smFRET study (37), supports the conclusion that we are indeed monitoring LBD cleft conformational states. More importantly, we introduce a model-free step transition and state identification method (STaSI) to identify additional cleft states in the isolated LBD that are too wide to be observed in the full hetero-tetramer.…”

Amino-terminal Domain Tetramer Organization and Structural Effects of Zinc Binding in the N-Methyl-d-aspartate (NMDA) Receptor

“…4 and 5). These findings and recent computational studies suggest that the NTDs of both GluN1 (37) and GluN2B undergo lateral twisting motions (16,38) as well as cleft closure movements (16,37). Our data demonstrate that zinc induces a cleft closure motion in GluN2A, but further work will be needed to explore and measure any three-dimensional twisting motions of these domains and the role of any GluN1/2A interactions in allosteric modulation.…”

“…Propping the ATD cleft open using thiol-reactive crosslinking agents increases open channel probability, suggesting that zinc binding to the ATD, which reduces open channel probability, proceeds through a cleft closure mechanism (3). Furthermore, molecular dynamics simulations support the premise that the ATD of GluN2A can undergo a cleft closure-type conformational change (16). Taken together, these data provide indirect evidence that zinc inhibits the NMDA receptor by closing the bilobed ATD and allosterically influencing conformational equilibrium between closed and open states.…”

The N-terminal Domain Modulates α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) Receptor Desensitization

“…In fact, crystal structures of the Zn 2ϩ -bound and free NTD of the GluN2B subunit indicate that the NTD also favors a closed conformation in the absence of Zn differs from that in NMDA receptors, and a significant closure of the putative ligand-binding cleft in the AMPA receptor NTD is thought to be unlikely. AMPA receptor NTDs have, however, been shown to display flexibility (a prerequisite for an allosteric role), ranging from large-scale domain movements to more subtle conformational fluctuations (6,8,(53)(54)(55). A wide range of NTD conformations, some differing substantially from the arrangement in GluA2 cryst, have been reported on the basis of electron microscopic (16, 53, 56 -58) and atomic force microscopic (55) analyses of purified AMPA and kainate receptor preparations, supporting the view that the NTD can assume different conformations, at least under the specific experimental conditions used.…”