The macro- and microarchitectures of the ligand-binding domain of glutamate receptors

doi:10.1016/S0166-2236(97)01184-3

Trends in Neurosciences

Volume 21, Issue 3, 1 March 1998, Pages 117-125

https://doi.org/10.1016/S0166-2236(97)01184-3 Get rights and content

Abstract

Over the last decade, a large body of information regarding the amino acid sequences and tertiary structures of many proteins has accumulated. Subtle similarities in sequence patterns identified between glutamate receptors and bacterial periplasmic substrate-binding proteins have suggested that structural kinship exists between these protein families. Many of the bacterial periplasmic binding proteins but none of the glutamate receptors have been crystallized so far. The following article reviews how the resemblance between these two protein families led to computer-assisted structural models of crucial elements involved in ligand binding by various glutamate receptors. A plausible dynamic model of the molecular mechanism of activation and desensitization of glutamate-receptor channels is also discussed.

Section snippets

Primary structure similarities between GluRs and distantly related proteins

Detailed amino acid sequence comparisons followed by multiple alignments of mGluRs and iGluRs with various bacterial periplasmic binding proteins (PBPs) led Nakanishi et al.[31] and O'Hara et al.[32] to recognize that several regions of amino acid sequence similarities exist between these protein families. Thus, it was proposed that: (1) the first ∼ 400 amino acids of mGluRs and iGluRs share a common folding pattern with the bacterial periplasmic leucine/isoleucine/ valine-binding protein

Deciphering the transmembrane-subunit topology of iGluRs

Based on hydrophobicity plots, at the time they were cloned each subunit of an oligomeric iGluR was considered to weave through the cell membrane four times, thus adopting the transmembrane topology that is typical of acetylcholine-, glycine- and γ-aminobutyric acid (GABA)-gated channels[8]. Such a topological organization placed the amino terminal domain (ATD) and the carboxyl-terminus region of an iGluR subunit (see Fig. 1A for definitions) facing the extracellular space where they could be

The regions that create the Glu-binding domain

Further work by Heinemann and his colleagues shed light on the relevance of the novel topology to the Glu-binding domain by showing that both segments, S1 and S2 (that were first defined by these researchers), determine the pharmacological specificity of AMPA–KA receptor chimeras (iGluR3-iGluR6 chimeras)[49]. For example, whereas AMPA does not bind and elicit currents in Xenopus oocytes expressing iGluR6, the simultaneous replacement of S1 and S2 segments by those of iGluR3 resulted in a

The modelled structure of the ligand-binding site of iGluRs

Attracted by the idea that S1 and S2 might share a similar folding pattern with PBPs, several groups have undertaken to identify residues involved in ligand binding to iGluRs.

Efficient activation of the NMDA receptor channel requires co-assembly of NR1 and NR2 subunits as well as simultaneous binding of both Glu and the co-agonist glycine (Gly)[8]. Because NR1 has a glycine-binding motif, FXY, and amino acid sequence similarities with LAOBP, extensive site-directed mutagenesis followed by

Ionotropic GluRs are allosteric proteins

In the case of allosteric regulation, conformational changes cause coupling of two spatially separated regulatory (such as a ligand-binding site) and active (such as a channel pore) sites. Hence, iGluRs could be viewed as allosteric integral-membrane proteins. Moreover, the activation of iGluRs by various agonists, including activation of the NMDAR by Gly, produce sigmoid (that is, co-operative) dose-response curves that exhibit Hill coefficient values of 1.2–2.2 (depending on the agonist type

A plausible model for the allosteric transitions of iGluRs

(1) The model includes four interacting subunits each possessing a LAOBP-like binding domain for glutamatergic ligands. In cases of homomeric assembly of AMPA or KA receptors, the receptor oligomer would be composed of four subunits carrying identical ligand-binding domains. The NMDA receptor complex would consist of two NR2 Glu-binding subunits and two NR1 Gly-binding subunits.

(2) In the absence of effectors, the four ligand-binding domains would simultaneously undergo transitions between an

Experimental support for the existence of the various allosteric states

As in the case of nearly all signal transduction systems, a rapid turnoff is characteristic of ligand-gated ion channels. After a short period of activation (ion permeation) the liganded receptor undergoes desensitization, that is, exhibits a closed-channel conformation and transiently becomes refractory to re- activation. Mano et al.[56] described mutations that impaired the ability of Glu and Quis to desensitize iGluR1 channels and to inhibit the currents evoked by the weakly desensitizing

The f lip/f lop segment of AMPA receptors might couple movements of the ligand-binding lobes to channel regions

The flip/flop region located upstream from M4 of AMPA receptors belongs, in terms of the primary structure, to the S2 region (Fig. 1B). Structural models49, 54, 55, 83 (Fig. 3) reveal that the segment homologous to the flip/flop region of AMPA receptors comes after the second hinge region that crosses from lobe II back to lobe I. This segment is not located in the vicinity of the interlobe cleft but forms a long, kinked α helix at the back of the molecule while forming contacts with components

Antibodies that mimic the action of glutamatergic agonists

Rabbits immunized with the ATD of iGluR3 develop high titres of anti-iGluR3 antibodies and symptoms reminiscent of those that appear in patients with Rasmussen's encephalitis[86], a progressive, rare childhood disease characterized by severe epilepsy, hemiplegia, dementia and inflammation of the brain[87]. Serum sampled from individuals who have this progressive disease was found to immunoreact against denatured and native iGluR3, but not against iGluR1, 2, 5 and 6, suggesting that Rasmussen's

Perspectives

In the absence of X-ray crystallographic data, the available model structures and future models of other iGluR subunits would probably provide a practical target for drug design. The finding of novel binding ligands might not only validate the structural models, assist with the refinement of their co-ordinates and lead to a better understanding of how channel activity is coupled to extracellular domain movements, but might also result in revealing compounds that are able to modify the activity

Note added in proof

At the time the current review article was in press, Swanson et al.[83] published results that demonstrate the involvement of two amino acids in the specific responses of the KA receptors iGluR5 and iGluR6 to different agonists. These two residues align with KA-binding residues located in the putative lobe II of cKBP. As has been noted by Swanson et al., their results validate the cKBP model structure (Fig. 3) as a useful construct for modelling the structure of the ligand-binding domain of

Acknowledgements

I wish to thank Jean-Pierre Changeux for critically reading the manuscript, stimulating discussion and his unfailing support; Lisa Marubio, Anne Devillers-Thiéry and Stuart J. Edelstein for critical reading of the manuscript and Pierre-Jean Corringer, Clément Léna and Vivian I. Teichberg for their judicious advice. This work was supported by long-term fellowships from the Federation of European Biochemical Societies and the Human Frontier Science Program Organization.

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Trends in Neurosciences

The macro- and microarchitectures of the ligand-binding domain of glutamate receptors

Abstract

Section snippets

Primary structure similarities between GluRs and distantly related proteins

Deciphering the transmembrane-subunit topology of iGluRs

The regions that create the Glu-binding domain

The modelled structure of the ligand-binding site of iGluRs

Ionotropic GluRs are allosteric proteins

A plausible model for the allosteric transitions of iGluRs

Experimental support for the existence of the various allosteric states

The f lip/f lop segment of AMPA receptors might couple movements of the ligand-binding lobes to channel regions

Antibodies that mimic the action of glutamatergic agonists

Perspectives

Note added in proof

Acknowledgements

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