Structural Insights Into NMDA Ionotropic Glutamate Receptors via Molecular Modelling

Chohan, Kamaldeep K.; Wo, Z.Galen; Oswald, Robert E.; Sutcliffe, Michael J.

doi:10.1007/pl00010721

Cited by 8 publications

(5 citation statements)

References 42 publications

(63 reference statements)

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“…Furthermore Paas et al (1996) found that the analogous mutation in a chick kainate‐binding protein (T268A) abolished detectable binding of kainate (though of course reduction of macroscopic binding does not constitute evidence for a change in the binding site; Colquhoun, 1998). The structure of the NMDA receptor has not been determined, but theoretical molecular modelling studies of the NR2C subunit by Chohan et al (2000) give particular importance to T671 in determination of agonist binding specificity (T671 in NR2A corresponds to T691 in their paper). This residue is proposed to form a hydrogen bond with glutamate, when it occupies its binding site.…”

Section: Discussionmentioning

confidence: 99%

Single‐channel analysis of an NMDA receptor possessing a mutation in the region of the glutamate binding site

Anson

Schoepfer

Colquhoun

et al. 2000

The Journal of Physiology

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Recombinant NR1a/NR2A(T671A) N‐methyl‐D‐aspartate (NMDA) receptor‐channels, which carry a point mutation in the putative glutamate binding site that reduces glutamate potency by around 1000‐fold, have been expressed in Xenopus laevis oocytes and their single‐channel properties examined using patch‐clamp recording techniques. Shut time distributions of channel activity were fitted with a mixture of five exponential components. The first three components in each distribution were considered to occur within a channel activation as they exhibited little or no dependence on agonist concentration. Bursts of single‐channel openings were defined by a critical gap length with a mean of 5.65 ± 0.37 ms. Shut intervals with a duration longer than this value were considered to occur between separate bursts of channel openings. Distributions of the lengths of bursts of openings were fitted with a mixture of four exponential components. The longest two components carried the majority of the charge transfer in the channel recordings and had means of 7.71 ± 1.1 and 37.7 ± 4.3 ms. The overall probability of a channel being open during a burst was high (mean 0.92 ± 0.01). Brief concentration jumps (1 ms) of 10 mm glutamate were applied to outside‐out patches so that a comparison between the macroscopic current relaxation and steady‐state single‐channel activity evoked by glutamate could be made. The decay of such macroscopic currents was fitted with a single exponential component with a mean of 32.0 ± 3.53 ms. The good agreement between macroscopic current decay following brief agonist exposure and the value for the slowest component of the burst length distribution suggests that the bursts of openings that we identified in steady‐state recordings represent individual activations of recombinant NR1a/NR2A(T671A) NMDA receptor‐channels. A new way of displaying geometric distributions is suggested, and the utility of a modified definition of the ‘probability of being open within a burst’ is discussed. The single‐channel data that we present in this paper support further the idea that the point mutation T671A in the NR2A NMDA receptor subunit affects mainly the ability of glutamate to remain bound to these channels.

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Section: Discussionmentioning

confidence: 99%

Single‐channel analysis of an NMDA receptor possessing a mutation in the region of the glutamate binding site

Anson

Schoepfer

Colquhoun

et al. 2000

The Journal of Physiology

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“…The crystal structures of the GluR2‐ or NR1‐binding pockets have served as templates for a number of homology models of the NR2‐glutamate‐binding site ( Chohan et al ., 2000 ; Tikhonova et al ., 2002 ; Blaise et al ., 2004 ; Laube et al ., 2004 ; Chen et al ., 2005 ; Kinarsky et al ., 2005 ; Hansen et al ., 2005 ). The NR2‐glutamate pocket shares similar features to the GluR2‐ and NR1‐binding pockets, although there are slight differences in loop and helical structure, the general pharmacophoric pattern formed by these residues is conserved among the ionotropic glutamate receptor family.…”

Section: Full and Partial Agonist Modelling In The Nr2 Nmda Receptor mentioning

confidence: 99%

Pharmacological insights obtained from structure–function studies of ionotropic glutamate receptors

Chen

Wyllie

2006

British J Pharmacology

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Ionotropic glutamate receptors mediate the vast majority of fast excitatory synaptic transmission in the CNS. Elucidating the structure of these proteins is central to understanding their overall function and in the last few years a tremendous amount of knowledge has been gained from the crystal structures of the ligand-binding domains of the receptor protein. These efforts have enabled us to unravel the possible mechanisms of partial agonism, agonist selectivity and desensitization. This review summarizes recent data obtained from structural studies of the binding pockets of the GluR2, GluR5/6, NR1 and NR2A subunits and discusses these studies together with homology modelling and molecular dynamics simulations that have suggested possible binding modes for full and partial agonists as well as antagonists within the binding pocket of various ionotropic glutamate receptor subunits. Comparison of the ligand-binding pockets suggests that the ligand-binding mechanisms may be conserved throughout the glutamate receptor family, although agonist selectivity may be explained by a number of features inherent to the AMPA, kainate and NMDA receptor-binding pockets such as steric occlusion, cavity size and the contribution of water-bridged interactions.

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“…X-ray diffraction studies have described the glycine binding domain of the NR1 subunit (Furukawa and Gouaux, 2003), but no equivalent structural data for any NR2 subunit exists, although some insight has been obtained from modeling studies (Chohan et al, 2000;Tikhonova et al, 2002;Laube et al, 2004). However, it is possible to make certain predictions about the nature of the contact residues in the NR2A NMDA receptor subunit with reference to studies of the AMPA receptor GluR2 S1S2 fragment (Armstrong et al, 1998;Armstrong and Gouaux, 2000).…”

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confidence: 99%

Structural Features of the Glutamate Binding Site in Recombinant NR1/NR2AN-Methyl-d-aspartate Receptors Determined by Site-Directed Mutagenesis and Molecular Modeling

Chen

Geballe²,

Stansfeld³

et al. 2005

Mol Pharmacol

143

133

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We have used site-directed mutagenesis of amino acids located within the S1 and S2 ligand binding domains of the NR2A N-methyl-D-aspartate (NMDA) receptor subunit to explore the nature of ligand binding. Wild-type or mutated NR1/NR2A NMDA receptors were expressed in Xenopus laevis oocytes and studied using two electrode voltage clamp. We investigated the effects of mutations in the S1 and S2 regions on the potencies of the agonists L-glutamate, L-aspartate, (R,S)-tetrazol-5yl-glycine, and NMDA. Mutation of each of the corresponding residues found in the NR2A receptor subunit, suggested to be contact residues in the GluR2 ␣-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit, caused a rightward shift in the concentration-response curve for each agonist examined. None of the mutations examined altered the efficacy of glutamate as assessed by methanethiosulfonate ethylammonium potentiation of agonist-evoked currents. In addition, none of the mutations altered the potency of glycine. Homology modeling and molecular dynamics were used to evaluate molecular details of ligand binding of both wild-type and mutant receptors, as well as to explore potential explanations for agonist selectivity between glutamate receptor subtypes. The modeling studies support our interpretation of the mutagenesis data and indicate a similar binding strategy for L-glutamate and NMDA when they occupy the binding site in NMDA receptors, as has been proposed for glutamate binding to the GluR2 AMPA receptor subunit. Furthermore, we offer an explanation as to why "charge conserving" mutations of two residues in the binding pocket result in nonfunctional receptor channels and suggest a contributing molecular determinant for why NMDA is not an agonist at AMPA receptors.The NMDA receptor channel is thought to be formed from the coassembly of two NR1 subunits and two NR2 subunits in a dimer of dimers configuration (Schorge and Colquhoun, 2003). NMDA receptors are unique among ligand-gated ion channels in that the binding of two different ligands is required for the activation of the receptor channel complex. Glycine, a coagonist, binds to residues located in the NR1 subunits, whereas glutamate binds to residues located in NR2 subunits (for review, see Erreger et al., 2004) of which there are four types (termed NR2A-D or ⑀ 1-4) and which are the major determinants of the pharmacological and biophysical properties of these receptors (Monyer et al., 1992(Monyer et al., , 1994Vicini et al., 1998;Wyllie et al., 1998). Ionotropic glutamate receptor subunits are comprised of distinct functional regions-an amino terminal domain, a ligand binding domain, a membrane-associated region, and an intracellular carboxyl-terminal domain (Fig. 1A). The ligand binding domain is thought to form a hinged clamshell-like structure (Armstrong et al., 1998) and is comprised of a region preceding the first membrane spanning domain (termed S1) and a region between the second and third membrane spanning domains (termed S2). In NR2 NMDA receptor s...

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Structural Insights Into NMDA Ionotropic Glutamate Receptors via Molecular Modelling

Cited by 8 publications

References 42 publications

Single‐channel analysis of an NMDA receptor possessing a mutation in the region of the glutamate binding site

Single‐channel analysis of an NMDA receptor possessing a mutation in the region of the glutamate binding site

Pharmacological insights obtained from structure–function studies of ionotropic glutamate receptors

Structural Features of the Glutamate Binding Site in Recombinant NR1/NR2AN-Methyl-d-aspartate Receptors Determined by Site-Directed Mutagenesis and Molecular Modeling

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