Data from: Molecular determinants of agonist selectivity in glutamate-gated chloride channels which likely explain the agonist selectivity of the vertebrate glycine and GABAA-ρ receptors

Orthologous Cys-loop glutamate-gated chloride channels (GluClR’s) have been cloned and described electrophysiologically and pharmacologically in arthropods and nematodes (both members of the invertebrate ecdysozoan superphylum). Recently, GluClR’s from Aplysia californica (a mollusc from the lophotrochozoan superphylum) have been cloned and similarly studied. In spite of sharing a common function, the ecdysozoan and lophotrochozoan receptors have been shown by phylogenetic analyses to have evolved independently. The recent crystallization of the GluClR from C. elegans revealed the binding pocket of the nematode receptor. An alignment of the protein sequences of the nematode and molluscan GluClRs showed that the Aplysia receptor does not contain all of the residues defining the binding mode of the ecdysozoan receptor. That the two receptors have slightly different binding modes is not surprising since earlier electrophysiological and pharmacological experiments had suggested that they were differentially responsive to certain agonists. Knowledge of the structure of the C. elegans GluClR has permitted us to generate a homology model of the binding pocket of the Aplysia receptor. We have analyzed the differences between the two binding modes and evaluated the relative significance of their non-common residues. We have compared the GluClRs electrophysiologically and pharmacologically and we have used site-directed mutagenesis on both receptor types to test predictions made from the model. Finally, we propose an explanation derived from the model for why the nematode receptors are gated only by glutamate, whereas the molluscan receptors can also be activated by β-alanine, GABA and taurine. Like the Aplysia receptor, the vertebrate glycine and GABAA-ρ receptors also respond to these other agonists. An alignment of the sequences of the molluscan and vertebrate receptors shows that the reasons we have given for the ability of the other agonists to activate the Aplysia receptor also explain the agonist profile seen in the glycine and GABAA-ρ receptors

Data from: Molecular determinants of agonist selectivity in glutamate-gated chloride channels which likely explain the agonist selectivity of the vertebrate glycine and GABAA-ρ receptors

Orthologous Cys-loop glutamate-gated chloride channels (GluClR’s) have been cloned and described electrophysiologically and pharmacologically in arthropods and nematodes (both members of the invertebrate ecdysozoan superphylum). Recently, GluClR’s from Aplysia californica (a mollusc from the lophotrochozoan superphylum) have been cloned and similarly studied. In spite of sharing a common function, the ecdysozoan and lophotrochozoan receptors have been shown by phylogenetic analyses to have evolved independently. The recent crystallization of the GluClR from C. elegans revealed the binding pocket of the nematode receptor. An alignment of the protein sequences of the nematode and molluscan GluClRs showed that the Aplysia receptor does not contain all of the residues defining the binding mode of the ecdysozoan receptor. That the two receptors have slightly different binding modes is not surprising since earlier electrophysiological and pharmacological experiments had suggested that they were differentially responsive to certain agonists. Knowledge of the structure of the C. elegans GluClR has permitted us to generate a homology model of the binding pocket of the Aplysia receptor. We have analyzed the differences between the two binding modes and evaluated the relative significance of their non-common residues. We have compared the GluClRs electrophysiologically and pharmacologically and we have used site-directed mutagenesis on both receptor types to test predictions made from the model. Finally, we propose an explanation derived from the model for why the nematode receptors are gated only by glutamate, whereas the molluscan receptors can also be activated by β-alanine, GABA and taurine. Like the Aplysia receptor, the vertebrate glycine and GABAA-ρ receptors also respond to these other agonists. An alignment of the sequences of the molluscan and vertebrate receptors shows that the reasons we have given for the ability of the other agonists to activate the Aplysia receptor also explain the agonist profile seen in the glycine and GABAA-ρ receptors

Vitamin K-dependent carboxylaseIn vitro inhibitory activity of cyclopentane and cyclohexane-derived analogues ofglutamic acid and their conformational study by NMR and molecular dynamics inaqueous solution

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Glutamate docked in the homology model of GluClAc2 (Aplysia californica)

Coordinates of the homology model of GluClAc2, the glutamate-gated chloride channel receptor of Aplysia californica with docked glutamate

Responses of mutated GluCl<i>Ac</i>2 and GluClα2b receptors to increasing concentrations of glutamate.

<p>A: Responses (in pA) of seven mutated GluCl<i>Ac</i>2 receptors to 1, 10, 50 and 100 mM glutamate. B: Responses of five mutated GluClα2B receptors to 1, 10, 50 and 100 mM glutamate.</p

Responses to 1 mM glutamate in both WT and mutated GluCl<i>Ac</i>2 and GluClα2b receptors.

<p>A. Mutations in four binding residues of GluCl<i>Ac</i>2: Y96, R98, R135 and Y161 (positions 54, 56, 93 and 119). B. Mutations in GluCl<i>Ac</i>2 of residues L79 alone and L79+R135. These two residues are found at positions 37 and 93 (see Figs. 3 and 4). Only one of the two (R135) belongs to the GluCl<i>Ac</i>2 binding pocket (see the R135A mutation alone in A). C. Mutations in GluClα2b of residues R111 and Q167 found at positions 37 and 93, respectively: R111 alone, and R111+Q167 in a double mutation. Only one of the residues (R111) belongs to the GluClα2b binding pocket. Calibration: A: 1 sec, 500 pA; B: 1 sec, 500 pA; C: 1 sec, 1000 pA.</p

Similar binding modes for the three additional ligands in GluCl<i>Ac</i>2.

<p>2D diagram representing the interactions between the binding pocket residues of the homology model for GluCl<i>Ac</i>2 and (A) β-alanine, (B) GABA and (C) taurine. Ligands are represented in lines. Only the polar hydrogens that are involved in interactions with the receptor are explicitly represented. Residues are depicted as circles in which the residue type, number and position (the latter in parentheses) are written on a colored background which indicates the subunit to which the residue belongs (see Fig. 3 and Fig. 4). Backbone and side chain hydrogen bonds are represented by green and blue arrows, respectively. Salt bridges are represented by purple arrows, π interactions are represented by orange lines. Atom colors as in Fig. 3B.</p

Glutamate bound to GluCl_Cryst and to the homology model of GluCl<i>Ac</i>2.

<p>A. 3D representation of the binding pocket of glutamate at the interface between the two subunits of the crystallographic structure of GluCl_Cryst (Left) and the model of GluCl<i>Ac</i>2 (Right). The Principal and Complementary subunits are displayed in violet and green/yellow, respectively. The bound glutamate is represented by a ball and stick display. The residues for four important positions in the alignment are represented as sticks, and their names and residue numbers are written in green. B. 2D diagram representing the interactions between glutamate and each of the two receptors: GluCl_Cryst (Left) and GluCl<i>Ac</i>2 (Right) as displayed in 3A. Glutamate is represented in lines, and adopts two different conformations reflecting the respective bindings at the two receptors. Only the polar hydrogens that are involved in interactions with the receptor are explicitly represented. Residues are depicted as circles in which the residue type, number and position (the latter in parentheses) are written on a colored background which indicates the subunit to which the residue belongs (see Fig. 3A). Backbone and side chain hydrogen bonds are represented by green and blue arrows, respectively. Salt bridges are represented by violet arrows and π interactions are represented by orange lines. Atom color code: carbon gray, oxygen red, nitrogen blue, hydogens white in A, black in B.</p