Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104

Melis, Claudio; Lummis, Sarah C. R.; Molteni, Carla

doi:10.1529/biophysj.107.127589

Cited by 30 publications

(34 citation statements)

References 31 publications

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“…Interestingly, the two mutations having the larg- est effect on the GABA binding rate (␣ 1 R67A and ␤ 2 R207A) had similar effects on the binding rate of the lower affinity agonist THIP, suggesting that those arginines may be part of a generic mechanism underlying agonist binding. Consistent with the idea that ␣ 1 Arg67 is generally involved in agonist binding, molecular dynamics simulations with GABA and glycine docked to homology models of the GABA C and glycine receptors, respectively, show the carboxylate group of both ligands in direct contact with the amide head group of an arginine in a homologous position to ␣ 1 Arg67 in the GABA A receptor (Grudzinska et al, 2005;Melis et al, 2008). A glutamate-gated chloride channel having 34% sequence identity to the human ␣1 glycine receptor has been crystallized with glutamate bound in the agonist binding site, in which its carboxylate groups are coordinated by two arginines, one of which is located similarly to ␣ 1 Arg67 in the GABA A receptor (Hibbs and Gouaux, 2011).…”

Section: Discussionsupporting

confidence: 54%

Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

Goldschen-Ohm

Wagner²,

Jones³

2011

Mol Pharmacol

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Binding of the agonist GABA to the GABA A receptor causes channel gating, whereas competitive antagonists that bind at the same site do not. The details of ligand binding are not well understood, including which residues interact directly with ligands, maintain the structure of the binding pocket, or transduce the action of binding into opening of the ion channel gate. Recent work suggests that the amine group of the GABA molecule may form a cation-bond with residues in a highly conserved "aromatic box" within the binding pocket. Although interactions with the carboxyl group of GABA remain unknown, three positively charged arginines (␣ 1 Arg67, ␣ 1 Arg132, and ␤ 2 Arg207) just outside of the aromatic box are likely candidates. To explore their roles in ligand binding, we individually mutated these arginines to alanine and measured the effects on microscopic ligand binding/unbinding rates and channel gating. The mutations ␣ 1 R67A or ␤ 2 R207A slowed agonist binding and sped unbinding with little effect on gating, demonstrating that these arginines are critical for both formation and stability of the agonist-bound complex. In addition, ␣ 1 R67A sped binding of the antagonist 2-(3-carboxypropyl)-3-amino-6-(4 methoxyphenyl)pyridazinium bromide (SR-95531), indicating that this arginine poses a barrier to formation of the antagonistbound complex. In contrast, ␤ 2 R207A and ␣ 1 R132A sped antagonist unbinding, indicating that these arginines stabilize the antagonist-bound state. ␣ 1 R132A also conferred a new longlived open state, indicating that this arginine influences the channel gate. Thus, each of these arginines plays a unique role in determining interactions with agonists versus antagonists and with the channel gate.

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Section: Discussionsupporting

confidence: 54%

Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

Goldschen-Ohm

Wagner²,

Jones³

2011

Mol Pharmacol

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“…11,39,40,45,46 We have also used this wealth of AChBP structural data and analysis for assessment against our study.…”

Section: Loop F Dynamics and Differencesmentioning

confidence: 99%

A Role for Loop F in Modulating GABA Binding Affinity in the GABAA Receptor

Carpenter

Lau

Lightstone

2012

Journal of Molecular Biology

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“…Nevertheless, homology-based computer modeling provides sufficiently accurate structural details to test the potential role of functional domains of the receptor (12)(13)(14)(15). We are interested in understanding the functional role of the carboxy-terminus of the TM4 segments of GABAρ receptors.…”

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confidence: 99%

Structure-function study of the fourth transmembrane segment of the GABAρ1 receptor

Estrada-Mondragón

Reyes-Ruiz

Martı́nez-Torres

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The Cys-loop family of receptors mediates synaptic neurotransmission in the central nervous system of vertebrates. These receptors share several structural characteristics and assemble in the plasma membrane as multimers with fivefold symmetry. Of these, the ionotropic GABA receptors are key players in the pathogenesis of diseases like epilepsy, anxiety, and schizophrenia. Different experimental approaches have shed some light on the mechanisms behind the function of these receptors; but little is known about their structure at high resolution. Sequence homology with the nicotinic acetylcholine receptor predicts that ionotropic GABA receptors possess four transmembrane segments (TM1-4) and that TM2 forms the wall of the ion channel. However, the role of the other three segments is unclear. The GABAρ1 receptor plays a fundamental role in the regulation of neurotransmission along the visual pathway, is highly sensitive to GABA, and exhibits little desensitization. In our recent investigations of the role of TM4 in receptor function, a key residue in this domain (W475) was found to be involved in activation of the receptor. Here we have generated a structural model of the GABAρ1 receptor in silico and assessed its validity by electrophysiologically testing nine amino acid substitutions of W475 and deletions of the neighboring residues (Y474 and S476). The results identify a critical linkage between the ligand-binding domain and the TM4 domain and provide a framework for more detailed structure-function analyses of ionotropic GABA receptors. GABAρ receptors play a central role in the visual pathway, negatively modulating glutamatergic transmission in the retina (1, 2). These receptors are located at the axon terminals of rod bipolar cells, where GABAergic input is received from amacrine neurons (3). There are three known genes coding for GABAρ receptors, GABAρ1 to -3, all of which form functional homomeric receptors with pharmacological properties very different from those of other GABA receptors. For example, they are highly sensitive to GABA, desensitize very little, and are essentially bicuculline/baclofen insensitive in situ (4, 5) and when expressed in heterologous systems, such as the Xenopus laevis oocyte (6, 7).The Cys-loop receptor superfamily, within which the GABAρ receptors are classified, includes cation-selective receptors, such as the nicotinic acetylcholine (nACh) and 5-hydroxytryptamine 3 (5-HT3) receptors, as well as anion-selective receptors, such as those for glycine and GABA (8). All these receptors share wellconserved amino acid sequences and presumably assemble in the plasma membrane as pentamers. Each subunit of the pentamer contains a large extracellular N-terminal ligand-binding domain (LBD), four transmembrane (TM1-4) helices, and a variable intracellular loop between TM3 and TM4 ( Fig. 1 A and B). The TM2 segment lines the pore domain and has subdomains that selectively discriminate ions according to their electric charge. The remaining three helices (TM1, -3, and -4) function as a "hydr...

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Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104

Cited by 30 publications

References 31 publications

Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

A Role for Loop F in Modulating GABA Binding Affinity in the GABAA Receptor

Structure-function study of the fourth transmembrane segment of the GABAρ1 receptor

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Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104

Cited by 30 publications

References 31 publications

Three Arginines in the GABAAReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

Three Arginines in the GABAAReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

A Role for Loop F in Modulating GABA Binding Affinity in the GABAA Receptor

Structure-function study of the fourth transmembrane segment of the GABAρ1 receptor

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Product

Resources

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Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes

Three Arginines in the GABA_AReceptor Binding Pocket Have Distinct Roles in the Formation and Stability of Agonist- versus Antagonist-Bound Complexes