Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models

Abstract

The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.

Heterogeneous expression of GABA receptor‐like subunits LCCH3 and GRD reveals functional diversity of GABA receptors in the honeybee Apis mellifera

“…All these polypeptide subunits present the general tertiary structure and the main features of the ligand‐gated ion channels, including (i) the four transmembrane segments, (ii) the two cysteines of the “Cys‐loop,” and (iii) the loops A, B, and C, on the principal subunit and the loops D, E, and F on the complementary one, which are involved in the agonist binding pocket located at the interface between extracellular domains of two subunits (Lummis, 2009) (Figure 1a). Seven amino acids are described in Drosophila RDL as specifically responsible for the GABA binding in this pocket (Ashby et al, 2012; Comitani et al, 2014; Comitani et al, 2016). These amino acids are all present on the A. mellifera RDL.…”

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

“…[26][27][28] Metadynamics has been successfully used to study a wide range of problems in the physical, chemical, biological, and material sciences. 26,[29][30][31][32][33][34] As metadynamics efficiency decreases with the number of biased CVs, the minimal CV set providing meaningful results should be chosen. To map the conformers of Asp, the three backbone torsional angles α, β, and γ are an obvious, but not adequate choice, as we observed with preliminary calculations.…”

Transcriptome Analysis of the Central and Peripheral Nervous Systems of the Spider Cupiennius salei Reveals Multiple Putative Cys-Loop Ligand Gated Ion Channel Subunits and an Acetylcholine Binding Protein

“…The only complete nACh receptor is a medium resolution electron microscopy structure from the electric ray Torpedo marmorata [ 17 ], but structural information for the channel extracellular domain has been inferred by homology with the molluscan acetylcholine binding protein AChBP [ 18 ]. All known Cys-loop receptors show remarkable structural similarities with conserved residues that are important for receptor function, making it possible to use a combination of several templates to infer information about other receptors to create homology models [ 19 ].…”