Comitani Federico, Cohen Netta, Ashby Jamie, Botten Dominic, Lummis Sarah C R, Molteni Carla
Physics Department, King's College London, Strand, London, WC2R 2LS, UK.
J Comput Aided Mol Des. 2014 Jan;28(1):35-48. doi: 10.1007/s10822-013-9704-0. Epub 2014 Jan 18.
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.
狄氏剂抗性（RDL）受体是一种昆虫五聚体配体门控离子通道（pLGIC）。它通过神经递质γ-氨基丁酸（GABA）与其细胞外结构域结合而被激活；因此，阐明这种相互作用的原子细节对于理解RDL受体的功能很重要。由于目前尚无高分辨率结构，我们使用不同的模板构建了RDL受体细胞外结构域的同源模型，包括广泛使用的乙酰胆碱结合蛋白以及两种pLGIC，即菊欧文氏菌配体门控离子通道（ELIC）和最近解析的谷氨酸氯离子通道（GluCl）。然后，我们将GABA对接至选定的三维结构中，将其用作经典分子动力学模拟的起点。这使我们能够详细分析GABA在结合位点的行为，包括其形成的氢键和阳离子-π相互作用网络、其访问的构象以及水分子在介导相互作用中的可能作用；我们还估算了结合自由能。这些模型都很稳定，并显示出共同特征，包括与实验数据一致且与其他pLGIC相似的相互作用；差异可归因于模型的质量，其随着序列同一性的增加而提高，以及pLGIC模板的使用。我们通过探索GABA与RDL受体结合的自由能景观，用元动力学（一种稀有事件方法）补充了分子动力学信息。总体而言，我们表明GluCl模板提供了最佳模型。GABA与Arg211和Glu204形成直接盐桥，并与包括Tyr109、Phe206和Tyr254的芳香笼形成阳离子-π相互作用，代表了一种有利的结合排列，并且与Glu204的相互作用也可以由一个水分子介导。
