Mapping the Ligand-Modulated Conformational Landscape of GPCRs

描述（由申请人提供）：G蛋白偶联受体（GPCR）是一种膜蛋白，可结合多种配体并调节许多重要的生物信号级联。了解这些GPCR的配体偏向性功能动力学可以指导更有效和靶向药物的设计。最近的GPCR结构为受体动力学的计算研究提供了机会。该研究项目研究了两种GPCR，即<$2肾上腺素能受体（<$2AR）和A2 A腺苷受体（A2 AR），模拟了嵌入洗涤剂胶束中的蛋白质，这是一种常用于生物物理实验的膜模拟物。具体目标是：1）预测<$2AR和A2 AR的激活和失活机制。凭借独特的分布式计算架构，我们将运行大规模并行的全原子，明确的溶剂，明确的脂质分子动力学模拟的<$2AR和A2 AR绑定到各种配体。通过在前所未有的时间尺度上进行稳健的参数化模拟，我们有望首次预测这些GPCR的非活性到活性的转变。我们使用马尔可夫状态模型（MSM）和转移路径理论的统计分析，以揭示最可能的途径和动力学的<$2AR和A2 AR激活和失活。这些方法使我们能够量化配体诱导的人口变化，选择G-蛋白和<$2AR，从构象景观的<$-arrestin途径。2)研究<$2AR和A2 AR构象景观的变构调节。GPCR的变构调节是非常有吸引力的，这是由于受体活性位点的普遍存在和不同的构象调节，其可用于产生位点特异性和事件特异性作用。然而，尚未鉴定出Δ 2AR和Δ 2AR的选择性小分子变构调节剂。我们计划利用MSM和信息论方法挖掘目标（1）中获得的大量2AR和A2 AR模拟数据，以识别指示变构网络的相关性和连接性。这些网络将引导靶向小分子对接到推定的变构位点。将通过实验评估最佳变构对接命中。

DESCRIPTION (provided by applicant): G-protein coupled receptors (GPCRs) are membrane proteins that bind a variety of ligands and modulate many important biological signal cascades. Understanding ligand-biased functional dynamics of these GPCRs can direct the design of more effective and targeted drugs. Recent GPCR structures give opportunity for computational study of receptor dynamics. This research project studies two GPCRs, the ¿2 adrenergic receptor (¿2AR) and the A2A adenosine receptor (A2AR) with simulations of the proteins embedded in detergent micelles, a membrane mimetic that is often used in biophysical experiments. The specific aims are: 1) To predict the full activation and deactivation mechanism for ¿2AR and A2AR. With unique distributed computing architectures, we will run massively parallel all-atom, explicit solvent, explicit lipid molecular dynamics simulations of ¿2AR and A2AR bound to a variety of ligands. With robustly parameterized simulations at unprecedented timescales, we expect to predict the inactive-to-active transitions for these GPCRs for the first time. We use statistical analysis with Markov State Models (MSMs) and Transition Path Theory to reveal the most probable pathways and the kinetics of ¿2AR and A2AR activation and deactivation. These methods allow us to quantify ligand-induced population shifts that select the G-protein and, for ¿2AR, the ¿-arrestin pathways from the conformational landscape. 2) To investigate allosteric modulation of ¿2AR and A2AR conformational landscapes. Allosteric modulation of GPCRs is very attractive due to the ubiquity of the receptor active sites and the diverse conformational tuning, which can be utilized to give site-specific and event specific action. However, no selective small molecule allosteric modulators have been identified for ¿2AR and A2AR. We plan to mine the wealth of ¿2AR and A2AR simulation data obtained in aim (1) with MSMs and information theory methods to identify correlations and connectivity indicative of allosteric networks. These networks will guide targeted small molecule docking to putative allosteric sites. Top allosteric docking hits will be evaluated with experiments.