Conformational and Thermodynamic Landscape of GPCR Activation from Theory and Computation.
Conformational and Thermodynamic Landscape of GPCR Activation from Theory and Computation.
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从理论和计算来看 GPCR 激活的构象和热力学景观。
DOI：
10.1016/j.bpj.2016.04.028
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发表时间：
2016
影响因子：
3.4
通讯作者：
Abrol,Ravinder
中科院分区：
文献类型：
--
作者：
Dong,SijiaS;Goddard3rd,WilliamA;Abrol,Ravinder
我们提出了一种混合计算方法来预测G蛋白偶联受体(GPCRs)的多种能量可及构象，这些构象可能在与配体和不同信号伙伴的结合中发挥作用。据我们所知，这种被称为ActiveGEnSeMBLE的方法，使得第一个GPCR激活的定量能量分布与从实验得出的定性分布相一致。ActiveGEnSeMBLE首先对螺旋倾斜/旋转(∼13万亿跨膜结构域构象)进行系统的粗网格采样，并基于能量选择构象景观。这个图谱识别了多个潜在的激活态能量井，TM3-TM6细胞内距离是一个近似的激活坐标。然后使用更精细的网格对这些能量井进行局部采样，以在每个能量井中找到局部最小化的构象。我们使用β-2肾上腺素能受体(h-β-2AR)和M2 M受体的非活性和活性实验结构来验证这一策略。用分子动力学方法对hβ2AR的活化坐标进行了分子动力学模拟和相互作用能分析，得到了hβ2AR活化的定量能谱.这幅图揭示了沿着这个坐标的几个亚稳态，表明对于hβ2AR，单靠激动剂不足以稳定活性状态，G蛋白是必要的，这与实验观察一致。该方法对生长抑素受体SSTR5(没有实验结构可用)的应用表明，要预测活性构象，最好从基于紧密同源的非活性结构模板开始，而不是从基于远距离同源的活性模板开始。HSSTR5激活的能量图谱与hβ2AR在G蛋白中的作用是一致的。这些结果证明了ActiveGEnSeMBLE方法在预测GPCRs激活途径上的多重构象和相应的能量景观方面的有效性，从而为GPCR功能的初始分子事件提供了详细的结构洞察，这些事件不容易通过实验获得。
We present a hybrid computational methodology to predict multiple energetically accessible conformations for G protein-coupled receptors (GPCRs) that might play a role in binding to ligands and different signaling partners. To our knowledge, this method, termed ActiveGEnSeMBLE, enables the first quantitative energy profile for GPCR activation that is consistent with the qualitative profile deduced from experiments. ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (∼13 trillion transmembrane-domain conformations) and selects the conformational landscape based on energy. This profile identifies multiple potential active-state energy wells, with the TM3–TM6 intracellular distance as an approximate activation coordinate. These energy wells are then sampled locally using a finer grid to find locally minimized conformation in each energy well. We validate this strategy using the inactive and active experimental structures ofβ2adrenergic receptor (hβ2AR) and M2 muscarinic acetylcholine receptor. Structures of membrane-embedded hβ2AR along its activation coordinate are subjected to molecular-dynamics simulations for relaxation and interaction energy analysis to generate a quantitative energy landscape for hβ2AR activation. This landscape reveals several metastable states along this coordinate, indicating that for hβ2AR,the agonist alone is not enough to stabilize the active state and that the G protein is necessary, consistent with experimental observations. The method's application to somatostatin receptor SSTR5 (no experimental structure available) shows thatto predict an active conformation it is better to start from an inactive structure template based on a close homolog than to start from an active template based on a distant homolog. The energy landscape for hSSTR5 activation is consistent with hβ2AR in the role of the G protein. These results demonstrate the utility of the ActiveGEnSeMBLE method for predicting multiple conformations along the pathways for activating GPCRs and the corresponding energy landscapes, thereby providing detailed structural insights into the initial molecular events of GPCR function that are not easily accessible by experiments.