We describe the first extensive energetic evaluation of GPCR dimerization on the atomistic level by means of potential of mean force (PMF) computations and implicit solvent/implicit membrane end‐point free energy calculations (MM‐PBSA approach). Free energies of association computed from the PMFs show that the formation of both the 1/8 and 4/5 interface is energetically favorable for TGR5, the first GPCR known to be activated by hydrophobic bile acids and neurosteroids. Furthermore, formation of the 1/8 interface is favored over that of the 4/5 interface. Both results are in line with our previous FRET experiments in live cells. Differences in lipid‐protein interactions are identified to contribute to the observed differences in free energies of association. A per‐residue decomposition of the MM‐PBSA effective binding energy reveals hot spot residues specific for both interfaces that form clusters. This knowledge may be used to guide the design of dimerization inhibitors or perform mutational studies to explore physiological consequences of distorted TGR5 association. Finally, we characterized the role of Y111, located in the conserved (D/E)RY motif, as a facilitator of TGR5 interactions. The types of computations performed here should be transferable to other transmembrane proteins that form dimers or higher oligomers as long as good structural models of the dimeric or oligomeric states are available. Such computations may help to overcome current restrictions due to an imperfect energetic representation of protein association at the coarse‐grained level. © 2019 Wiley Periodicals, Inc.

中文翻译：

---

来自全原子模拟的 G 蛋白偶联胆汁酸受体 TGR5 的二聚化能量学

我们通过平均力势 (PMF) 计算和隐式溶剂/隐式膜端点自由能计算（MM-PBSA 方法）描述了原子水平上 GPCR 二聚化的首次广泛能量评估。从 PMF 计算出的结合自由能表明，1/8 和 4/5 界面的形成在能量上有利于 TGR5，这是已知第一个被疏水胆汁酸和神经类固醇激活的 GPCR。此外，1/8 界面的形成优于 4/5 界面的形成。这两个结果都与我们之前在活细胞中的 FRET 实验一致。脂质-蛋白质相互作用的差异被确定有助于观察到的结合自由能的差异。MM-PBSA 有效结合能的每个残基分解揭示了形成簇的两个界面特异性的热点残基。该知识可用于指导二聚化抑制剂的设计或进行突变研究以探索扭曲的 TGR5 关联的生理后果。最后，我们描述了位于保守 (D/E)RY 基序中的 Y111 作为 TGR5 相互作用促进剂的作用。只要二聚体或寡聚体状态的良好结构模型可用，此处执行的计算类型应可转移到形成二聚体或更高寡聚体的其他跨膜蛋白。由于粗粒度水平的蛋白质关联的不完美能量表示，这种计算可能有助于克服当前的限制。© 2019 威利期刊公司。