Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
J Mol Biol. 2022 Sep 15;434(17):167690. doi: 10.1016/j.jmb.2022.167690. Epub 2022 Jun 18.
Accurate development of allosteric modulators of GPCRs require a thorough assessment of their sequence, structure, and dynamics, toward gaining insights into their mechanisms of actions shared by family members, as well as dynamic features that distinguish subfamilies. Building on recent progress in the characterization of the signature dynamics of proteins, we analyzed here a dataset of 160 Class A GPCRs to determine their sequence similarities, structural landscape, and dynamic features across different species (human, bovine, mouse, squid, and rat), different activation states (active/inactive), and different subfamilies. The two dominant directions of variability across experimentally resolved structures, identified by principal component analysis of the dataset, shed light to cooperative mechanisms of activation, subfamily differentiation, and speciation of Class A GPCRs. The analysis reveals the functional significance of the conformational flexibilities of specific structural elements, including: the dominant role of the intracellular loop 3 (ICL3) together with the cytoplasmic ends of the adjoining helices TM5 and TM6 in enabling allosteric activation; the role of particular structural motifs at the extracellular loop 2 (ECL2) connecting TM4 and TM5 in binding ligands specific to different subfamilies; or even the differentiation of the N-terminal conformation across different species. Detailed analyses of the modes of motions accessible to the members of the dataset and their variations across members demonstrate how the active and inactive states of GPCRs obey distinct conformational dynamics. The collective fluctuations of the GPCRs are robustly defined in the active state, while the inactive conformers exhibit broad variance among members.
准确开发 GPCR 的别构调节剂需要对其序列、结构和动力学进行全面评估，以深入了解家族成员共有的作用机制，以及区分亚家族的动态特征。基于近年来对蛋白质特征动力学的研究进展，我们在这里分析了 160 个 A 类 GPCR 的数据集，以确定它们在不同物种（人、牛、鼠、鱿鱼和鼠）、不同激活状态（激活/失活）和不同亚家族中的序列相似性、结构景观和动态特征。通过对数据集的主成分分析，确定了跨实验解析结构的两个主要变化方向，这揭示了 A 类 GPCR 激活的协同机制、亚家族分化和物种形成。该分析揭示了特定结构元素构象灵活性的功能意义，包括：细胞内环 3（ICL3）与相邻 TM5 和 TM6 胞质末端一起在别构激活中的主导作用；连接 TM4 和 TM5 的细胞外环 2（ECL2）中特定结构模体在结合不同亚家族特异性配体中的作用；甚至在不同物种中 N 端构象的分化。对数据集成员可及的运动模式及其在成员间的变化进行详细分析，展示了 GPCR 的激活和失活状态如何遵循不同的构象动力学。GPCR 的集体波动在激活状态下是稳健定义的，而失活构象在成员间表现出广泛的变化。
