Activation and Speciation Mechanisms in Class A GPCRs

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 dif-ferent species (human, bovine, mouse, squid, and rat), different activation states (active/inactive), and dif-ferent 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 activa-tion, subfamily differentiation, and speciation of Class A GPCRs. The analysis reveals the functional sig-nificance 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) con-necting 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 inac-tive 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.(c) 2022 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecom-mons.org/licenses/by/4.0/).