GPCRome-wide analysis of G-protein-coupling diversity using a computational biology approach

Marin Matic, Pasquale Miglionico, Manae Tatsumi, Asuka Inoue () and Francesco Raimondi ()
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Marin Matic: Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore
Pasquale Miglionico: Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore
Manae Tatsumi: Tohoku University
Asuka Inoue: Tohoku University
Francesco Raimondi: Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract GPCRs are master regulators of cell signaling by transducing extracellular stimuli into the cell via selective coupling to intracellular G-proteins. Here we present a computational analysis of the structural determinants of G-protein-coupling repertoire of experimental and predicted 3D GPCR-G-protein complexes. Interface contact analysis recapitulates structural hallmarks associated with G-protein-coupling specificity, including TM5, TM6 and ICLs. We employ interface contacts as fingerprints to cluster Gs vs Gi complexes in an unsupervised fashion, suggesting that interface residues contribute to selective coupling. We experimentally confirm on a promiscuous receptor (CCKAR) that mutations of some of these specificity-determining positions bias the coupling selectivity. Interestingly, Gs-GPCR complexes have more conserved interfaces, while Gi/o proteins adopt a wider number of alternative docking poses, as assessed via structural alignments of representative 3D complexes. Binding energy calculations demonstrate that distinct structural properties of the complexes are associated to higher stability of Gs than Gi/o complexes. AlphaFold2 predictions of experimental binary complexes confirm several of these structural features and allow us to augment the structural coverage of poorly characterized complexes such as G12/13.

Date: 2023
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DOI: 10.1038/s41467-023-40045-y

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