Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling

• Published in: The Journal of biological chemistry 2024-06, Vol.300 (6), p.107362, Article 107362
• Main Authors: Mukhaleva, Elizaveta, Ma, Ning, van der Velden, Wijnand J.C., Gogoshin, Grigoriy, Branciamore, Sergio, Bhattacharya, Supriyo, Rodin, Andrei S., Vaidehi, Nagarajan
• Format: Article
• Language: English
• Subjects: Bayesian network; cooperativity; G protein selectivity; GPCR:G protein interaction; GPCRs; Gα protein selectivity; machine learning; MD simulations and network; molecular dynamics; network modeling; protein-protein interactions
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1016/j.jbc.2024.107362

Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces, it is challenging to determine which amino acid pair interactions are cooperative. In this work, we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein–coupled receptor (GPCR) complexes with Gα subunits. Our results reveal six GPCR:Gα contacts that are common to the different Gα subtypes and show strong cooperativity in the formation of interface. Both the C terminus helix5 and the core of the G protein are codependent entities and play an important role in GPCR coupling. We show that a promiscuous GPCR coupling to different Gα subtypes, makes all the GPCR:Gα contacts that are specific to each Gα subtype (Gαs, Gαi, and Gαq). This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.