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1. Ligand-Dependent Conformational Transitions in Molecular Dynamics Trajectories of GPCRs Revealed by a New Machine Learning Rare Event Detection Protocol

   https://doi.org/10.3390/molecules26103059  

   Plante, Ambrose; Weinstein, Harel (May 2021, Molecules)

   null (Ed.)

   Central among the tools and approaches used for ligand discovery and design are Molecular Dynamics (MD) simulations, which follow the dynamic changes in molecular structure in response to the environmental condition, interactions with other proteins, and the effects of ligand binding. The need for, and successes of, MD simulations in providing this type of essential information are well documented, but so are the challenges presented by the size of the resulting datasets encoding the desired information. The difficulty of extracting information on mechanistically important state-to-state transitions in response to ligand binding and other interactions is compounded by these being rare events in the MD trajectories of complex molecular machines, such as G-protein-coupled receptors (GPCRs). To address this problem, we have developed a protocol for the efficient detection of such events. We show that the novel Rare Event Detection (RED) protocol reveals functionally relevant and pharmacologically discriminating responses to the binding of different ligands to the 5-HT2AR orthosteric site in terms of clearly defined, structurally coherent, and temporally ordered conformational transitions. This information from the RED protocol offers new insights into specific ligand-determined functional mechanisms encoded in the MD trajectories, which opens a new and rigorously reproducible path to understanding drug activity with application in drug discovery. 

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2. Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein

   https://doi.org/10.1073/pnas.2215916120  

   Han, Yanxiao; Dawson, John R.; DeMarco, Kevin R.; Rouen, Kyle C.; Bekker, Slava; Yarov-Yarovoy, Vladimir; Clancy, Colleen E.; Xiang, Yang K.; Vorobyov, Igor (March 2023, Proceedings of the National Academy of Sciences)

   G protein-coupled receptors (GPCRs) represent the largest group of membrane receptors for transmembrane signal transduction. Ligand-induced activation of GPCRs triggers G protein activation followed by various signaling cascades. Understanding the structural and energetic determinants of ligand binding to GPCRs and GPCRs to G proteins is crucial to the design of pharmacological treatments targeting specific conformations of these proteins to precisely control their signaling properties. In this study, we focused on interactions of a prototypical GPCR, beta-2 adrenergic receptor (β 2 AR), with its endogenous agonist, norepinephrine (NE), and the stimulatory G protein (G s ). Using molecular dynamics (MD) simulations, we demonstrated the stabilization of cationic NE, NE(+), binding to β 2 AR by G s protein recruitment, in line with experimental observations. We also captured the partial dissociation of the ligand from β 2 AR and the conformational interconversions of G s between closed and open conformations in the NE(+)–β 2 AR–G s ternary complex while it is still bound to the receptor. The variation of NE(+) binding poses was found to alter G s α subunit (G s α) conformational transitions. Our simulations showed that the interdomain movement and the stacking of G s α α1 and α5 helices are significant for increasing the distance between the G s α and β 2 AR, which may indicate a partial dissociation of G s α The distance increase commences when G s α is predominantly in an open state and can be triggered by the intracellular loop 3 (ICL3) of β 2 AR interacting with G s α, causing conformational changes of the α5 helix. Our results help explain molecular mechanisms of ligand and GPCR-mediated modulation of G protein activation. 

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3. Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

   https://doi.org/10.3389/fendo.2024.1348465  

   Buckley, Sean J; Nguyen, Tuan Viet; Cummins, Scott F; Elizur, Abigail; Fitzgibbon, Quinn P; Smith, Gregory S; Mykles, Donald L; Ventura, Tomer (February 2024, Frontiers in Endocrinology)

   None (Ed.)

   G protein-coupled receptors (GPCRs) are an ancient family of signal transducers that are both abundant and consequential in metazoan endocrinology. The evolutionary history and function of the GPCRs of the decapod superfamilies of gonadotropin-releasing hormone (GnRH) are yet to be fully elucidated. As part of which, the use of traditional phylogenetics and the recycling of a diminutive set of mis-annotated databases has proven insufficient. To address this, we have collated and revised eight existing and three novel GPCR repertoires for GnRH of decapod species. We developed a novel bioinformatic workflow that included clustering analysis to capture likely GnRH receptor-like proteins, followed by phylogenetic analysis of the seven transmembrane-spanning domains. A high degree of conservation of the sequences and topology of the domains and motifs allowed the identification of species-specific variation (up to ~70%, especially in the extracellular loops) that is thought to be influential to ligand-binding and function. Given the key functional role of the DRY motif across GPCRs, the classification of receptors based on the variation of this motif can be universally applied to resolve cryptic GPCR families, as was achieved in this work. Our results contribute to the resolution of the evolutionary history of invertebrate GnRH receptors and inform the design of bioassays in their deorphanization and functional annotation. 

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4. What Makes GPCRs from Different Families Bind to the Same Ligand?

   https://doi.org/10.3390/biom12070863  

   Dankwah, Kwabena Owusu; Mohl, Jonathon E.; Begum, Khodeza; Leung, Ming-Ying (July 2022, Biomolecules)

   G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs. 

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5. Differential regulation of G protein signaling in Arabidopsis through two distinct pathways that internalize AtRGS1

   https://doi.org/10.1126/scisignal.abe4090  

   Watkins, Justin M.; Ross-Elliott, Timothy J.; Shan, Xiaoyi; Lou, Fei; Dreyer, Bernd; Tunc-Ozdemir, Meral; Jia, Haiyan; Yang, Jing; Oliveira, Celio Cabral; Wu, Luguang; et al (August 2021, Science Signaling)

   In animals, endocytosis of a seven-transmembrane GPCR is mediated by arrestins to propagate or arrest cytoplasmic G protein–mediated signaling, depending on the bias of the receptor or ligand, which determines how much one transduction pathway is used compared to another. InArabidopsis thaliana, GPCRs are not required for G protein–coupled signaling because the heterotrimeric G protein complex spontaneously exchanges nucleotide. Instead, the seven-transmembrane protein AtRGS1 modulates G protein signaling through ligand-dependent endocytosis, which initiates derepression of signaling without the involvement of canonical arrestins. Here, we found that endocytosis of AtRGS1 initiated from two separate pools of plasma membrane: sterol-dependent domains and a clathrin-accessible neighborhood, each with a select set of discriminators, activators, and candidate arrestin-like adaptors. Ligand identity (either the pathogen-associated molecular pattern flg22 or the sugar glucose) determined the origin of AtRGS1 endocytosis. Different trafficking origins and trajectories led to different cellular outcomes. Thus, in this system, compartmentation with its associated signalosome architecture drives biased signaling. 

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