Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations

Saleh, Noureldin; Saladino, Giorgio; Gervasio, Francesco Luigi; Clark, Timothy

doi:10.1039/c6sc04647a

Cited by 42 publications

(55 citation statements)

References 51 publications

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“…Umbrella sampling has been used to calculate free energy profiles of the TM6 outward movement during receptor coupling to the G proteins. 17 Metadynamics simulations have been performed to investigate the dynamic effects of different GPCR ligands and intracellular binding partners 24 and examine differences of GPCRs coupled by the G protein versus its mimetic nanobody. 25 Nevertheless, these enhanced simulation methods require predefined collective variables and may apply constrains on the conformational space of the proteins.…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Wang

Miao

2019

Preprint

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Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR-G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ~1/3 of currently marketed drugs. Here, we have employed all-atom molecular simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR-G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A1AR and A2AAR coupled with the Gi and Gs proteins, respectively. Changing the Gi protein to the Gs led to increased fluctuations in the A1AR and agonist adenosine (ADO), while agonist 5'-N-ethylcarboxamidoadenosine (NECA) binding in the A2AAR could be still stabilized upon changing the Gs protein to the Gi. Free energy calculations identified one stable low-energy conformation for each of the ADO-A1AR-Gi and NECA-A2AAR-Gs complexes as in the cryo-EM structures, similarly for the NECA-A2AAR-Gi complex. In contrast, the ADO agonist and Gs protein sampled multiple conformations in the ADO-A1AR-Gs system. GaMD simulations thus indicated that the ADO-bound A1AR preferred to couple with the Gi protein to the Gs, while the A2AAR could couple with both the Gs and Gi proteins, being highly consistent with experimental findings of the ARs. More importantly, detailed analysis of the atomic simulations showed that the specific AR-G protein coupling resulted from remarkably complementary residue interactions at the protein interface, involving mainly the receptor transmembrane 6 helix and the Gα α5 helix and α4-β6 loop. In summary, the GaMD simulations have provided unprecedented insights into the dynamic mechanism of specific GPCR-G protein interactions at an atomistic level, which is expected to facilitate future drug design efforts of the GPCRs.

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Section: Introductionmentioning

confidence: 99%

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Wang

Miao

2019

Preprint

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“…We recently described am etadynamics-based protocol for studying ligand/GPCR binding and modulation that allows us to study diverse processes from subtype selectivity to the cooperativity between ligand and intracellular binding partner (IBP) and negative allosteric modulation with aroot mean square error (RMSE) between calculated and experimental free energies of binding of less than 1.1 kcal mol À1 and R 2 = 0.74. [34][35][36][37][38] In this work, we built on our previous success in investigating the allostery and cooperativity of GPCR ligands by employing metadynamics simulations to determine binding sites of the agonist CP 55,940 and the Ago-PAM GAT228. We have also determined their binding modes and affinities to delineate the mode of action of 2-phenylindole Ago-PAMs.…”

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confidence: 99%

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor

et al. 2018

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The cannabinoid CB1 receptor (CB1R) is an abundant metabotropic G-protein-coupled receptor that has been difficult to address therapeutically because of CNS side effects exerted by orthosteric drug candidates.R ecent efforts have focused on developing allosteric modulators that target CB1R. Compounds from the recently discovered class of mixed agonistic and positive allosteric modulators (Ago-PAMs) based on 2-phenylindoles have shown promising functional and binding properties as CB1R ligands.H ere,w e identify binding modes of both the CP 55,940 agonist and GAT228, a2 -phenylindole allosteric modulator,b yu sing our metadynamics simulation protocol, and quantify their affinity and cooperativity by atomistic simulations.Wedemonstrate the involvement of multiple adjunct binding sites in the Ago-PAM characteristics of the 2-phenylindole modulators and explain their ability to compete with orthosteric agonists at higher concentrations.W ev alidate these results experimentally by showing the contribution of multiple sites on the allosteric binding of ZCZ011, another homologous member of the class, together with the orthosteric agonist.

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“…This means that we can obtain complete free-energy profiles along the binding path for both ligands and IBPs [39]. This, in turn, allows us to validate the simulations by comparison with experimental free energies of binding obtained from measured binding constants.…”

Section: Reviewmentioning

confidence: 99%

G-Protein coupled receptors: answers from simulations

Clark¹

2017

Beilstein J. Org. Chem.

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Molecular-dynamics (MD) simulations are playing an increasingly important role in research into the modes of action of G-protein coupled receptors (GPCRs). In this field, MD simulations are unusually important as, because of the difficult experimental situation, they often offer the only opportunity to determine structural and mechanistic features in atomistic detail. Modern combinations of soft- and hardware have made MD simulations a powerful tool in GPCR research. This is important because GPCRs are targeted by approximately half of the drugs on the market, so that computer-aided drug design plays a major role in GPCR research.

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Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations

Abstract: We propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and intracellular binding partner (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias.

Cited by 42 publications

References 51 publications

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor

G-Protein coupled receptors: answers from simulations

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