scholarly journals Universal activation mechanism of class A GPCRs

2019 ◽  
Author(s):  
Qingtong Zhou ◽  
Dehua Yang ◽  
Meng Wu ◽  
Yu Guo ◽  
Wangjing Guo ◽  
...  
Keyword(s):  
Ligand Binding ◽  
G Protein ◽  
Transmembrane Helix ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coupling Region ◽  
Activation Pathway ◽  
Class A ◽  
Gpcr Activation

AbstractClass A G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. GPCR activation is an allosteric process that links agonist binding to G protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue-level changes of this trigger remain less well understood. Here, by analyzing over 230 high-resolution structures of class A GPCRs, we discovered a modular, universal GPCR activation pathway that unites previous findings into a common activation mechanism, directly linking the bottom of ligand-binding pocket with G protein-coupling region. We suggest that the modular nature of the universal GPCR activation pathway allowed for the decoupling of the evolution of the ligand binding site, G protein binding region and the residues important for receptor activation. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.

scholarly journals Common activation mechanism of class A GPCRs

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Qingtong Zhou ◽  
Dehua Yang ◽  
Meng Wu ◽  
Yu Guo ◽  
Wanjing Guo ◽  
...  
Keyword(s):  
Ligand Binding ◽  
G Protein ◽  
Conformational Changes ◽  
Receptor Activation ◽  
Site Directed Mutagenesis ◽  
Activation Mechanism ◽  
Activation Pathway ◽  
Class A ◽  
Gpcr Activation ◽  
The Common

Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.

scholarly journals Receptor-wide Determinants of G Protein Coupling Selectivity in Aminergic GPCRs

2021 ◽  
Author(s):  
Berkay Selçuk ◽  
Ismail Erol ◽  
Serdar Durdağı ◽  
Ogun Adebali
Keyword(s):  
Ligand Binding ◽  
G Protein ◽  
Md Simulations ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Selective Activation ◽  
G Protein Coupling ◽  
Protein Coupling ◽  
Gpcr Activation ◽  
Activation Mechanisms

AbstractG protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Here, we identified conserved G protein selective activation mechanisms determining receptors’ ability to couple to a type of G protein. Herein, we performed an extensive phylogenetic analysis and identified specifically conserved residues for the receptors having similar coupling profiles in each aminergic receptor. By integrating our methodology of differential evolutionary conservation of G protein-specific amino acids with structural analyses, we identified selective activation networks for Gs, Gi1, Go, and Gq. We found that G protein selectivity is determined by not only the G protein interaction site but also other parts of the receptor including the ligand binding pocket. To validate our findings, we further studied an amino acid residue that we revealed as a selectivity-determining in Gs coupling and performed molecular dynamics (MD) simulations. We showed that previously uncharacterized Glycine at position 7×41 plays an important role in both receptor activation and Gs coupling. Finally, we gathered our results into a comprehensive model of G protein selectivity called “sequential switches of activation” describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms and G protein contact. We believe that our work provides a broader view on receptor-level determinants of G protein coupling selectivity.

scholarly journals Correlated motions of conserved polar motifs lay out a plausible mechanism of G protein-coupled receptor activation.

2020 ◽  
Author(s):  
Argha Mitra ◽  
Arijit Sarkar ◽  
Marton Richard Szabo ◽  
Attila Borics
Keyword(s):  
G Protein ◽  
Intracellular Signaling ◽  
Transmembrane Helix ◽  
Receptor Activation ◽  
Current Theory ◽  
Activation Mechanism ◽  
Structural Basis ◽  
Binding Interface ◽  
Gpcr Activation ◽  
G Protein Coupled

Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism on an entirely structural basis gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the mu-opioid receptor in a physiological environment revealed that external stimulus is propagated to the intracellular surface of the receptor through subtle, concerted movements of highly conserved polar amino acid side chains along the 7th transmembrane helix. To amend the widely accepted theory we suggest that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface.

scholarly journals Structural basis of bile acid receptor activation and Gs coupling

2020 ◽  
Author(s):  
Fan Yang ◽  
Chunyou Mao ◽  
Lulu Guo ◽  
Jingyu Lin ◽  
Qianqian Ming ◽  
...  
Keyword(s):  
Bile Acid ◽  
Ligand Binding ◽  
Bile Acids ◽  
G Protein ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Structural Features ◽  
Ligand Binding Pocket ◽  
Bile Acid Receptor ◽  
Key Residues

AbstractG protein-coupled bile acid receptor (GPBAR) is a membrane receptor that senses bile acids to regulate diverse functions through Gs activation. Here, we report the cryo-EM structures of GPBAR–Gs complexes stabilized by either high-affinity P395 or the semisynthesized bile acid derivative INT-777 at 3-Å resolution. These structures revealed a large oval-shaped ligand pocket with several sporadic polar groups to accommodate the amphipathic cholic core of bile acids. A fingerprint of key residues recognizing diverse bile acids in the orthosteric site, a putative second bile acid binding site with allosteric properties and structural features contributing to bias property were identified through structural analysis and mutagenesis studies. Moreover, structural comparison of GPBAR with other GPCRs uncovered an atypical mode of receptor activation and G-protein– coupling, featuring a different set of key residues connecting the ligand binding pocket to the Gs coupling site, and a specific interaction motif localized in intracellular loop 3. Overall, our study not only provides unique structural features of GPBAR in bile acid recognition, allosteric effects and biased signaling, but also suggests that distinct allosteric connecting mechanisms between the ligand binding pocket and the G protein binding site exist in the GPCR superfamily.

scholarly journals Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shaoyong Lu ◽  
Xinheng He ◽  
Zhao Yang ◽  
Zongtao Chai ◽  
Shuhua Zhou ◽  
...  
Keyword(s):  
G Protein ◽  
Large Scale ◽  
Receptor Activation ◽  
Site Directed Mutagenesis ◽  
Therapeutic Drug ◽  
Activation Pathway ◽  
Transition Mechanism ◽  
Gpcr Activation ◽  
State Models ◽  
G Protein Coupled

AbstractG protein-coupled receptors (GPCRs) are the most common proteins targeted by approved drugs. A complete mechanistic elucidation of large-scale conformational transitions underlying the activation mechanisms of GPCRs is of critical importance for therapeutic drug development. Here, we apply a combined computational and experimental framework integrating extensive molecular dynamics simulations, Markov state models, site-directed mutagenesis, and conformational biosensors to investigate the conformational landscape of the angiotensin II (AngII) type 1 receptor (AT1 receptor) — a prototypical class A GPCR—activation. Our findings suggest a synergistic transition mechanism for AT1 receptor activation. A key intermediate state is identified in the activation pathway, which possesses a cryptic binding site within the intracellular region of the receptor. Mutation of this cryptic site prevents activation of the downstream G protein signaling and β-arrestin-mediated pathways by the endogenous AngII octapeptide agonist, suggesting an allosteric regulatory mechanism. Together, these findings provide a deeper understanding of AT1 receptor activation at an atomic level and suggest avenues for the design of allosteric AT1 receptor modulators with a broad range of applications in GPCR biology, biophysics, and medicinal chemistry.

scholarly journals Nucleic acid ligands act as a PAM and agonist depending on the intrinsic ligand binding state of P2RY2

2021 ◽  
Vol 118 (18) ◽  
pp. e2019497118
Author(s):  
Masaki Takahashi ◽  
Ryo Amano ◽  
Michiru Ozawa ◽  
Anna Martinez ◽  
Kazumasa Akita ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Purinergic Receptor ◽  
Partial Agonist ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Gpcr Activation ◽  
Virus Like Particle ◽  
A Cell ◽  
Biochemical Analyses

G protein–coupled receptors (GPCRs) play diverse roles in physiological processes, and hence the ligands to modulate GPCRs have served as important molecules in biological and pharmacological approaches. However, the exploration of novel ligands for GPCR still remains an arduous challenge. In this study, we report a method for the discovery of nucleic acid ligands against GPCRs by an advanced RNA aptamer screening technology that employs a virus-like particle (VLP), exposing the GPCR of interest. An array of biochemical analyses coupled with a cell-based assay revealed that one of the aptamers raised against purinergic receptor P2Y2 (P2RY2), a GPCR, exhibits an activation potency to unliganded receptor and prohibits a further receptor activation by endogenous ligand, behaving like a partial agonist. However, the aptamer enhances the activity of intrinsic ligand-binding P2RY2, thereby acting as a positive allosteric modulator (PAM) to liganded receptor. Our findings demonstrate that the nucleic acid aptamer conditionally exerts PAM and agonist effects on GPCRs, depending on their intrinsic ligand binding state. These results indicate the validity of our VLP-based aptamer screening targeting GPCR and reemphasize the great potential of nucleic acid ligands for exploring the GPCR activation mechanism and therapeutic applications.

scholarly journals Allosteric effect of nanobody binding on ligand-specific active states of the β2-Adrenergic Receptor

2021 ◽  
Author(s):  
Yue Chen ◽  
Oliver Fleetwood ◽  
Sergio Perez-Conesa ◽  
Lucie Delemotte
Keyword(s):  
G Protein ◽  
Conformational Changes ◽  
Adrenergic Receptor ◽  
Partial Agonist ◽  
Transmembrane Helix ◽  
Active State ◽  
Supervised Machine Learning ◽  
Activation Mechanism ◽  
Gpcr Activation ◽  
Loop 2

Nanobody binding stabilizes the active state of G-protein-coupled receptor (GPCR) and modulates its affinity for bound ligands. However, the atomic level basis for this allosteric regulation remains elusive. Here, we investigate the conformational changes induced by the binding of a nanobody (Nb80) on the active-like beta2 adrenergic receptor (beta2AR) via enhanced sampling molecular dynamics simulations. Dimensionality reduction analysis shows that Nb80 stabilizes a highly active state of the beta2AR with a ~14 A outward movement of transmembrane helix 6 and close proximity of transmembrane (TM) helices 5 and 7. This is further supported by the residues located at hotspots located on TMs 5, 6 and 7, as shown by supervised machine learning methods. Besides, ligand-specific subtle differences in the conformations assumed by intercellular loop 2 and extracellular loop 2 are captured from the trajectories of various ligand-bound receptors in the presence of Nb80. Dynamic network analysis further reveals that Nb80 binding can enhance the communication between the binding sites of Nb80 and of the ligand. We identify unique allosteric signal transmission mechanisms between the Nb80-binding site and the extracellular domains in presence of full agonist and G-protein biased partial agonist, respectively. Altogether, our results provide insights into the effect of intracellular binding partners on the GPCR activation mechanism, which could be useful for structure-based drug discovery.

Ligand binding and activation of the CGRP receptor

2007 ◽  
Vol 35 (4) ◽  
pp. 729-732 ◽  
Author(s):  
A.C. Conner ◽  
J. Simms ◽  
J. Barwell ◽  
M. Wheatley ◽  
D.R. Poyner
Keyword(s):  
G Protein ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Extracellular Loop ◽  
C Terminus ◽  
Calcitonin Gene ◽  
The Family ◽  
N Terminus ◽  
G Protein Coupled

The receptor for CGRP (calcitonin gene-related peptide) is a heterodimer between a GPCR (G-protein-coupled receptor), CLR (calcitonin receptor-like receptor) and an accessory protein, RAMP1 (receptor activity-modifying protein 1). Models have been produced of RAMP1 and CLR. It is likely that the C-terminus of CGRP interacts with the extracellular N-termini of CLR and RAMP1; the extreme N-terminus of CLR is particularly important and may interact directly with CGRP and also with RAMP1. The N-terminus of CGRP interacts with the TM (transmembrane) portion of the receptor; the second ECL (extracellular loop) is especially important. Receptor activation is likely to involve the relative movements of TMs 3 and 6 to create a G-protein-binding pocket, as in Family A GPCRs. Pro321 in TM6 appears to act as a pivot. At the base of TMs 2 and 3, Arg151, His155 and Glu211 may form a loose equivalent of the Family A DRY (Asp-Arg-Tyr) motif. Although the details of this proposed activation mechanism clearly do not apply to all Family B GPCRs, the broad outlines may be conserved.

scholarly journals Buried ionizable networks are an ancient hallmark of G protein-coupled receptor activation

2015 ◽  
Vol 112 (18) ◽  
pp. 5702-5707 ◽  
Author(s):  
Daniel G. Isom ◽  
Henrik G. Dohlman
Keyword(s):  
G Protein ◽  
Sequence Similarity ◽  
Transmembrane Helix ◽  
Binding Pocket ◽  
Receptor Activation ◽  
Transmembrane Receptors ◽  
Domains Of Life ◽  
G Protein Coupled ◽  
Ionizable Groups

Seven-transmembrane receptors (7TMRs) have evolved in prokaryotes and eukaryotes over hundreds of millions of years. Comparative structural analysis suggests that these receptors may share a remote evolutionary origin, despite their lack of sequence similarity. Here we used structure-based computations to compare 221 7TMRs from all domains of life. Unexpectedly, we discovered that these receptors contain spatially conserved networks of buried ionizable groups. In microbial 7TMRs these networks are used to pump ions across the cell membrane in response to light. In animal 7TMRs, which include light- and ligand-activated G protein-coupled receptors (GPCRs), homologous networks were found to be characteristic of activated receptor conformations. These networks are likely relevant to receptor function because they connect the ligand-binding pocket of the receptor to the nucleotide-binding pocket of the G protein. We propose that agonist and G protein binding facilitate the formation of these electrostatic networks and promote important structural rearrangements such as the displacement of transmembrane helix-6. We anticipate that robust classification of activated GPCR structures will aid the identification of ligands that target activated GPCR structural states.

scholarly journals Correlated Motions of Conserved Polar Motifs Lay out a Plausible Mechanism of G Protein-Coupled Receptor Activation

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 670
Author(s):  
Argha Mitra ◽  
Arijit Sarkar ◽  
Márton Richárd Szabó ◽  
Attila Borics
Keyword(s):  
G Protein ◽  
Intracellular Signaling ◽  
Transmembrane Domain ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Structural Basis ◽  
Binding Interface ◽  
Gpcr Activation ◽  
Macroscopic Polarization ◽  
G Protein Coupled

Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism, on an entirely structural basis, gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the μ opioid receptor (MOP) revealed that transmission of external stimulus to the intracellular surface of the receptor is accompanied by subtle, concerted movements of highly conserved polar amino acid side chains along the 7th transmembrane helix. This may entail the rearrangement of polar species and the shift of macroscopic polarization in the transmembrane domain, triggered by agonist binding. Based on our observations and numerous independent indications, we suggest amending the widely accepted theory that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface.

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