α1A-adrenoceptor inverse agonists and agonists modulate receptor signalling through a conformational selection mechanism

AbstractG-Protein Coupled Receptors (GPCRs) transmit signals across the cell membrane via an allosteric network from the ligand-binding site to the G-protein binding site via a series of conserved microswitches. Crystal structures of GPCRs provide snapshots of inactive and active states, but poorly describe the conformational dynamics of the allosteric network that underlies GPCR activation. Here we analyse the correlation between ligand binding and receptor conformation of the α1A-adrenoceptor, known for stimulating smooth muscle contraction in response to binding noradrenaline. NMR of 13CεH3-methionine labelled α1A-adrenoreceptor mutants, each exhibiting differing signalling capacities, revealed how different classes of ligands modulate receptor conformational equilibria. 13CεH3-methionine residues near the microswitches revealed distinct states that correlated with ligand efficacies, supporting a conformational selection mechanism. We propose that allosteric coupling between the microswitches controls receptor conformation and underlies the mechanism of ligand modulation of GPCR signalling in cells.

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Probing the correlation between ligand efficacy and conformational diversity at the α1A-adrenoreceptor reveals allosteric coupling of its microswitches

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.012842 ◽

2020 ◽

Vol 295 (21) ◽

pp. 7404-7417 ◽

Cited By ~ 3

Author(s):

Feng-Jie Wu ◽

Lisa M. Williams ◽

Alaa Abdul-Ridha ◽

Avanka Gunatilaka ◽

Tasneem M. Vaid ◽

...

Keyword(s):

Ligand Binding ◽

Binding Site ◽

G Protein ◽

Conformational Dynamics ◽

Smooth Muscle Contraction ◽

Allosteric Coupling ◽

Gpcr Activation ◽

Methionine Residues ◽

G Protein Coupled ◽

Receptor Conformation

G protein–coupled receptors (GPCRs) use a series of conserved microswitches to transmit signals across the cell membrane via an allosteric network encompassing the ligand-binding site and the G protein-binding site. Crystal structures of GPCRs provide snapshots of their inactive and active states, but poorly describe the conformational dynamics of the allosteric network that underlies GPCR activation. Here, we analyzed the correlation between ligand binding and receptor conformation of the α1A-adrenoreceptor, a GPCR that stimulates smooth muscle contraction in response to binding noradrenaline. NMR of [13CϵH3]methionine-labeled α1A-adrenoreceptor variants, each exhibiting differing signaling capacities, revealed how different classes of ligands modulate the conformational equilibria of this receptor. [13CϵH3]Methionine residues near the microswitches exhibited distinct states that correlated with ligand efficacies, supporting a conformational selection mechanism. We propose that allosteric coupling among the microswitches controls the conformation of the α1A-adrenoreceptor and underlies the mechanism of ligand modulation of GPCR signaling in cells.

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Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190708103132 ◽

2020 ◽

Vol 16 (4) ◽

pp. 451-459 ◽

Cited By ~ 1

Author(s):

Fortunatus C. Ezebuo ◽

Ikemefuna C. Uzochukwu

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Binding Energy ◽

Binding Site ◽

Conformational Dynamics ◽

Side Chain ◽

Amino Acid Residues ◽

Conformational Selection ◽

Hybrid Mechanism ◽

Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

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Generation of an agonistic binding site for blockers of the M3 muscarinic acetylcholine receptor

Biochemical Journal ◽

10.1042/bj20071366 ◽

2008 ◽

Vol 412 (1) ◽

pp. 103-112 ◽

Cited By ~ 10

Author(s):

Doreen Thor ◽

Angela Schulz ◽

Thomas Hermsdorf ◽

Torsten Schöneberg

Keyword(s):

Ligand Binding ◽

Binding Site ◽

G Protein ◽

Binding Sites ◽

Expression System ◽

Muscarinic Acetylcholine Receptor ◽

Intracellular Loop ◽

Inverse Agonists ◽

Yeast Expression System ◽

High Affinity

GPCRs (G-protein-coupled receptors) exist in a spontaneous equilibrium between active and inactive conformations that are stabilized by agonists and inverse agonists respectively. Because ligand binding of agonists and inverse agonists often occurs in a competitive manner, one can assume an overlap between both binding sites. Only a few studies report mutations in GPCRs that convert receptor blockers into agonists by unknown mechanisms. Taking advantage of a genetically modified yeast strain, we screened libraries of mutant M3Rs {M3 mAChRs [muscarinic ACh (acetylcholine) receptors)]} and identified 13 mutants which could be activated by atropine (EC50 0.3–10 μM), an inverse agonist on wild-type M3R. Many of the mutations sensitizing M3R to atropine activation were located at the junction of intracellular loop 3 and helix 6, a region known to be involved in G-protein coupling. In addition to atropine, the pharmacological switch was found for other M3R blockers such as scopolamine, pirenzepine and oxybutynine. However, atropine functions as an agonist on the mutant M3R only when expressed in yeast, but not in mammalian COS-7 cells, although high-affinity ligand binding was comparable in both expression systems. Interestingly, we found that atropine still blocks carbachol-induced activation of the M3R mutants in the yeast expression system by binding at the high-affinity-binding site (Ki ∼10 nM). Our results indicate that blocker-to-agonist converting mutations enable atropine to function as both agonist and antagonist by interaction with two functionally distinct binding sites.

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A common ligand-binding site in G-protein coupled receptors

Peptides for the New Millennium - American Peptide Symposia ◽

10.1007/0-306-46881-6_229 ◽

2006 ◽

pp. 581-582

Author(s):

Laerte Oliveira ◽

Gerrit Vriend ◽

Antonio C.M. Paiva

Keyword(s):

Ligand Binding ◽

Binding Site ◽

G Protein ◽

G Protein Coupled Receptors ◽

Ligand Binding Site ◽

G Protein Coupled

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A structural basis for how ligand binding site changes can allosterically regulate GPCR signaling and engender functional selectivity

Science Signaling ◽

10.1126/scisignal.aaw5885 ◽

2020 ◽

Vol 13 (617) ◽

pp. eaaw5885 ◽

Cited By ~ 5

Author(s):

Marta Sanchez-Soto ◽

Ravi Kumar Verma ◽

Blair K. A. Willette ◽

Elizabeth C. Gonye ◽

Annah M. Moore ◽

...

Keyword(s):

Ligand Binding ◽

Binding Site ◽

G Protein ◽

Structural Basis ◽

Protein Signaling ◽

Ligand Binding Site ◽

Intracellular Loop ◽

Gpcr Signaling ◽

Biased Signaling ◽

Dynamics Simulations

Signaling bias is the propensity for some agonists to preferentially stimulate G protein–coupled receptor (GPCR) signaling through one intracellular pathway versus another. We previously identified a G protein–biased agonist of the D2 dopamine receptor (D2R) that results in impaired β-arrestin recruitment. This signaling bias was predicted to arise from unique interactions of the ligand with a hydrophobic pocket at the interface of the second extracellular loop and fifth transmembrane segment of the D2R. Here, we showed that residue Phe189 within this pocket (position 5.38 using Ballesteros-Weinstein numbering) functions as a microswitch for regulating receptor interactions with β-arrestin. This residue is relatively conserved among class A GPCRs, and analogous mutations within other GPCRs similarly impaired β-arrestin recruitment while maintaining G protein signaling. To investigate the mechanism of this signaling bias, we used an active-state structure of the β2-adrenergic receptor (β2R) to build β2R-WT and β2R-Y1995.38A models in complex with the full β2R agonist BI-167107 for molecular dynamics simulations. These analyses identified conformational rearrangements in β2R-Y1995.38A that propagated from the extracellular ligand binding site to the intracellular surface, resulting in a modified orientation of the second intracellular loop in β2R-Y1995.38A, which is predicted to affect its interactions with β-arrestin. Our findings provide a structural basis for how ligand binding site alterations can allosterically affect GPCR-transducer interactions and result in biased signaling.

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Coactivator Proteins as Determinants of Estrogen Receptor Structure and Function: Spectroscopic Evidence for a Novel Coactivator-Stabilized Receptor Conformation

Molecular Endocrinology ◽

10.1210/me.2004-0458 ◽

2005 ◽

Vol 19 (6) ◽

pp. 1516-1528 ◽

Cited By ~ 34

Author(s):

Anobel Tamrazi ◽

Kathryn E. Carlson ◽

Alice L. Rodriguez ◽

John A. Katzenellenbogen

Keyword(s):

Estrogen Receptor ◽

Ligand Binding ◽

Conformational Dynamics ◽

Development Of Resistance ◽

Coactivator Binding Inhibitors ◽

High Concentrations ◽

Vitro Model ◽

And Function ◽

Receptor Conformation

Abstract The direct regulation of gene transcription by nuclear receptors, such as the estrogen receptor (ER), involves not just ligand and DNA binding but the recruitment of coregulators. Typically, recruitment of p160 coactivator proteins to agonist-liganded ER is considered to be unidirectional, with ligand binding stabilizing an ER ligand binding domain (LBD) conformation that favors coactivator interaction. Using fluorophore-labeled ERα-LBDs, we present evidence for a pronounced stabilization of ER conformation that results from coactivator binding, manifest by decreased ER sensitivity to proteases and reduced conformational dynamics, as well as for the formation of a novel coactivator-stabilized (costabilized) receptor conformation, that can be conveniently monitored by the generation of an excimer emission from pyrene-labeled ERα-LBDs. This costabilized conformation may embody features required to support ER transcriptional activity. Different classes of coactivator proteins combine with estrogen agonists of different structure to elicit varying degrees of this receptor stabilization, and antagonists and coactivator binding inhibitors disfavor the costabilized conformation. Remarkably, high concentrations of coactivators engender this conformation even in apo- and antagonist-bound ERs (more so with selective ER modulators than with pure antagonists), providing an in vitro model for the development of resistance to hormone therapy in breast cancer.

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Energy landscapes reveal agonist control of GPCR activation via microswitches

10.1101/627026 ◽

2019 ◽

Cited By ~ 2

Author(s):

Oliver Fleetwood ◽

Pierre Matricon ◽

Jens Carlsson ◽

Lucie Delemotte

Keyword(s):

Binding Site ◽

G Protein ◽

Conformational Changes ◽

Energy Landscapes ◽

Agonist Binding ◽

Transmembrane Region ◽

Gpcr Activation ◽

Simulation Protocol ◽

Dynamics Simulations ◽

Intracellular Region

AbstractAgonist binding to G protein-coupled receptors (GPCRs) leads to conformational changes in the transmembrane region that activate cytosolic signaling pathways. Al-though high resolution structures of different receptor states are available, atomistic details of the allosteric signalling across the membrane remain elusive. We calculated free energy landscapes of the β2 adrenergic receptors activation using atomistic molecular dynamics simulations in an optimized string of swarms framework, which sheds new light on how microswitches govern the equilibrium between conformational states. Contraction of the extracellular binding site in the presence of the agonist BI-167107 is obligatorily coupled to conformational changes in a connector motif located in the core of the transmembrane region. The connector is probabilistically coupled to the conformation of the intracellular region. An active connector promotes desolvation of a buried cavity, a twist of the conserved NPxxY motif, and an interaction between two conserved tyrosines in transmembrane helices 5 and 7 (Y-Y motif), which leads to a larger population of active-like states at the G protein binding site. This coupling is augmented by protonation of the strongly conserved Asp792.50. The agonist binding site hence communicates with the intracellular region via a cascade of locally connected microswitches. Characterization of these can be used to understand how ligands stabilize distinct receptor states and contribute to development drugs with specific signaling properties. The developed simulation protocol is likely transferable to other class A GPCRs.Graphical TOC Entry

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

10.1101/2021.09.15.460528 ◽

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.

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