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.

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 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.

G-protein-coupled receptor dynamics: dimerization and activation models compared with experiment

2012 ◽  
Vol 40 (2) ◽  
pp. 394-399 ◽  
Author(s):  
Bruck Taddese ◽  
Lisa M. Simpson ◽  
Ian D. Wall ◽  
Frank E. Blaney ◽  
Nathan J. Kidley ◽  
...  
Keyword(s):  
G Protein ◽  
Adrenergic Receptor ◽  
Transmembrane Helix ◽  
Active State ◽  
Toggle Switch ◽  
X Ray ◽  
Active Model ◽  
Β2 Adrenergic Receptor ◽  
Implicit And Explicit ◽  
G Protein Coupled

Our previously derived models of the active state of the β2-adrenergic receptor are compared with recently published X-ray crystallographic structures of activated GPCRs (G-protein-coupled receptors). These molecular dynamics-based models using experimental data derived from biophysical experiments on activation were used to restrain the receptor to an active state that gave high enrichment for agonists in virtual screening. The β2-adrenergic receptor active model and X-ray structures are in good agreement over both the transmembrane region and the orthosteric binding site, although in some regions the active model is more similar to the active rhodopsin X-ray structures. The general features of the microswitches were well reproduced, but with minor differences, partly because of the unexpected X-ray results for the rotamer toggle switch. In addition, most of the interacting residues between the receptor and the G-protein were identified. This analysis of the modelling has also given important additional insight into GPCR dimerization: re-analysis of results on photoaffinity analogues of rhodopsin provided additional evidence that TM4 (transmembrane helix 4) resides at the dimer interface and that ligands such as bivalent ligands may pass between the mobile helices. A comparison, and discussion, is also carried out between the use of implicit and explicit solvent for active-state modelling.

scholarly journals Kinetic analysis of ASIC1a delineates conformational signaling from proton-sensing domains to the channel gate

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Sabrina Vullo ◽  
Nicolas Ambrosio ◽  
Jan P Kucera ◽  
Olivier Bignucolo ◽  
Stephan Kellenberger
Keyword(s):  
Ion Channels ◽  
Kinetic Analysis ◽  
Conformational Changes ◽  
Transmembrane Helix ◽  
Activation Mechanism ◽  
Pain Sensation ◽  
Channel Activation ◽  
Channel Pore ◽  
Acid Sensing Ion Channels ◽  
Channel Gate

Acid-sensing ion channels (ASICs) are neuronal Na+ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.

scholarly journals Conformational changes in the G protein Gs induced by the β2 adrenergic receptor

Nature ◽  
2011 ◽  
Vol 477 (7366) ◽  
pp. 611-615 ◽  
Author(s):  
Ka Young Chung ◽  
Søren G. F. Rasmussen ◽  
Tong Liu ◽  
Sheng Li ◽  
Brian T. DeVree ◽  
...  
Keyword(s):  
G Protein ◽  
Conformational Changes ◽  
Adrenergic Receptor ◽  
Β2 Adrenergic Receptor

scholarly journals Analysis of full and partial agonists binding to β2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes

2009 ◽  
Vol 22 (4) ◽  
pp. 307-318 ◽  
Author(s):  
Vsevolod Katritch ◽  
Kimberly A. Reynolds ◽  
Vadim Cherezov ◽  
Michael A. Hanson ◽  
Christopher B. Roth ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Adrenergic Receptor ◽  
Transmembrane Helix ◽  
Partial Agonists ◽  
Β2 Adrenergic Receptor

scholarly journals Structural insights into ligand efficacy and activation of the glucagon receptor

2019 ◽  
Author(s):  
Daniel Hilger ◽  
Kaavya Krishna Kumar ◽  
Hongli Hu ◽  
Mie Fabricius Pedersen ◽  
Lise Giehm ◽  
...  
Keyword(s):  
G Protein ◽  
Partial Agonist ◽  
Transmembrane Helix ◽  
Peptide Hormone ◽  
Receptor Activation ◽  
Glucagon Receptor ◽  
Structural Framework ◽  
Class B ◽  
Treatment Of Diabetes ◽  
Sugar Levels

AbstractThe glucagon receptor family comprises Class B G protein-coupled receptors (GPCRs) that play a crucial role in regulating blood sugar levels. Receptors of this family represent important therapeutic targets for the treatment of diabetes and obesity. Despite intensive structural studies, we only have a poor understanding of the mechanism of peptide hormone-induced Class B receptor activation. This process involves the formation of a sharp kink in transmembrane helix 6 that moves out to allow formation of the nucleotide-free G protein complex. Here, we present the cryo-EM structure of the glucagon receptor (GCGR), a prototypical Class B GPCR, in complex with an engineered soluble glucagon derivative and the heterotrimeric G-protein, Gs. Comparison with the previously determined crystal structures of GCGR bound to a partial agonist reveals a structural framework to explain the molecular basis of ligand efficacy that is further supported by mutagenesis data.

scholarly journals Molecular insights into phosphorylation-induced allosteric conformational changes in β2-adrenergic receptor

2021 ◽  
Author(s):  
Midhun K Madhu ◽  
Annesha Debroy ◽  
Rajesh K. Murarka
Keyword(s):  
G Protein ◽  
Conformational Changes ◽  
Adrenergic Receptor ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Specific Binding ◽  
Experimental Studies ◽  
Residue Interaction ◽  
Β2 Adrenergic Receptor ◽  
Experimental Findings

The large conformational flexibility of G protein-coupled receptors (GPCRs) has been a puzzle in structural and pharmacological studies for the past few decades. Apart from structural rearrangements induced by ligands, enzymatic phosphorylations by GPCR kinases (GRKs) at the carboxy-terminal tail (C-tail) of a GPCR also makes conformational alterations to the transmembrane helices and facilitates the binding of one of its transducer proteins named β-arrestin. Phosphorylation-induced conformational transition of the receptor that causes specific binding to β-arrestin but prevents the association of other transducers such as G proteins lacks atomistic understanding and is elusive to experimental studies. Using microseconds of all-atom conventional and Gaussian accelerated molecular dynamics (GaMD) simulations, we investigate the allosteric mechanism of phosphorylation induced-conformational changes in β2-adrenergic receptor, a well-characterized GPCR model system. Free energy profiles reveal that the phosphorylated receptor samples a new conformational state in addition to the canonical active state corroborating with recent nuclear magnetic resonance experimental findings. The new state has a smaller intracellular cavity that is likely to accommodate β-arrestin better than G protein. Using contact map and inter-residue interaction energy calculations, we found the phosphorylated C-tail adheres to the cytosolic surface of the transmembrane domain of the receptor. Transfer entropy calculations show that the C-tail residues drive the correlated motions of TM residues, and the allosteric signal is relayed via several residues at the cytosolic surface. Our results also illustrate how the redistribution of inter-residue nonbonding interaction couples with the allosteric communication from the phosphorylated C-tail to the transmembrane. Atomistic insight into phosphorylation-induced β-arrestin specific conformation is therapeutically important to design drugs with higher efficacy and fewer side effects. Our results therefore open novel opportunities to fine-tune β-arrestin bias in GPCR signaling.

scholarly journals Energy landscapes reveal agonist control of GPCR activation via microswitches

2019 ◽  
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

Sign in / Sign up

Export Citation Format

Share Document