Prediction and targeting of GPCR oligomer interfaces

Expression and purification of Gpr33, a candidate membrane receptor for cortisol

Membrane receptors for the sex steroids progesterone, estrogen, and androgens have been identified, and membrane receptors for the adrenocortical steroids glucocorticoids and mineralocorticoids have also been suggested to exist but have not yet been identified. Because of their diverse physiological actions, corticoids have been artificially synthesized and widely used as steroid drugs, and membrane receptors for corticoids are expected to become new drug targets. Therefore, there is a need to identify membrane glucocorticoid receptors (mGRs). To screen candidate mGRs, we identified two common amino acid sequences between membrane progesterone receptor (mPR) and membrane estrogen receptor (mER). We searched the protein database PROSITE for these common sequences. This led us to select GPR33 as a candidate mGR. To determine whether GPR33 can bind to corticoids, recombinant mouse Gpr33 (MGpr33) was expressed in Pichia yeast. Recombinant MGpr33, which was present as an oligomer in the membrane fraction, was found to bind to cortisol (hydrocortisone), a type of glucocorticoid. These results verified that GPR33 is a candidate membrane corticoid receptor. Denaturation by urea resulted in the generation of MGpr33 monomers and reduced the cortisol-binding activity of MGpr33, suggesting that MGpr33 may function as an oligomer. MGpr33 oligomers purified by two-step column chromatography using a Ni-NTA column and a Sephacryl S-300 gel filtration column retained the ability to bind cortisol. The purified fraction bound to cortisol with a Kd = 11.9 nM and Bmax = 1.19 nM. Furthermore, MGpr33 specifically bound to cortisol but not to estradiol, progesterone or testosterone. MGpr33 was found to be a candidate mGR that may function as an oligomer.

Research approaches for exploring the hidden conversations of G protein-coupled receptor transactivation

G protein-coupled receptor (GPCR) signaling is a crucial physiological mechanism that encompasses a wide range of signaling phenomena. Although traditional GPCR signaling involves G protein or arrestin-related activation, other modes such as biphasic activation, dimer or oligomeric activation, and transactivation have also been observed. Herein, we focus on the increasingly recognized process of GPCR-transactivation. Transactivation refers to the ability of GPCRs to activate other receptor types, especially receptor tyrosine kinases, without engaging their own specific ligands. This cross-talk between GPCRs and other receptors facilitates the integration of multiple signaling pathways, thereby regulating diverse cellular responses, which underscores its physiological significance. In this review, we provide a comprehensive overview of the role of GPCR-transactivation in physiology. We also discuss the growing interest in this field and examine the various tools available for studying transactivation. Additionally, we highlight recent advancements in emerging tools and their application to GPCR-transactivation research. Finally, we propose future research directions and consider the potential impact of new technologies in this rapidly evolving field. SIGNIFICANCE STATEMENT: G protein-coupled receptor transactivation plays a key role in integrating multiple signaling pathways by activating other proteins, like receptor tyrosine kinases, without binding their specific ligands. Here, we focus on the significance of transactivation and the various approaches used to study this phenomenon.

GPCR oligomerization across classes: A2AR-mediated regulation of mGlu5R activation

The adenosine A2A receptor (A2AR), a class A GPCR, is a known player in neurological diseases, including Parkinson's disease and Alzheimer's disease, and is also implicated in SARS-CoV-2 infection. Recent studies have revealed its oligomerization with metabotropic glutamate receptor type 5 (mGlu5R), a class C G protein coupled receptor (GPCR) that exists in the homodimeric form. Simultaneous activation of both receptors synergistically enhances mGlu5R-mediated effects in the hippocampus. Despite their importance, the molecular mechanisms governing these interactions remain unclear. In this study, we used molecular modelling techniques, including molecular docking, extensive molecular dynamics (MD) simulations, and detailed analysis, to elucidate the interactions between mGlu5R and A2AR in the inactive and active states. Our findings provide molecular-level insights into the permissive role of A2AR in mGlu5R activation, demonstrating that the inactive A2AR interface within the oligomer blocks the mGlu5R transmembrane helix 6 (TM6), which is crucial for activation. Upon A2AR activation, the oligomer interface undergoes conformational rearrangement, exposing mGlu5R-TM6 and allowing for mGlu5R activation. Furthermore, we identified a pivotal role of the mGlu5R-TM4:A2AR-TM4 interface in facilitating mGlu5R activation. These results highlight the intricate architecture of the mGlu5R:A2AR oligomer, advancing our understanding of GPCR oligomerization and its regulatory mechanisms on receptor activity.

Early Events in β2AR Dimer Dynamics Mediated by Activation-Related Microswitches

G-Protein-Coupled Receptors (GPCRs) make up around 3-4% of the human genome and are the targets of one-third of FDA-approved drugs. GPCRs typically exist as monomers but also aggregate to form higher-order oligomers, including dimers. β2AR, a pharmacologically relevant GPCR, is known to be targeted for the treatment of asthma and cardiovascular diseases. The activation of β2AR at the dimer level remains under-explored. In the current study, molecular dynamics (MD) simulations have been performed to understand activation-related structural changes in β2AR at the dimer level. The transition from inactive to active and vice versa has been studied by starting the simulations in the apo, agonist-bound, and inverse agonist-bound β2AR dimers for PDB ID: 2RH1 and PDB ID: 3P0G, respectively. A cumulative total of around 21-μs simulations were performed. Residue-based distances, RMSD, and PCA calculations suggested that either of the one monomer attained activation-related features for the apo and agonist-bound β2AR dimers. The TM5 and TM6 helices within the two monomers were observed to be in significant variation in all the simulations. TM5 bulge and proximity of TM2 and TM7 helices may be contributing to one of the early events in activation. The dimeric interface between TM1 and helix 8 were observed to be well maintained in the apo and agonist-bound simulations. The presence of inverse agonists favored inactive features in both the monomers. These key features of activation known for monomers were observed to have an impact on β2AR dimers, thereby providing an insight into the oligomerization mechanism of GPCRs.

Utility of FRET in studies of membrane protein oligomerization: The concept of the effective dissociation constant

The activity of many membrane receptors is controlled through their lateral association into dimers or higher-order oligomers. Although Förster resonance energy transfer (FRET) measurements have been used extensively to characterize the stability of receptor dimers, the utility of FRET in studies of larger oligomers has been limited. Here we introduce an effective equilibrium dissociation constant that can be extracted from FRET measurements for EphA2, a receptor tyrosine kinase (RTK) known to form active oligomers of heterogeneous distributions in response to its ligand ephrinA1-Fc. The newly introduced effective equilibrium dissociation constant has a well-defined physical meaning and biological significance. It denotes the receptor concentration for which half of the receptors are monomeric and inactive, and the other half are associated into oligomers and are active, irrespective of the exact oligomer size. This work introduces a new dimension to the utility of FRET in studies of membrane receptor association and signaling in the plasma membrane.

Chemokine Binding to Tenascin-C Influences Chemokine-Induced Immune Cell Migration

Tenascin-C (TNC) is a complex glycoprotein of the extracellular matrix (ECM) involved in a plethora of (patho-)physiological processes, such as oncogenesis and inflammation. Since chemokines play an essential role in both disease processes, we have investigated here the binding of TNC to some of the key chemokines, namely CCL2, CCL26, CXCL8, CXCL10, and CXCL12. Thereby, a differential chemokine-TNC binding pattern was observed, with CCL26 exhibiting the highest and CCL2 the lowest affinity for TNC. Heparan sulfate (HS), another member of the ECM, proved to be a similarly high-affinity ligand of TNC, with a Kd value of 730 nM. Chemokines use glycosa-minoglycans such as HS as co-receptors to induce immune cell migration. Therefore, we assumed an influence of TNC on immune cell chemotaxis due to co-localization within the ECM. CCL26- and CCL2-induced mobilization experiments of eosinophils and monocytes, respectively, were thus performed in the presence and the absence of TNC. Pre-incubation of the immune cells with TNC resulted in a 3.5-fold increase of CCL26-induced eosinophil chemotaxis, whereas a 1.3-fold de-crease in chemotaxis was observed when monocytes were pre-incubated with CCL2. As both chemokines have similar HS binding but different TNC binding affinities, we speculate that TNC acts as an attenuator in monocyte and as an amplifier in eosinophil mobilization by impeding CCL2 from binding to HS on the one hand, and by reinforcing CCL26 to bind to HS on the other hand.

Therapeutic potential of opioid receptor heteromers in chronic pain and associated comorbidities

Chronic pain affects 20% to 45% of the global population and is often associated with the development of anxio-depressive disorders. Treatment of this debilitating condition remains particularly challenging with opioids prescribed to alleviate moderate to severe pain. However, despite strong antinociceptive properties, numerous adverse effects limit opioid use in the clinic. Moreover, opioid misuse and abuse have become a major health concern worldwide. This prompted efforts to design original strategies that would efficiently and safely relieve pain. Targeting of opioid receptor heteromers is one of these. This review summarizes our current knowledge on the role of heteromers involving opioid receptors in the context of chronic pain and anxio-depressive comorbidities. It also examines how heteromerization in native tissue affects ligand binding, receptor signalling and trafficking properties. Finally, the therapeutic potential of ligands designed to specifically target opioid receptor heteromers is considered. LINKED ARTICLES: This article is part of a themed issue on Advances in Opioid Pharmacology at the Time of the Opioid Epidemic. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v180.7/issuetoc.

Beyond sequence: Structure-based machine learning

Recent breakthroughs in protein structure prediction demarcate the start of a new era in structural bioinformatics. Combined with various advances in experimental structure determination and the uninterrupted pace at which new structures are published, this promises an age in which protein structure information is as prevalent and ubiquitous as sequence. Machine learning in protein bioinformatics has been dominated by sequence-based methods, but this is now changing to make use of the deluge of rich structural information as input. Machine learning methods making use of structures are scattered across literature and cover a number of different applications and scopes; while some try to address questions and tasks within a single protein family, others aim to capture characteristics across all available proteins. In this review, we look at the variety of structure-based machine learning approaches, how structures can be used as input, and typical applications of these approaches in protein biology. We also discuss current challenges and opportunities in this all-important and increasingly popular field.

The M1 muscarinic receptor is present in situ as a ligand-regulated mixture of monomers and oligomeric complexes

Although it is appreciated that members of the large family of rhodopsin-like cell surface receptors can form dimeric or larger protein complexes when expressed at high levels in cultured cells, their organizational state within native cells and tissues of the body is largely unknown. We assessed this in neurons of the central nervous system by replacing the M₁ muscarinic acetylcholine receptor in mice with a form of this receptor with an added fluorescent protein. Receptor function was unaltered by this change, and the biophysical approach we used demonstrated that the receptor exists as a mixture of monomers and dimers or oligomers. Drug treatments that target this receptor promote its monomerization, which may have significance for receptor function.

The quaternary organization of rhodopsin-like G protein-coupled receptors in native tissues is unknown. To address this we generated mice in which the M₁ muscarinic acetylcholine receptor was replaced with a C-terminally monomeric enhanced green fluorescent protein (mEGFP)–linked variant. Fluorescence imaging of brain slices demonstrated appropriate regional distribution, and using both anti-M₁ and anti–green fluorescent protein antisera the expressed transgene was detected in both cortex and hippocampus only as the full-length polypeptide. M₁-mEGFP was expressed at levels equal to the M₁ receptor in wild-type mice and was expressed throughout cell bodies and projections in cultured neurons from these animals. Signaling and behavioral studies demonstrated M₁-mEGFP was fully active. Application of fluorescence intensity fluctuation spectrometry to regions of interest within M₁-mEGFP–expressing neurons quantified local levels of expression and showed the receptor was present as a mixture of monomers, dimers, and higher-order oligomeric complexes. Treatment with both an agonist and an antagonist ligand promoted monomerization of the M₁-mEGFP receptor. The quaternary organization of a class A G protein-coupled receptor in situ was directly quantified in neurons in this study, which answers the much-debated question of the extent and potential ligand-induced regulation of basal quaternary organization of such a receptor in native tissue when present at endogenous expression levels.

Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery

Great progress has been made over the past decade in understanding the structural, functional, and pharmacological diversity of lipid GPCRs. From the first determination of the crystal structure of bovine rhodopsin in 2000, much progress has been made in the field of GPCR structural biology. The extraordinary progress in structural biology and pharmacology of GPCRs, coupled with rapid advances in computational approaches to study receptor dynamics and receptor-ligand interactions, has broadened our comprehension of the structural and functional facets of the receptor family members and has helped usher in a modern age of structure-based drug design and development. First, we provide a primer on lipid mediators and lipid GPCRs and their role in physiology and diseases as well as their value as drug targets. Second, we summarize the current advancements in the understanding of structural features of lipid GPCRs, such as the structural variation of their extracellular domains, diversity of their orthosteric and allosteric ligand binding sites, and molecular mechanisms of ligand binding. Third, we close by collating the emerging paradigms and opportunities in targeting lipid GPCRs, including a brief discussion on current strategies, challenges, and the future outlook.

Neural network strategies for plasma membrane selection in fluorescence microscopy images

In recent years, there has been an explosion of fluorescence microscopy studies of live cells in the literature. The analysis of the images obtained in these studies often requires labor-intensive manual annotation to extract meaningful information. In this study, we explore the utility of a neural network approach to recognize, classify, and select plasma membranes in high-resolution images, thus greatly speeding up data analysis and reducing the need for personnel training for highly repetitive tasks. Two different strategies are tested: 1) a semantic segmentation strategy, and 2) a sequential application of an object detector followed by a semantic segmentation network. Multiple network architectures are evaluated for each strategy, and the best performing solutions are combined and implemented in the Recognition Of Cellular Membranes software. We show that images annotated manually and with the Recognition Of Cellular Membranes software yield identical results by comparing Förster resonance energy transfer binding curves for the membrane protein fibroblast growth factor receptor 3. The approach that we describe in this work can be applied to other image selection tasks in cell biology.

GPCR oligomerization as a target for antidepressants: Focus on GPR39

At present most of the evidence for the relevance of oligomerization for the pharmacology of depression comes from in vitro studies which identified oligomers, and from neuropsychopharmacological studies of receptors which participate in oligomerization. For example, behavioural and biochemical studies in knockout animals suggest that GPR39 may mediate the antidepressant action of monoaminergic antidepressants. We have recently found long-lasting antidepressant-like effects of GPR39 agonist, thus suggesting GPR39 as a target for the development of novel antidepressant drugs. In vitro studies have shown that GPR39 oligomerizes with other GPCRs. Oligomerization of GPR39 should thus be considered in relation to the development of new antidepressants targeting this receptor as well as antidepressants targeting other receptors that may form complexes with GPR39. Here, we summarize recent data suggestive of the importance of oligomerization for the pharmacology of depression and discuss approaches for validation of this phenomenon.

Structural Complexity and Plasticity of Signaling Regulation at the Melanocortin-4 Receptor

The melanocortin-4 receptor (MC4R) is a class A G protein-coupled receptor (GPCR), essential for regulation of appetite and metabolism. Pathogenic inactivating MC4R mutations are the most frequent cause of monogenic obesity, a growing medical and socioeconomic problem worldwide. The MC4R mediates either ligand-independent or ligand-dependent signaling. Agonists such as α-melanocyte-stimulating hormone (α-MSH) induce anorexigenic effects, in contrast to the endogenous inverse agonist agouti-related peptide (AgRP), which causes orexigenic effects by suppressing high basal signaling activity. Agonist action triggers the binding of different subtypes of G proteins and arrestins, leading to concomitant induction of diverse intracellular signaling cascades. An increasing number of experimental studies have unraveled molecular properties and mechanisms of MC4R signal transduction related to physiological and pathophysiological aspects. In addition, the MC4R crystal structure was recently determined at 2.75 Å resolution in an inactive state bound with a peptide antagonist. Underpinned by structural homology models of MC4R complexes simulating a presumably active-state conformation compared to the structure of the inactive state, we here briefly summarize the current understanding and key players involved in the MC4R switching process between different activity states. Finally, these perspectives highlight the complexity and plasticity in MC4R signaling regulation and identify gaps in our current knowledge.