Biology subjects

Selent, J.

Publications and source records attributed to Selent, J..

18 recordsLinked to original sources

bioRxiv2026

Dynamic Pocketome of Trace Amine-Associated Receptors

Trace amine-associated receptors (TAARs) are class A GPCRs that span two distinct physiological roles: TAAR1 is a CNS drug target, whereas TAAR2 to TAAR9 detect volatile amines in the olfactory epithelium. Recent experimental structures resolve their architecture and ligand-binding mode, but capture only static snapshots, which cannot address how the binding site and the overall pocketome respond to ligand binding. Here, we present a simulation library comprising 26 experimental structures of four human and murine genes in the apo and holo states, each in triplicate (total aggregate time of 156 microseconds). Cavities were detected and analysed across the entire receptor surface throughout each trajectory. Orthosteric changes did not follow a single direction when comparing the states: apo sites were neither uniformly smaller nor uniformly more flexible than their holo counterparts, instead pointing to a receptor- specific ligand-receptor interplay that propagates beyond the orthosteric pocket. This plasticity is further highlighted by the size composition and stability of allosteric pockets, which proves that some regions are larger in the apo state while others are larger when a ligand is present. Resolving such trends required pockets to be comparable across trajectories, which a novel global identifier (GID) provides. Although agnostic to functional annotation, the GID recovered the orthosteric site as a single region in both states and matched pockets across replicates of the same receptor-state pair. The result is a dynamic pocketome map of the TAAR family obtained by an approach transferable to other membrane proteins.

bioinformatics↗

bioRxiv2025

Reverse-engineering B-Arrestin Bias in the d-Opioid Receptor

G protein-coupled receptors (GPCRs) form the largest family of cell-surface receptors and remain prime targets in drug discovery. A central challenge in modern GPCR drug discovery is understanding and exploiting biased agonism: the ability of ligands to favor signaling via therapeutically beneficial pathways while avoiding those that trigger side effects. Therefore, pinpointing the structural determinants of signaling bias is crucial for rational drug design. Biased agonists are particularly compelling for targeting opioid receptors, as in this family, ligands that limit {beta}-arrestin ({beta}-arr) recruitment are believed to preserve analgesia while reducing respiratory depression and addiction liabilities. Here, we use extensive all-atom molecular dynamics (MD) simulations to dissect signaling bias in the {delta}-opioid receptor ({delta}OR). Focusing on a receptor mutant with a strong {beta}-arr bias, we employed a reverse-engineering approach to reveal the conformational mechanisms that promote {beta}-arr recruitment. Building on these insights, engineer new mutations that reshape the receptors signaling profile. Importantly, this approach allowed us to pinpoint signaling bias to motions of a single microswitch and identify how structural receptor motions induced by the mutations and ligand contacts cooperate to promote a specific functional response. In this proof-of-concept study, we not only provide structural insights into {delta}OR pharmacology but also demonstrate how computational methods can be leveraged to probe structural mechanisms of signaling specificity across GPCRs, paving the way for the rational design of tailored receptor variants and novel, safer, and more effective therapeutics.

bioinformatics↗

bioRxiv2025

Molecular mechanism of naturally-encoded signaling-bias at the complement anaphylatoxin receptors

The conceptual framework of biased signaling has revolutionized our understanding of GPCR signaling and regulatory paradigms, and greatly impacted the efforts focused on the discovery of GPCR-targeted therapeutics. However, the mechanistic basis of biased signaling remains primarily defined based on synthetic ligands and receptor mutants with relatively limited progress in understanding naturally-encoded signaling-bias. Here, we present fundamental molecular and structural insights into naturally-encoded signaling-bias at the complement anaphylatoxin C5a receptors namely, C5aR1 and C5aR2. We first discover that C5a-d-Arg, the naturally-occurring version of C5a lacking the terminal arginine, exhibits robust G-protein signaling-bias at C5aR1, characterised by attenuated {beta}arr recruitment. This signaling-bias manifests in both cytokine release from primary human immune cells, and in vivo, during neutrophil mobilization. We combine the cryo-EM structures of C5a/C5a-d-Arg-C5aR1 complexes with MD simulation, site-directed mutagenesis, and cellular experiments to elucidate that the G-protein-bias exhibited by C5a-d-Arg results from a distinct orientation of TM7 and helix 8 in C5aR1 leading to inefficient GRK recruitment and receptor phosphorylation. Next, we determine the first cryo-EM structures of C5aR2, a naturally-encoded {beta}-arrestin-biased receptor, in an apo state, complexed with the natural agonists C5a and C5a-d-Arg, and three peptide agonists including a first-in-class, newly discovered C5aR2-selective agonist, R8Y. These structural snapshots reveal key differences between the binding of C5a and C5a- d-Arg to C5aR1 and C5aR2, and provide a molecular basis of functional specialization at these two receptors. Moreover, the structural insights also allow us to decipher the molecular basis of naturally-encoded signaling-bias at C5aR2 originating from a shallower cytoplasmic interface with hydrophobic interior pocket that is not permissive to efficient G-protein-coupling and activation. Finally, we also engineer and characterize loss-of-function and gain-of-function variants of C5aR1 and C5aR2, which in turn corroborate and validate the structural observations presented here. Collectively, our findings offer crucial insights into previously lacking molecular mechanisms of the naturally-encoded signaling-bias at GPCRs, which have broad implications not only for the general framework of biased-signaling, but also for novel therapeutic design.

biochemistry↗

bioRxiv2025

Integrative Biophysical Illumination of the 3D GPCRome Dynamics

Achieving high-resolution insights into protein dynamics remains a major challenge, particularly for membrane proteins such as G protein-coupled receptors (GPCRs) - a highly dynamic class of cell surface receptors and key drug targets. Here, we present an integrative strategy that bridges computational and experimental biophysical methods for probing protein dynamics. To illustrate its potential, we developed GPCRmd-NMR, a platform that synergistically combines molecular dynamics (MD) simulations with high-resolution nuclear magnetic resonance (NMR) spectroscopy across the 3D GPCRome. The resulting dataset maps over 20 billion NMR signals to more than 7 million conformational snapshots of GPCRs, enabling structure-resolved analysis at an unprecedented scale. Application across multiple GPCRs provides access to previously underexplored functional GPCR dynamics, receptor states, and sites, including microswitches and hidden ligand entrance gateways. Our integrated framework offers a powerful solution to long-standing challenges faced by both experimental and computational researchers. To support broad accessibility, GPCRmd-NMR is available as an open-access, web-based framework equipped with user-friendly analysis tools (https://www.gpcrmd.org/gpcrmd-nmr-tool) and is readily applicable to other dynamic protein families beyond GPCRs and other types of biophysical data.

bioinformatics↗

bioRxiv2025

Assessing the ligand native-like pose using a quantum mechanical-derived hydropathic score for protein-ligand complementarity

Elucidating the correct binding mode of drug-like compounds is crucial to disclose the molecular determinants that underline the recognition by the target protein and estimate the binding affinity, thus guiding the ensuing hit-to-lead optimization. However, the choice of the near-native binding pose in docking experiments remains a major hurdle. Assuming that the hydropathic complementarity principle is the major driving force in ligand-protein recognition, the suitability of simple hydropathicity-based scoring functions to reveal the near-native pose was examined. A benchmarking dataset of 1000 ligand-protein complexes purposely designed to encompass bioactive and decoy poses was used to assess the performance of 3D hydropathicity atomic descriptors derived from empirical and quantum mechanical models. This strategy led to a predictive accuracy of ca. 90% when the non-negligible influence of the conformational stress is also considered. The results reveal the need to leverage nonpolar/polar chemical features for the successful discrimination of the near-native pose.

bioinformatics↗

bioRxiv2025

An arginine switch drives the stepwise activation of β-arrestin

{beta}-arrestins ({beta}arrs) play a crucial role in regulating G protein-coupled receptor (GPCR) signaling and trafficking. Canonically, interactions of {beta}arr with the phosphorylated intracellular GPCR-tail induce a multi-step conformational transition that results in the activation of {beta}arr. Depending on the specific interaction pattern with the receptor, {beta}arrs adopt multiple conformational states, each tightly linked to a specific functional outcome of {beta}arr recruitment. Despite its physiological relevance, the structural determinants of {beta}arr activation remain poorly understood. Using a combination of molecular dynamics simulations, biochemical and cell-based experiments, we reveal how specific interactions with a prototypical GPCR promote the unbinding of the {beta}arr2 C-tail--a crucial step in arrestin activation. Importantly, we observe that the expulsion of the C-tail is promoted by the displacement of a conserved arginine residue (Arg394) within the {beta}arr polar core, which we dub "the arginine switch." Our study uncovers a previously unknown molecular switch that, upon engagement, destabilizes the polar core as a crucial step in the GPCR-induced {beta}arr activation.

biochemistry↗

bioRxiv2024

A Structural Mechanism for Noncanonical GPCRSignal Transduction in the Hedgehog Pathway

SUMMARY PARAGRAPHThe Hedgehog (Hh) signaling pathway is fundamental to embryogenesis, tissue homeostasis, and cancer. Hh signals are transduced via an unusual mechanism: upon agonist-induced phosphorylation, the noncanonical G protein-coupled receptor SMOOTHENED (SMO) binds the catalytic subunit of protein kinase A (PKA-C) and physically blocks its enzymatic activity. By combining computational structural approaches with biochemical and functional studies, we show that SMO mimics strategies prevalent in canonical GPCR and PKA signaling complexes, despite little sequence or secondary structural homology. An intrinsically disordered region of SMO binds the PKA-C active site, resembling the PKA regulatory subunit (PKA-R) / PKA-C holoenzyme, while the SMO transmembrane domain binds a conserved PKA-C interaction hub, similar to other GPCR-effector complexes. In contrast with prevailing GPCR signal transduction models, phosphorylation of SMO promotes intramolecular electrostatic interactions that stabilize key structural elements within the SMO cytoplasmic domain, thereby remodeling it into a PKA-inhibiting conformation. Our work provides a structural mechanism for a central step in the Hh cascade and defines a paradigm for disordered GPCR domains to transmit signals intracellularly.

biochemistry↗

bioRxiv2024

Location-biased β-arrestin conformations direct GPCR signaling

{beta}-arrestins are multifunctional intracellular proteins that regulate the desensitization, internalization and signaling of over 800 different G protein-coupled receptors (GPCRs) and interact with a diverse array of cellular partners1,2. Beyond the plasma membrane, GPCRs can initiate unique signaling cascades from various subcellular locations, a phenomenon known as "location bias"3,4. Here, we investigate how {beta}-arrestins direct location-biased signaling of the angiotensin II type I receptor (AT1R). Using novel bioluminescence resonance energy transfer (BRET) conformational biosensors and extracellular signal-regulated kinase (ERK) activity reporters, we reveal that in response to the endogenous agonist Angiotensin II and the {beta}-arrestin-biased agonist TRV023, {beta}-arrestin 1 and {beta}-arrestin 2 adopt distinct conformations across different subcellular locations, which are intricately linked to differential ERK activation profiles. We also uncover a population of receptor-free catalytically activated {beta}-arrestins in the plasma membrane that exhibits insensitivity to different agonists and promotes ERK activation on the plasma membrane independent of G proteins. These findings deepen our understanding of GPCR signaling complexity and also highlight the nuanced roles of {beta}-arrestins beyond traditional G protein pathways.

biochemistry↗

bioRxiv2024

Multiple triggers converge to preferential effector coupling in the CB2R through a complex allosteric communication network

G protein-coupled receptors are important therapeutic drug targets for a wide range of diseases. Their ability to preferentially engage specific signaling pathways over others can be exploited to design drugs that target only disease-associated pathways leading to an improved safety profile. However, the underlying molecular mechanisms for preferential pathway engagement are complex and remain largely elusive. To elucidate the multifaceted actions at the receptor level that lead to preferential coupling, we employ a combination of techniques. Our approach integrates systematic mutagenesis of the CB2R and comprehensive profiling of Gi2 and {beta}-arrestin1 engagements with computer simulations to track mutant-induced impacts on receptor dynamics. Most importantly, our research discloses multiple triggers on a complex allosteric communication network (ACN) that converge to preferential CB2R coupling by modulating evolutionary conserved motifs (e.g., CWxP, NPxxY, sodium binding site). Potent triggers for a preferential Gi2 response exhibit high levels of connectivity and are located in proximity to connections with high information transmission. Our insights highlight the complexity of GPCR signaling and can guide the rational design of drug candidates tailored to evoke specific functional responses that can enhance the precision and efficacy of therapeutic interventions.

cell biology↗

bioRxiv2024

Exploring human rare disease variants from a multidimensional perspective illuminates receptor - G protein coupling diversity

G protein-coupled receptors (GPCRs) are transmembrane proteins capable of detecting signals as diverse as odours, neurotransmitters, and hormones. Upon activation, receptor signalling converges onto four G protein subtypes to regulate intracellular responses. Therefore, variation in a single G protein gene can potentially impact the function of numerous receptors. In this work, we have performed a multidimensional study of rare disease mutations in Gs, a prototypical G protein. By integrating data from 3D structures, GPCR / G protein functional pairings, transcriptomics, biophysics, and molecular dynamics with systems pharmacology modelling, our results reveal why mutations impairing receptor / Gs coupling result in highly specific context-based signalling defects. Furthermore, we show that mutations leading to the same rare disease can alter different signal transduction steps, highlighting the importance of patient-specific treatment strategies. By closely dissecting G protein coupling, our study provides a blueprint to interrogate GPCR pathway signalling diversity in different (patho)physiological contexts.

systems biology↗

bioRxiv2023

Molecular insights into atypical modes of beta-arrestin interaction with seven transmembrane receptors

{beta}-arrestins are multifunctional proteins that are critically involved in regulating spatio-temporal aspects of GPCR signaling. The interaction of {beta}-arrestins with GPCRs is typically conceptualized in terms of receptor activation and phosphorylation primarily in the carboxyl-terminus. Interestingly however, there are several GPCRs that harbor majority of phosphorylation sites in their 3rd intracellular loop (ICL3) instead of carboxyl-terminus but still robustly engage {beta}-arrestins. Moreover, there are several 7TMRs that are now characterized as intrinsically-biased, {beta}-arrestin-coupled receptors (ACRs) due to lack of functional G-protein-coupling but robust {beta}-arrestin binding leading to functional outcomes. The molecular basis of {beta}-arrestin interaction and activation upon binding to these types of 7TMRs is currently elusive, and it represents a major knowledge gap in our current understanding of this signaling system. Here, we present seven cryo-EM structures of {beta}-arrestins in basal state, activated by the muscarinic M2 receptor (M2R) through its ICL3, and a {beta}-arrestin-coupled receptor known as decoy D6 receptor (D6R). These structural snapshots combined with biochemical, cellular, and biophysical experiments including HDX-MS and MD simulation provide novel insights into the ability of {beta}-arrestins to preferentially select specific phosphorylation patterns in the receptors, and also illuminate the structural diversity in 7TMR-{beta}-arrestin interaction. Surprisingly, we also observe that the carboxyl-terminus of {beta}-arrestin2 but not {beta}-arrestin1 undergoes structural transition from a {beta}-strand to -helix upon activation by D6R, which may preclude the core-interaction with the activated receptor. Taken together, our study elucidates previously unappreciated aspects of 7TMR-{beta}-arrestin interaction, and provides important mechanistic clues about how the two isoforms of {beta}-arrestins can recognize and regulate a large repertoire of GPCRs.

biochemistry↗

bioRxiv2023

Phosphorylation barcodes direct biased chemokine signaling at CXCR3

G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered {beta}-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.

biochemistry↗

bioRxiv2022

Single-molecule analysis of receptor-beta-arrestin interactions in living cells

{beta}-arrestin plays a key role in G protein-coupled receptor (GPCR) signaling and desensitization. Despite recent structural advances, the mechanisms that govern receptor-{beta}-arrestin interactions at the plasma membrane of living cells remain elusive. Here, we combine single-molecule microscopy with molecular dynamics simulations to dissect the complex sequence of events involved in {beta}-arrestin interactions with both receptors and the lipid bilayer. In contrast to the currently widely accepted model, we show that {beta}-arrestin spontaneously inserts into the lipid bilayer and transiently interacts with receptors via lateral diffusion on the plasma membrane. Moreover, we show that following receptor interaction, the plasma membrane stabilizes {beta}-arrestin in a membrane-bound, active-like conformation, allowing it to diffuse to clathrin coated pits separately from the activating receptor. These results challenge our current understanding of {beta}-arrestin function at the plasma membrane, revealing a new critical role for {beta}-arrestin pre-association with the lipid bilayer in facilitating its interactions with receptors and subsequent activation.

cell biology↗

bioRxiv2022

Allosteric modulation of GPCR-induced β-arrestin trafficking and signaling by a synthetic intrabody

Agonist-induced phosphorylation of G protein-coupled receptors (GPCRs) is a primary determinant of {beta}-arrestin ({beta}arr) recruitment and trafficking. For several GPCRs, such as the vasopressin type II receptor (V2R), which exhibit high affinity for {beta}arrs, agonist-stimulation first drives the translocation of {beta}arrs to the plasma membrane, followed by endosomal trafficking. We previously found that mutation of a single phosphorylation site in V2R (i.e., V2RT360A) results in near-complete loss of {beta}arr translocation to endosomes although {beta}arrs are robustly recruited to the plasma membrane. Here, we show that a synthetic intrabody referred to as intrabody30 (Ib30), which selectively recognizes an active-like {beta}arr1 conformation, rescues endosomal translocation of {beta}arr1 for V2RT360A. In addition, Ib30 also rescues agonist-induced ERK1/2 MAP kinase activation for V2RT360A to levels similar to that of the wild-type V2R. Molecular dynamics simulations reveal that Ib30 binding promotes active-like conformation in {beta}arr1 with respect to the inter-domain rotation. Interestingly, we also observe that Ib30 enhances the interaction of {beta}arr1 with {beta}2-adaptin, which provides a mechanistic basis for the ability of Ib30 to promote endosomal trafficking of {beta}arr1. Taken together, our data provide a novel mechanism to positively modulate the receptor-transducer-effector axis for GPCRs using intrabodies, which can potentially be integrated in the current paradigm of GPCR-targeted drug discovery. SignificanceThe interaction of G protein-coupled receptors (GPCRs) with {beta}-arrestins ({beta}arrs) is a critical step in their regulatory and signaling paradigms. While intrabodies that bind to GPCRs, G proteins and {beta}arrs have been utilized as biosensors and regulators of functional outcomes, allosteric targeting of receptor-transducer complexes to encode gain of function has not been documented so far. Here, we discover that a conformation-specific synthetic intrabody recognizing GPCR-bound {beta}arr1 can allosterically enhance endosomal trafficking of {beta}arr1 and agonist-induced ERK1/2 MAP kinase activation. This intrabody promotes an active-like {beta}arr1 conformation and enhances the interaction of {beta}2-adaptin with {beta}arr1. Our findings establish a conceptual framework to allosterically modulate protein-protein interactions in GPCR signaling cascade to modulate their trafficking and signaling responses.

biochemistry↗

bioRxiv2022

Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling

The heterogenous and dynamic constitution of the membrane fine-tunes signal transduction. In particular, the polyunsaturated fatty acid (PUFA) tails of phospholipids influence the biophysical properties of the membrane, production of second messengers, or membrane partitioning. Few evidence mostly originating from studies of rhodopsin suggest that PUFAs directly modulate the conformational dynamic of transmembrane proteins. However, whether such properties translate to other G protein-coupled receptors remains unclear. We focused on the dopamine D2 receptor (D2R), a main target of antipsychotics. Membrane enrichment in n-3, but not n-6, PUFAs potentiates ligand binding. Molecular dynamics simulations show that the D2R preferentially interacts with n-3 over n-6 PUFAs. Furthermore, even though this mildly affects signalling in heterologous systems, in vivo n-3 PUFA deficiency blunts the effects of D2R ligands. These results suggest that n-3 PUFAs act as allosteric modulators of the D2R and provide a putative mechanism for their potentiating effect on antipsychotic efficacy.

cell biology↗

bioRxiv2021

Entrectinib - a SARS-CoV-2 inhibitor in Human Lung Tissue (HLT) cells

Since the start of the COVID-19 outbreak, pharmaceutical companies and research groups have focused on the development of vaccines and antiviral drugs against SARS-CoV-2. Here, we apply a drug repurposing strategy to identify potential drug candidates that are able to block the entrance of the virus into human cells. By combining virtual screening with in vitro pseudovirus assays and antiviral assays in Human Lung Tissue (HLT) cells, we identify entrectinib as a promising antiviral drug. We found that part of the antiviral action of entrectinib is mediated by a non-specific mechanism, likely occurring at the viral membrane level. Such a profile could provide entrectinib with protection against the development of drug resistance by emerging SARS-CoV-2 variants.

cell biology↗

bioRxiv2019

Conformational sensors and domain-swapping reveal structural and functional differences between β-arrestin isoforms

Desensitization, signaling and trafficking of G protein-coupled receptors (GPCRs) are critically regulated by multifunctional adaptor proteins, {beta}-arrestins ({beta}arrs). The two isoforms of {beta}arrs ({beta}arr1 and 2) share a high degree of sequence and structural similarity, still however, they often mediate distinct functional outcomes in the context of GPCR signaling and regulation. A mechanistic basis for such a functional divergence of {beta}arr isoforms is still lacking. Using a set of complementary approaches including antibody fragment based conformational sensors, we discover structural differences between {beta}arr1 and 2 upon their interaction with activated and phosphorylated receptors. Interestingly, domain swapped chimeras of {beta}arrs display robust complementation in functional assays thereby, linking the structural differences between the receptor-bound {beta}arr1 and 2 with their divergent functional outcomes. Our findings reveal important insights into the ability of {beta}arr isoforms to drive distinct functional outcomes, and underscore the importance of integrating this aspect in the current framework of biased agonism.

biophysics↗

bioRxiv2019

Genetically encoded intrabody sensors illuminate structural and functional diversity in GPCR-β-arrestin complexes

Interaction of {beta}-arrestins ({beta}arrs) upon agonist-stimulation is a hallmark of G protein-coupled receptors (GPCRs) resulting in receptor desensitization, endocytosis and signaling. Although overall functional roles of {beta}arrs are typically believed to be conserved across different receptors, emerging data now clearly unveils receptor-specific functional contribution of {beta}arrs. The underlying mechanism however remains mostly speculative and represents a key missing link in our current understanding of GPCR signaling and regulatory paradigms. Here, we develop synthetic intrabody-based conformational sensors that help us visualize the assembly and trafficking of GPCR-{beta}arr1 complexes in cellular context for a broad set of receptors with spatio-temporal resolution. Surprisingly, these conformational sensors reveal a previously unappreciated level of diversity in GPCR-{beta}arr complexes that extends beyond the current framework of affinity-based classification and phosphorylation-code-based interaction patterns. More importantly, this conformational diversity arising from spatial signature of phosphorylation sites manifests directly in the form of distinct functional outcomes, including even opposite contribution of {beta}arrs in signal-transduction for different receptors. Taken together, these findings uncover that despite an overall similar interaction and trafficking patterns; critical structural and functional differences exist in {beta}arr complexes for different GPCRs that define and fine-tune receptor-specific downstream responses.

cell biology↗