Biology subjects

Gooley, P. R.

Publications and source records attributed to Gooley, P. R..

11 recordsLinked to original sources

bioRxiv2026

The rabies virus interferon antagonist P protein selectively modulates interferon signalling to inhibit antiviral gene expression while supporting proviral gene expression

Type-I IFNs mediate the principle antiviral response of cells by controlling the expression of hundreds of IFN-regulated genes (IRGs), many of which have antiviral functions. The best understood mediators of IFN signalling are STAT1 and STAT2, and STAT1/2-dependent gene induction is conventionally viewed as the primary outcome of type-I IFN signalling. To overcome the IFN response, viruses express proteins called IFN-antagonists, which target IFN signalling pathways (e.g. rabies virus P-protein (RABV-P) binds and inhibits IFN-activated STAT1/2) and so are typically considered to mediate shutdown of the IFN response. However, IFN signalling is not exclusively antiviral, with many IRGs reported to be required for or to facilitate infection by certain viruses. How viruses coordinate the apparent need to suppress certain antiviral IRGs, while presumably permitting the expression of others, including proviral IRGs is poorly defined. However, it has been shown that type-I IFN can activate multiple pathways other than classical STAT1/2, so discriminatory targeting of specific pathways by IFN-antagonists may enable highly selective regulation of distinct IRGs, dependent on the requirements of the specific virus. Here, we analyse the global effects of RABV-P protein on the IFN-regulated transcriptome. We confirm that IFN not only stimulates (IFN-stimulated genes, ISGs) but also represses (IFN-repressed genes, IRepGs) a large number of IRGs. Notably, our data indicate that RABV-P protein can antagonize both the IFN-dependent stimulation and repression of certain ISGs and IRepGs, without significantly impacting the expression of large proportion of IRGs. Antagonized ISGs included classical antiviral genes, while non-antagonized ISGs include genes with pro-viral effects on RABV. Transcription factor analysis indicated that RABV-P antagonizes STAT1/2-regulated IRGs, but not IRGs regulated by other pathways including MAP-kinase pathways, which are important to process such as cell survival and inflammatory response. These data indicate that selective modulation rather than global inhibition of IFN-signalling has beneficial outcomes for replication. The data also support the significance of IRepGs, and their modulation by IFN antagonists in viral infection. Significance StatementThe ability of viruses to evade immunity is critical to disease and so presents targets for the development of interventions. The principle antiviral response of cells is mediated by interferons (IFNs), which activate STAT proteins to induce hundreds of genes including antiviral genes. Viruses counter this by expressing IFN-antagonist proteins, many of which directly inhibit STATs. IFN-antagonists are typically considered to shut down IFN responses, but many IRGs have pro-viral functions. How viruses coordinate the apparent need to antagonise some IRGs but not others are poorly understood. Using a well-characterised viral IFN-antagonist, we find that by selectively targeting certain IFN-activated pathways, IFN-antagonists can inhibit effects of IFN on specific subsets of IRGs (including antiviral genes) without affecting others (including proviral genes); thus, IFN-antagonists may be redefined as selective IFN-modulators.

systems biology↗

bioRxiv2026

Rabies virus antagonizes interferon signaling by targeting phosphorylated STAT1 tetramers

AO_SCPLOWBSTRACTC_SCPLOWRabies virus phosphoprotein (P protein) antagonizes interferon signalling by selectively targeting activated STAT1 protein, but the structural basis for the selective recognition of activated STAT1 has remained unclear. Here we report cryo-EM structures of tyrosine-phosphorylated STAT1 (pY-STAT1) in complex with the C-terminal domain of P protein (P-CTD). P-CTD engages the pY-STAT1 tetramer through three discrete interfaces, contacting two DNA-binding domains within a pY-mediated STAT1 dimer and the N-terminal domain of a third STAT1 protomer. This binding mode explains how P-CTD selectively recognizes activated STAT1, occludes surfaces required for importin 5 and DNA binding, and stabilizes the compact tetrameric state, thereby restricting the conformational transition required for cooperative DNA binding. Cell-based assays further indicate that distinct P-CTD surfaces differentially contribute to antagonism of type I and type II interferon signalling. Further, by acting as an anchoring molecule, P-CTD also enabled structural elucidation of the complete STAT1 structures in the tetramer. Together, these data reveal critical mechanisms in viral immune evasion and pathogenesis, and fundamental innate immune signaling.

molecular biology↗

bioRxiv2025

The allosteric mechanism of G-protein-coupled receptors is induced fit, not conformational selection

The allosteric mechanism of G-protein-coupled receptors (GPCRs) involves a population shift from inactive to active receptor conformations in response to the binding of ligand agonists. Two possible kinetic mechanisms for this population shift are induced fit and conformational selection. The two mechanisms differ in the temporal sequence of binding events and conformational changes: Ligand bindings occurs prior to the change from the inactive to the active receptor conformation in the induced-fit mechanism, and after the conformational change in the conformational-selection mechanism. In this article, we discuss the current evidence from experiments that probe the binding kinetics of GPCRs to identify the allosteric mechanism. For the peptide-activated neurotensin receptor 1, the modeling of kinetic data from stopped-flow mixing experiments indicates an induced-fit mechanism 1. The conformational exchange rates of the induced-fit mechanism obtained from this modeling agree with rates measured by saturation transfer difference NMR experiments of the peptide-receptor complex, which corroborates the mechanism. For the small-molecule-activated {beta}2-andrenergic receptor, an induced-fit mechanism has been inferred from a comparison of ligand-association rates for the inactive and the active receptor conformation 2. A stabilization of the active receptor conformation by G proteins or nanobodies leads to a decrease of ligand association rates, which indicates that ligand binding occurs in the inactive conformation and, thus, prior to the change from the inactive to the active conformation as in the induced-fit mechanism. A structural explanation for the induced-fit mechanism of the {beta}2-andrenergic receptor is a closed lid over the binding site that blocks ligand entry in the active conformation. Since constriction and closing of the ligand-binding site in the active conformation is rather common for small-molecule-activated and peptide-activated GPCRs, induced fit likely is shared as allosteric mechanism by these GPCRs.

biophysics↗

bioRxiv2022

The dynamic nature of neurotensin receptor 1 (NTS1) allostery and signaling bias

The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13C{varepsilon}H3-methionine NMR spectroscopy to show that phosphatidylinositol-4,5-bisphosphate (PIP2) promotes transducer complexation not by dramatically altering the receptor structure but by strengthening long-range allosteric connections, in the form of correlated conformational kinetics, between the orthosteric pocket and highly-conserved activation motifs. {beta}-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on the rate. A {beta}-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.

biochemistry↗

bioRxiv2022

Ligands tune the local and global motions of neurotensin receptor 1 (NTS1): a DFT-guided solution NMR analysis

Unlike many signaling proteins that function as binary switches between on and off states, G protein-coupled receptors (GPCRs) exhibit basal activity that can be increased or decreased by numerous ligands. A given receptor can recognize multiple ligands, allosteric modulators, and transducers to create a complex free energy landscape. Many of the lowest energy states have been captured by static structural techniques while detailing the wells widths, metastable states, and the transition between them, is still in its infancy. Nuclear magnetic resonance (NMR) spectroscopy can monitor the structure and dynamics of GPCR ensembles across fifteen orders-of-magnitude, but technical challenges have limited its application to super-microsecond timescales. Focusing on a prototypical peptide-binding GPCR, the neurotensin receptor 1 (NTS1), we employed NMR and density functional theory (DFT) to probe global sub-nanosecond motions. The near random coil chemical shifts of the apo receptor produced a poor correlation with theoretical predictions that may indicate a high degree of conformational averaging in solution, a crystallization artifact, or both. Whereas orthosteric agonists and antagonists both rigidified the receptor, but to varying degrees, which suggests conformational entropy differentially contributes to their respective pharmacology. The strong correlations of observed and theoretical chemical shifts lend confidence to interpreting spectra in terms of local structure, methyl dihedral angle geometry, and pico-second timescale transitions. Together, our results suggest a role for sub-nanosecond dynamics and conformational entropy in GPCR ligand discrimination.

biophysics↗

bioRxiv2022

Structures of the interleukin 11 signalling complex reveal dynamics of gp130 extracellular domains and the inhibitory mechanism of a cytokine variant

Interleukin (IL-)11, an IL-6 family cytokine, has pivotal roles in numerous autoimmune diseases, fibrotic complications, and solid cancers. Despite intense therapeutic targeting efforts, structural understanding of IL-11 signalling and mechanistic insights into current inhibitors is lacking. Here we present cryo-EM and crystal structures of the IL-11 signalling complex, including the complex containing the complete extracellular domains of the shared IL-6 family {beta}-receptor, gp130. We show that the membrane-proximal domains of gp130 are dynamic and do not participate in complex assembly. We demonstrate that the cytokine mutant IL-11 Mutein competitively inhibits signalling in human cell lines. Structural shifts in IL-11 Mutein underlie inhibitory activity by altering cytokine binding interactions at all three receptor-engaging sites and abrogating the final gp130 binding step. Our results reveal the structural basis of IL-11 signalling, define the molecular mechanisms of an inhibitor, and advance understanding of gp130-containing receptor complexes, with potential applications in therapeutic development.

cell biology↗

bioRxiv2021

Structural insights into the modes of relaxin-binding and tethered-agonist activation of RXFP1 and RXFP2

Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signalling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.

biophysics↗

bioRxiv2021

Membrane permeabilization is mediated by distinct epitopes in mouse and human orthologs of the necroptosis effector, MLKL

Necroptosis is a lytic programmed cell death pathway with origins in innate immunity that is frequently dysregulated in inflammatory diseases. The terminal effector of the pathway, MLKL, is licensed to kill following phosphorylation of its pseudokinase domain by the upstream regulator, RIPK3 kinase. Phosphorylation provokes the unleashing of MLKLs N-terminal four-helix bundle (4HB or HeLo) domain, which binds and permeabilizes the plasma membrane to cause cell death. The precise mechanism by which the 4HB domain permeabilizes membranes, and how the mechanism differs between species, remains unclear. Here, we identify the membrane binding epitope of mouse MLKL using NMR spectroscopy. Using liposome permeabilization and cell death assays, we validate K69 in the 3 helix, W108 in the 4 helix, and R137/Q138 in the first brace helix as crucial residues for necroptotic signaling. This epitope differs from the phospholipid binding site reported for human MLKL, which comprises basic residues primarily located in the 1 and 2 helices. In further contrast to human and plant MLKL orthologs, in which the 3-4 loop forms a helix, this loop is unstructured in mouse MLKL in solution. Together, these findings illustrate the versatility of the 4HB domain fold, whose lytic function can be mediated by distinct epitopes in different orthologs.

cell biology↗

bioRxiv2021

Copper signaling promotes proteostasis and animal development via allosteric activation of ubiquitin E2D conjugases

Nutrient copper supply is critical for cell growth and differentiation, and its disturbance is associated with major pathologies including cancer and neurodegeneration. Although increasing copper bioavailability in late Precambrian facilitated emergence of novel cuproproteins, their intricate regulation by this essential trace element remains largely cryptic. We found that subtle rises in cellular copper strikingly increase polyubiquitination and accelerate protein degradation within 30 minutes in numerous mammalian cell lines. We track this surprising observation to allostery induced in the UBE2D ubiquitin conjugase clade through a conserved CXXXC sub-femtomolar-affinity Cu+ binding motif. Thus, physiologic fluctuation in cytoplasmic Cu+ is coupled to the prompt degradation of UBE2D protein targets, including p53. In Drosophila harboring a larval-lethal knockdown of the nearly identical fly orthologue UbcD1, complementation with human UBE2D2 restored near-normal development, but mutation of its CXXXC Cu+ binding motif profoundly disrupted organogenesis. Nutrient Cu+ emerges as a trophic allosteric modulator of UBE2D activity through a structural motif whose evolution coincides with animal multicellularity. One Sentence SummaryModulation of nutrient copper impacts protein turnover and animal morphogenesis through conserved allostery of ubiquitin E2D conjugases. HilightsO_LINutrient copper supply is critical for cell growth and differentiation C_LIO_LIThe E2D clade of ubiquitin conjugases contains a sub-femtomolar-affinity Cu+ binding motif C_LIO_LIAllosteric activation by Cu+ markedly accelerates protein polyubiquitination C_LIO_LIThis sensor couples physiologic fluctuations in cytoplasmic Cu+ with the degradation rate of E2D targets, including p53 C_LIO_LIThis metazoan signaling mechanism is critical for drosophila morphogenesis C_LI In BriefConserved allostery of ubiquitin E2D conjugases links nutrient copper signaling to protein degradation and animal morphogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/431211v2_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@17009fforg.highwire.dtl.DTLVardef@a07f8eorg.highwire.dtl.DTLVardef@11664c7org.highwire.dtl.DTLVardef@1327ab7_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

biochemistry↗

bioRxiv2019

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

G-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 1A-adrenoceptor, known for stimulating smooth muscle contraction in response to binding noradrenaline. NMR of 13C{varepsilon}H3-methionine labelled 1A-adrenoreceptor mutants, each exhibiting differing signalling capacities, revealed how different classes of ligands modulate receptor conformational equilibria. 13C{varepsilon}H3-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.

biochemistry↗

bioRxiv2017

Tadpole-like conformations of huntingtin exon 1 with expanded polyglutamine engenders novel interactions in cells

Soluble huntingtin exon 1 (Httex1) with expanded polyglutamine (polyQ) engenders neurotoxicity in Huntingtons disease. To uncover the physical basis of this toxicity, we performed structural studies of soluble Httex1 for wild type and mutant polyQ lengths. Nuclear magnetic resonance experiments show evidence for conformational rigidity across the polyQ region. In contrast, hydrogen-deuterium exchange shows absence of backbone amide protection, suggesting negligible persistence of hydrogen bonds. The seemingly conflicting results are explained by all-atom simulations, which show that Httex1 adopts tadpole-like structures with a globular head encompassing the N-terminal amphipathic and polyQ regions and the tail encompassing the C-terminal proline-rich region. The surface area of the globular domain increases monotonically with polyQ length. This stimulates sharp increases in gain-of-function interactions in cells for expanded polyQ, and one of these interactions is with the stress-granule protein Fus. Our results highlight plausible connections between Httex1 structure and routes to neurotoxicity.

biochemistry↗