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1.
Cell ; 185(23): 4361-4375.e19, 2022 11 10.
Article in English | MEDLINE | ID: mdl-36368306

ABSTRACT

Morphine and fentanyl are among the most used opioid drugs that confer analgesia and unwanted side effects through both G protein and arrestin signaling pathways of µ-opioid receptor (µOR). Here, we report structures of the human µOR-G protein complexes bound to morphine and fentanyl, which uncover key differences in how they bind the receptor. We also report structures of µOR bound to TRV130, PZM21, and SR17018, which reveal preferential interactions of these agonists with TM3 side of the ligand-binding pocket rather than TM6/7 side. In contrast, morphine and fentanyl form dual interactions with both TM3 and TM6/7 regions. Mutations at the TM6/7 interface abolish arrestin recruitment of µOR promoted by morphine and fentanyl. Ligands designed to reduce TM6/7 interactions display preferential G protein signaling. Our results provide crucial insights into fentanyl recognition and signaling of µOR, which may facilitate rational design of next-generation analgesics.


Subject(s)
Fentanyl , Morphine , Humans , Analgesics, Opioid/pharmacology , Arrestin/metabolism , Fentanyl/pharmacology , GTP-Binding Proteins/metabolism , Morphine/pharmacology , Receptors, Opioid, mu
2.
Nat Immunol ; 22(2): 128-139, 2021 02.
Article in English | MEDLINE | ID: mdl-33398182

ABSTRACT

Complement hyperactivation, angiopathic thrombosis and protein-losing enteropathy (CHAPLE disease) is a lethal disease caused by genetic loss of the complement regulatory protein CD55, leading to overactivation of complement and innate immunity together with immunodeficiency due to immunoglobulin wasting in the intestine. We report in vivo human data accumulated using the complement C5 inhibitor eculizumab for the medical treatment of patients with CHAPLE disease. We observed cessation of gastrointestinal pathology together with restoration of normal immunity and metabolism. We found that patients rapidly renormalized immunoglobulin concentrations and other serum proteins as revealed by aptamer profiling, re-established a healthy gut microbiome, discontinued immunoglobulin replacement and other treatments and exhibited catch-up growth. Thus, we show that blockade of C5 by eculizumab effectively re-establishes regulation of the innate immune complement system to substantially reduce the pathophysiological manifestations of CD55 deficiency in humans.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Complement Activation/drug effects , Complement C5/antagonists & inhibitors , Complement Inactivating Agents/therapeutic use , Energy Metabolism/drug effects , Hypoproteinemia/drug therapy , Immunity, Innate/drug effects , Protein-Losing Enteropathies/drug therapy , Antibodies, Monoclonal, Humanized/adverse effects , Antibodies, Monoclonal, Humanized/pharmacokinetics , Biomarkers/blood , CD55 Antigens/deficiency , CD55 Antigens/genetics , Complement C5/metabolism , Complement Inactivating Agents/adverse effects , Complement Inactivating Agents/pharmacokinetics , Genetic Predisposition to Disease , Humans , Hypoproteinemia/genetics , Hypoproteinemia/immunology , Hypoproteinemia/metabolism , Mutation , Phenotype , Protein-Losing Enteropathies/genetics , Protein-Losing Enteropathies/immunology , Protein-Losing Enteropathies/metabolism , Treatment Outcome
3.
Nat Immunol ; 19(6): 547-560, 2018 06.
Article in English | MEDLINE | ID: mdl-29777223

ABSTRACT

The adaptor CARD9 functions downstream of C-type lectin receptors (CLRs) for the sensing of microbial infection, which leads to responses by the TH1 and TH17 subsets of helper T cells. The single-nucleotide polymorphism rs4077515 at CARD9 in the human genome, which results in the substitution S12N (CARD9S12N), is associated with several autoimmune diseases. However, the function of CARD9S12N has remained unknown. Here we generated CARD9S12N knock-in mice and found that CARD9S12N facilitated the induction of type 2 immune responses after engagement of CLRs. Mechanistically, CARD9S12N mediated CLR-induced activation of the non-canonical transcription factor NF-κB subunit RelB, which initiated production of the cytokine IL-5 in alveolar macrophages for the recruitment of eosinophils to drive TH2 cell-mediated allergic responses. We identified the homozygous CARD9 mutation encoding S12N in patients with allergic bronchopulmonary aspergillosis and revealed activation of RelB and production of IL-5 in peripheral blood mononuclear cells from these patients. Our study provides genetic and functional evidence demonstrating that CARD9S12N can turn alveolar macrophages into IL-5-producing cells and facilitates TH2 cell-mediated pathologic responses.


Subject(s)
Aspergillosis, Allergic Bronchopulmonary/immunology , CARD Signaling Adaptor Proteins/immunology , Interleukin-5/biosynthesis , Macrophages, Alveolar/immunology , Th2 Cells/immunology , Animals , Aspergillosis, Allergic Bronchopulmonary/genetics , CARD Signaling Adaptor Proteins/genetics , Humans , Interleukin-5/immunology , Macrophages, Alveolar/metabolism , Mice , Polymorphism, Single Nucleotide , Signal Transduction/immunology
4.
Nature ; 630(8015): 247-254, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38750358

ABSTRACT

The noradrenaline transporter has a pivotal role in regulating neurotransmitter balance and is crucial for normal physiology and neurobiology1. Dysfunction of noradrenaline transporter has been implicated in numerous neuropsychiatric diseases, including depression and attention deficit hyperactivity disorder2. Here we report cryo-electron microscopy structures of noradrenaline transporter in apo and substrate-bound forms, and as complexes with six antidepressants. The structures reveal a noradrenaline transporter dimer interface that is mediated predominantly by cholesterol and lipid molecules. The substrate noradrenaline binds deep in the central binding pocket, and its amine group interacts with a conserved aspartate residue. Our structures also provide insight into antidepressant recognition and monoamine transporter selectivity. Together, these findings advance our understanding of noradrenaline transporter regulation and inhibition, and provide templates for designing improved antidepressants to treat neuropsychiatric disorders.


Subject(s)
Antidepressive Agents , Cryoelectron Microscopy , Norepinephrine Plasma Membrane Transport Proteins , Norepinephrine , Protein Multimerization , Humans , Antidepressive Agents/chemistry , Antidepressive Agents/metabolism , Antidepressive Agents/pharmacology , Apoproteins/chemistry , Apoproteins/metabolism , Apoproteins/ultrastructure , Aspartic Acid/chemistry , Aspartic Acid/metabolism , Binding Sites , Cholesterol/metabolism , Cholesterol/chemistry , Models, Molecular , Norepinephrine/metabolism , Norepinephrine/chemistry , Norepinephrine Plasma Membrane Transport Proteins/antagonists & inhibitors , Norepinephrine Plasma Membrane Transport Proteins/chemistry , Norepinephrine Plasma Membrane Transport Proteins/metabolism , Norepinephrine Plasma Membrane Transport Proteins/ultrastructure , Protein Binding , Substrate Specificity
5.
Nature ; 620(7974): 676-681, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37532940

ABSTRACT

Phosphorylation of G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) desensitizes G-protein signalling and promotes arrestin signalling, which is also modulated by biased ligands1-6. The molecular assembly of GRKs on GPCRs and the basis of GRK-mediated biased signalling remain largely unknown owing to the weak GPCR-GRK interactions. Here we report the complex structure of neurotensin receptor 1 (NTSR1) bound to GRK2, Gαq and the arrestin-biased ligand SBI-5537. The density map reveals the arrangement of the intact GRK2 with the receptor, with the N-terminal helix of GRK2 docking into the open cytoplasmic pocket formed by the outward movement of the receptor transmembrane helix 6, analogous to the binding of the G protein to the receptor. SBI-553 binds at the interface between GRK2 and NTSR1 to enhance GRK2 binding. The binding mode of SBI-553 is compatible with arrestin binding but clashes with the binding of Gαq protein, thus providing a mechanism for its arrestin-biased signalling capability. In sum, our structure provides a rational model for understanding the details of GPCR-GRK interactions and GRK2-mediated biased signalling.


Subject(s)
G-Protein-Coupled Receptor Kinase 2 , Receptors, G-Protein-Coupled , Signal Transduction , Arrestins/metabolism , Phosphorylation , Receptors, G-Protein-Coupled/metabolism , G-Protein-Coupled Receptor Kinase 2/biosynthesis , G-Protein-Coupled Receptor Kinase 2/chemistry , G-Protein-Coupled Receptor Kinase 2/metabolism , GTP-Binding Protein alpha Subunits, Gq-G11/metabolism , Ligands , Protein Binding , Receptors, Neurotensin/metabolism
6.
Mol Cell ; 77(3): 669-680.e4, 2020 02 06.
Article in English | MEDLINE | ID: mdl-32004470

ABSTRACT

Corticotropin-releasing factor (CRF) and the three related peptides urocortins 1-3 (UCN1-UCN3) are endocrine hormones that control the stress responses by activating CRF1R and CRF2R, two members of class B G-protein-coupled receptors (GPCRs). Here, we present two cryoelectron microscopy (cryo-EM) structures of UCN1-bound CRF1R and CRF2R with the stimulatory G protein. In both structures, UCN1 adopts a single straight helix with its N terminus dipped into the receptor transmembrane bundle. Although the peptide-binding residues in CRF1R and CRF2R are different from other members of class B GPCRs, the residues involved in receptor activation and G protein coupling are conserved. In addition, both structures reveal bound cholesterol molecules to the receptor transmembrane helices. Our structures define the basis of ligand-binding specificity in the CRF receptor-hormone system, establish a common mechanism of class B GPCR activation and G protein coupling, and provide a paradigm for studying membrane protein-lipid interactions for class B GPCRs.


Subject(s)
Receptors, Corticotropin-Releasing Hormone/ultrastructure , Amino Acid Sequence , Binding Sites , Corticotropin-Releasing Hormone , Cryoelectron Microscopy/methods , GTP-Binding Protein alpha Subunits, Gs/metabolism , GTP-Binding Proteins/metabolism , Humans , Peptides/metabolism , Receptors, Corticotropin-Releasing Hormone/metabolism , Urocortins/metabolism
7.
EMBO J ; 42(22): e113383, 2023 Nov 15.
Article in English | MEDLINE | ID: mdl-37807845

ABSTRACT

Notch signaling pathway activity, particularly fluctuations in the biologically active effector fragment NICD, is required for rapid and efficient dynamic regulation of proper fate decisions in stem cells. In this study, we identified NEDD4-binding protein 1 (N4BP1), which is highly expressed in the developing mouse cerebral cortex, as a negative modulator of Notch signaling dynamics in neural progenitor cells. Intriguingly, N4BP1 regulated NICD stability specifically after Notch1 S3 cleavage through ubiquitin-mediated degradation that depended on its RAM domain, not its PEST domain, as had been extensively and previously described. The CoCUN domain in N4BP1, particularly the "Phe-Pro" motif (862/863 amino acid), was indispensable for mediating NICD degradation. The Ring family E3 ligase Trim21 was, in contrast to other NEDD4 family members, required for N4BP1-regulated NICD degradation. Overexpression of N4BP1 in cortical neural progenitors promoted neural stem cell differentiation, whereas neural progenitor cells lacking N4BP1 were sensitized to Notch signaling, resulting in the maintenance of stem-like properties in neural progenitor cells and lower production of cortical neurons.


Subject(s)
Neocortex , Neural Stem Cells , Animals , Mice , Cell Differentiation/physiology , Neocortex/metabolism , Neural Stem Cells/metabolism , Neurons/metabolism , Receptor, Notch1/metabolism , Receptors, Notch/genetics , Receptors, Notch/metabolism , Signal Transduction/physiology
8.
Nature ; 599(7886): 605-610, 2021 11.
Article in English | MEDLINE | ID: mdl-34819683

ABSTRACT

Solids in nature can be generally classified into crystalline and non-crystalline states1-7, depending on whether long-range lattice periodicity is present in the material. The differentiation of the two states, however, could face fundamental challenges if the degree of long-range order in crystals is significantly reduced. Here we report a paracrystalline state of diamond that is distinct from either crystalline or amorphous diamond8-10. The paracrystalline diamond reported in this work, consisting of sub-nanometre-sized paracrystallites that possess a well-defined crystalline medium-range order up to a few atomic shells4,5,11-13, was synthesized in high-pressure high-temperature conditions (for example, 30 GPa and 1,600 K) employing face-centred cubic C60 as a precursor. The structural characteristics of the paracrystalline diamond were identified through a combination of X-ray diffraction, high-resolution transmission microscopy and advanced molecular dynamics simulation. The formation of paracrystalline diamond is a result of densely distributed nucleation sites developed in compressed C60 as well as pronounced second-nearest-neighbour short-range order in amorphous diamond due to strong sp3 bonding. The discovery of paracrystalline diamond adds an unusual diamond form to the enriched carbon family14-16, which exhibits distinguishing physical properties and can be furthered exploited to develop new materials. Furthermore, this work reveals the missing link in the length scale between amorphous and crystalline states across the structural landscape, having profound implications for recognizing complex structures arising from amorphous materials.

9.
Nature ; 594(7864): 583-588, 2021 06.
Article in English | MEDLINE | ID: mdl-34135510

ABSTRACT

The metabotropic glutamate receptors (mGlus) have key roles in modulating cell excitability and synaptic transmission in response to glutamate (the main excitatory neurotransmitter in the central nervous system)1. It has previously been suggested that only one receptor subunit within an mGlu homodimer is responsible for coupling to G protein during receptor activation2. However, the molecular mechanism that underlies the asymmetric signalling of mGlus remains unknown. Here we report two cryo-electron microscopy structures of human mGlu2 and mGlu4 bound to heterotrimeric Gi protein. The structures reveal a G-protein-binding site formed by three intracellular loops and helices III and IV that is distinct from the corresponding binding site in all of the other G-protein-coupled receptor (GPCR) structures. Furthermore, we observed an asymmetric dimer interface of the transmembrane domain of the receptor in the two mGlu-Gi structures. We confirmed that the asymmetric dimerization is crucial for receptor activation, which was supported by functional data; this dimerization may provide a molecular basis for the asymmetric signal transduction of mGlus. These findings offer insights into receptor signalling of class C GPCRs.


Subject(s)
GTP-Binding Proteins/chemistry , Receptors, Metabotropic Glutamate/chemistry , Binding Sites , Cryoelectron Microscopy , Humans , Protein Multimerization , Protein Structure, Tertiary , Signal Transduction
10.
Proc Natl Acad Sci U S A ; 121(17): e2314353121, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38635634

ABSTRACT

Auxin regulates plant growth and development through downstream signaling pathways, including the best-known SCFTIR1/AFB-Aux/IAA-ARF pathway and several other less characterized "noncanonical" pathways. Recently, one SCFTIR1/AFB-independent noncanonical pathway, mediated by Transmembrane Kinase 1 (TMK1), was discovered through the analyses of its functions in Arabidopsis apical hook development. Asymmetric accumulation of auxin on the concave side of the apical hook triggers DAR1-catalyzed release of the C-terminal of TMK1, which migrates into the nucleus, where it phosphorylates and stabilizes IAA32/34 to inhibit cell elongation, which is essential for full apical hook formation. However, the molecular factors mediating IAA32/34 degradation have not been identified. Here, we show that proteins in the CYTOKININ INDUCED ROOT WAVING 1 (CKRW1)/WAVY GROWTH 3 (WAV3) subfamily act as E3 ubiquitin ligases to target IAA32/34 for ubiquitination and degradation, which is inhibited by TMK1c-mediated phosphorylation. This antagonistic interaction between TMK1c and CKRW1/WAV3 subfamily E3 ubiquitin ligases regulates IAA32/34 levels to control differential cell elongation along opposite sides of the apical hook.


Subject(s)
Arabidopsis Proteins , Arabidopsis , F-Box Proteins , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Indoleacetic Acids/metabolism , Signal Transduction , Ubiquitins/metabolism , Gene Expression Regulation, Plant , F-Box Proteins/genetics , F-Box Proteins/metabolism
11.
Proc Natl Acad Sci U S A ; 121(2): e2219352120, 2024 Jan 09.
Article in English | MEDLINE | ID: mdl-38165927

ABSTRACT

High levels of mitochondrial reactive oxygen species (mROS) are linked to cancer development, which is tightly controlled by the electron transport chain (ETC). However, the epigenetic mechanisms governing ETC gene transcription to drive mROS production and cancer cell growth remain to be fully characterized. Here, we report that protein demethylase PHF8 is overexpressed in many types of cancers, including colon and lung cancer, and is negatively correlated with ETC gene expression. While it is well known to demethylate histones to activate transcription, PHF8 demethylates transcription factor YY1, functioning as a co-repressor for a large set of nuclear-coded ETC genes to drive mROS production and cancer development. In addition to genetically ablating PHF8, pharmacologically targeting PHF8 with a specific chemical inhibitor, iPHF8, is potent in regulating YY1 methylation, ETC gene transcription, mROS production, and cell growth in colon and lung cancer cells. iPHF8 exhibits potency and safety in suppressing tumor growth in cell-line- and patient-derived xenografts in vivo. Our data uncover a key epigenetic mechanism underlying ETC gene transcriptional regulation, demonstrating that targeting the PHF8/YY1 axis has great potential to treat cancers.


Subject(s)
Lung Neoplasms , Transcription Factors , Humans , Transcription Factors/metabolism , Reactive Oxygen Species/metabolism , Histone Demethylases/metabolism , Histones/metabolism , Cell Transformation, Neoplastic , Lung Neoplasms/genetics , YY1 Transcription Factor/genetics , YY1 Transcription Factor/metabolism
12.
Nat Chem Biol ; 20(4): 484-492, 2024 Apr.
Article in English | MEDLINE | ID: mdl-37945893

ABSTRACT

GPR101 is an orphan G protein-coupled receptor actively participating in energy homeostasis. Here we report the cryo-electron microscopy structure of GPR101 constitutively coupled to Gs heterotrimer, which reveals unique features of GPR101, including the interaction of extracellular loop 2 within the 7TM bundle, a hydrophobic chain packing-mediated activation mechanism and the structural basis of disease-related mutants. Importantly, a side pocket is identified in GPR101 that facilitates in silico screening to identify four small-molecule agonists, including AA-14. The structure of AA-14-GPR101-Gs provides direct evidence of the AA-14 binding at the side pocket. Functionally, AA-14 partially restores the functions of GH/IGF-1 axis and exhibits several rejuvenating effects in wild-type mice, which are abrogated in Gpr101-deficient mice. In summary, we provide a structural basis for the constitutive activity of GPR101. The structure-facilitated identification of GPR101 agonists and functional analysis suggest that targeting this orphan receptor has rejuvenating potential.


Subject(s)
Receptors, G-Protein-Coupled , Mice , Animals , Cryoelectron Microscopy , Receptors, G-Protein-Coupled/metabolism , Ligands
13.
Nature ; 577(7790): 432-436, 2020 01.
Article in English | MEDLINE | ID: mdl-31915381

ABSTRACT

Class B G-protein-coupled receptors are major targets for the treatment of chronic diseases, including diabetes and obesity1. Structures of active receptors reveal peptide agonists engage deep within the receptor core, leading to an outward movement of extracellular loop 3 and the tops of transmembrane helices 6 and 7, an inward movement of transmembrane helix 1, reorganization of extracellular loop 2 and outward movement of the intracellular side of transmembrane helix 6, resulting in G-protein interaction and activation2-6. Here we solved the structure of a non-peptide agonist, TT-OAD2, bound to the glucagon-like peptide-1 (GLP-1) receptor. Our structure identified an unpredicted non-peptide agonist-binding pocket in which reorganization of extracellular loop 3 and transmembrane helices 6 and 7 manifests independently of direct ligand interaction within the deep transmembrane domain pocket. TT-OAD2 exhibits biased agonism, and kinetics of G-protein activation and signalling that are distinct from peptide agonists. Within the structure, TT-OAD2 protrudes beyond the receptor core to interact with the lipid or detergent, providing an explanation for the distinct activation kinetics that may contribute to the clinical efficacy of this compound series. This work alters our understanding of the events that drive the activation of class B receptors.


Subject(s)
Glucagon-Like Peptide-1 Receptor/agonists , Isoquinolines/pharmacology , Phenylalanine/analogs & derivatives , Pyridines/pharmacology , Animals , CHO Cells , Cricetinae , Cricetulus , Glucagon-Like Peptide-1 Receptor/chemistry , Glucagon-Like Peptide-1 Receptor/metabolism , Humans , Isoquinolines/chemistry , Kinetics , Models, Molecular , Phenylalanine/chemistry , Phenylalanine/pharmacology , Protein Structure, Quaternary , Protein Structure, Tertiary , Pyridines/chemistry , Structural Homology, Protein
14.
Nucleic Acids Res ; 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38967001

ABSTRACT

Small RNAs (sRNAs) are essential for normal plant development and range in size classes of 21-24 nucleotides. The 22nt small interfering RNAs (siRNAs) and miRNAs are processed by Dicer-like 2 (DCL2) and DCL1 respectively and can initiate secondary siRNA production from the target transcript. 22nt siRNAs are under-represented due to competition between DCL2 and DCL4, while only a small number of 22nt miRNAs exist. Here we produce abundant 22nt siRNAs and other siRNA size classes using long hairpin RNA (hpRNA) transgenes. By introducing asymmetric bulges into the antisense strand of hpRNA, we shifted the dominant siRNA size class from 21nt of the traditional hpRNA to 22, 23 and 24nt of the asymmetric hpRNAs. The asymmetric hpRNAs effectively silenced a ß-glucuronidase (GUS) reporter transgene and the endogenous ethylene insensitive-2 (EIN2) and chalcone synthase (CHS) genes. Furthermore, plants containing the asymmetric hpRNA transgenes showed increased amounts of 21nt siRNAs downstream of the hpRNA target site compared to plants with the traditional hpRNA transgenes. This indicates that these asymmetric hpRNAs are more effective at inducing secondary siRNA production to amplify silencing signals. The 22nt asymmetric hpRNA constructs enhanced virus resistance in plants compared to the traditional hpRNA constructs.

15.
Proc Natl Acad Sci U S A ; 120(33): e2303696120, 2023 08 15.
Article in English | MEDLINE | ID: mdl-37549266

ABSTRACT

Glucagon-like peptide-1 receptor (GLP-1R) and glucagon receptor (GCGR), two members of class B1 G protein-coupled receptors, play important roles in glucose homeostasis and energy metabolism. They share a high degree of sequence homology but have different functionalities. Unimolecular dual agonists of both receptors developed recently displayed better clinical efficacies than that of monotherapy. To study the underlying molecular mechanisms, we determined high-resolution cryo-electron microscopy structures of GLP-1R or GCGR in complex with heterotrimeric Gs protein and three GLP-1R/GCGR dual agonists including peptide 15, MEDI0382 (cotadutide) and SAR425899 with variable activating profiles at GLP-1R versus GCGR. Compared with related structures reported previously and supported by our published pharmacological data, key residues responsible for ligand recognition and dual agonism were identified. Analyses of peptide conformational features revealed a difference in side chain orientations within the first three residues, indicating that distinct engagements in the deep binding pocket are required to achieve receptor selectivity. The middle region recognizes extracellular loop 1 (ECL1), ECL2, and the top of transmembrane helix 1 (TM1) resulting in specific conformational changes of both ligand and receptor, especially the dual agonists reshaped ECL1 conformation of GLP-1R relative to that of GCGR, suggesting an important role of ECL1 interaction in executing dual agonism. Structural investigation of lipid modification showed a better interaction between lipid moiety of MEDI0382 and TM1-TM2 cleft, in line with its increased potency at GCGR than SAR425899. Together, the results provide insightful information for the design and development of improved therapeutics targeting these two receptors simultaneously.


Subject(s)
Glucagon-Like Peptide-1 Receptor , Receptors, Glucagon , Cryoelectron Microscopy , Glucagon-Like Peptide-1 Receptor/agonists , Ligands , Lipids , Peptides/chemistry , Receptors, Glucagon/agonists
16.
Proc Natl Acad Sci U S A ; 120(34): e2304071120, 2023 08 22.
Article in English | MEDLINE | ID: mdl-37585458

ABSTRACT

Class IA phosphoinositide 3-kinase alpha (PI3Kα) is an important drug target because it is one of the most frequently mutated proteins in human cancers. However, small molecule inhibitors currently on the market or under development have safety concerns due to a lack of selectivity. Therefore, other chemical scaffolds or unique mechanisms of catalytic kinase inhibition are needed. Here, we report the cryo-electron microscopy structures of wild-type PI3Kα, the dimer of p110α and p85α, in complex with three Y-shaped ligands [cpd16 (compound 16), cpd17 (compound 17), and cpd18 (compound 18)] of different affinities and no inhibitory effect on the kinase activity. Unlike ATP-competitive inhibitors, cpd17 adopts a Y-shaped conformation with one arm inserted into a binding pocket formed by R770 and W780 and the other arm lodged in the ATP-binding pocket at an angle that is different from that of the ATP phosphate tail. Such a special interaction induces a conformation of PI3Kα resembling that of the unliganded protein. These observations were confirmed with two isomers (cpd16 and cpd18). Further analysis of these Y-shaped ligands revealed the structural basis of differential binding affinities caused by stereo- or regiochemical modifications. Our results may offer a different direction toward the design of therapeutic agents against PI3Kα.


Subject(s)
Phosphatidylinositol 3-Kinase , Phosphatidylinositol 3-Kinases , Humans , Phosphatidylinositol 3-Kinases/metabolism , Ligands , Cryoelectron Microscopy , Adenosine Triphosphate/metabolism
17.
Proc Natl Acad Sci U S A ; 120(41): e2306145120, 2023 10 10.
Article in English | MEDLINE | ID: mdl-37792509

ABSTRACT

Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a potential drug target for metabolic disorders. It works with glucagon-like peptide-1 receptor and glucagon receptor in humans to maintain glucose homeostasis. Unlike the other two receptors, GIPR has at least 13 reported splice variants (SVs), more than half of which have sequence variations at either C or N terminus. To explore their roles in endogenous peptide-mediated GIPR signaling, we determined the cryoelectron microscopy (cryo-EM) structures of the two N terminus-altered SVs (referred as GIPR-202 and GIPR-209 in the Ensembl database, SV1 and SV2 here, respectively) and investigated the outcome of coexpressing each of them in question with GIPR in HEK293T cells with respect to ligand binding, receptor expression, cAMP (adenosine 3,5-cyclic monophosphate) accumulation, ß-arrestin recruitment, and cell surface localization. It was found that while both N terminus-altered SVs of GIPR neither bound to the hormone nor elicited signal transduction per se, they suppressed ligand binding and cAMP accumulation of GIPR. Meanwhile, SV1 reduced GIPR-mediated ß-arrestin 2 responses. The cryo-EM structures of SV1 and SV2 showed that they reorganized the extracellular halves of transmembrane helices 1, 6, and 7 and extracellular loops 2 and 3 to adopt a ligand-binding pocket-occupied conformation, thereby losing binding ability to the peptide. The results suggest a form of signal bias that is constitutive and ligand-independent, thus expanding our knowledge of biased signaling beyond pharmacological manipulation (i.e., ligand specific) as well as constitutive and ligand-independent (e.g., SV1 of the growth hormone-releasing hormone receptor).


Subject(s)
Gastric Inhibitory Polypeptide , Receptors, Gastrointestinal Hormone , Humans , Gastric Inhibitory Polypeptide/genetics , Gastric Inhibitory Polypeptide/metabolism , Gastric Inhibitory Polypeptide/pharmacology , Ligands , Cryoelectron Microscopy , HEK293 Cells , Signal Transduction/physiology , Receptors, Gastrointestinal Hormone/genetics , Receptors, Gastrointestinal Hormone/chemistry , Receptors, Gastrointestinal Hormone/metabolism , Peptides , Glucagon-Like Peptide-1 Receptor/metabolism
18.
Proc Natl Acad Sci U S A ; 120(30): e2216329120, 2023 07 25.
Article in English | MEDLINE | ID: mdl-37478163

ABSTRACT

To accomplish concerted physiological reactions, nature has diversified functions of a single hormone at at least two primary levels: 1) Different receptors recognize the same hormone, and 2) different cellular effectors couple to the same hormone-receptor pair [R.P. Xiao, Sci STKE 2001, re15 (2001); L. Hein, J. D. Altman, B.K. Kobilka, Nature 402, 181-184 (1999); Y. Daaka, L. M. Luttrell, R. J. Lefkowitz, Nature 390, 88-91 (1997)]. Not only these questions lie in the heart of hormone actions and receptor signaling but also dissecting mechanisms underlying these questions could offer therapeutic routes for refractory diseases, such as kidney injury (KI) or X-linked nephrogenic diabetes insipidus (NDI). Here, we identified that Gs-biased signaling, but not Gi activation downstream of EP4, showed beneficial effects for both KI and NDI treatments. Notably, by solving Cryo-electron microscope (cryo-EM) structures of EP3-Gi, EP4-Gs, and EP4-Gi in complex with endogenous prostaglandin E2 (PGE2)or two synthetic agonists and comparing with PGE2-EP2-Gs structures, we found that unique primary sequences of prostaglandin E2 receptor (EP) receptors and distinct conformational states of the EP4 ligand pocket govern the Gs/Gi transducer coupling selectivity through different structural propagation paths, especially via TM6 and TM7, to generate selective cytoplasmic structural features. In particular, the orientation of the PGE2 ω-chain and two distinct pockets encompassing agonist L902688 of EP4 were differentiated by their Gs/Gi coupling ability. Further, we identified common and distinct features of cytoplasmic side of EP receptors for Gs/Gi coupling and provide a structural basis for selective and biased agonist design of EP4 with therapeutic potential.


Subject(s)
Dinoprostone , Signal Transduction , Dinoprostone/metabolism , Signal Transduction/physiology , Receptors, Prostaglandin/metabolism , GTP-Binding Protein alpha Subunits, Gs/metabolism , Hormones , Receptors, Prostaglandin E, EP4 Subtype/metabolism , Receptors, Prostaglandin E, EP2 Subtype/metabolism , Receptors, Prostaglandin E, EP3 Subtype/metabolism
19.
Plant J ; 117(4): 1206-1222, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38038953

ABSTRACT

MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.


Subject(s)
Arabidopsis , MicroRNAs , Base Pairing/genetics , Plants, Genetically Modified/genetics , RNA, Small Interfering/genetics , MicroRNAs/genetics , RNA Interference , RNA, Messenger/genetics , RNA, Double-Stranded , Arabidopsis/genetics
20.
J Virol ; 98(5): e0035024, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38591900

ABSTRACT

Feline calicivirus (FCV) is one of the few members of the Caliciviridae family that grows well in cell lines and, therefore, serves as a surrogate to study the biology of other viruses in the family. Conley et al. (14) demonstrated that upon the receptor engagement to the capsid, FCV VP2 forms a portal-like assembly, which might provide a channel for RNA release. However, the process of calicivirus RNA release is not yet fully understood. Our findings suggest that the separation of the FCV capsid from its genome RNA (gRNA) occurs rapidly in the early endosomes of infected cells. Using a liposome model decorated with the FCV cell receptor fJAM-A, we demonstrate that FCV releases its gRNA into the liposomes by penetrating membranes under low pH conditions. Furthermore, we found that VP2, which is rich in hydrophobic residues at its N-terminus, functions as the pore-forming protein. When we substituted the VP2 N-terminal hydrophobic residues, the gRNA release efficacy of the FCV mutants decreased. In conclusion, our results suggest that in the acidic environment of early endosomes, FCV VP2 functions as the pore-forming protein to mediate gRNA release into the cytoplasm of infected cells. This provides insight into the mechanism of calicivirus genome release.IMPORTANCEResearch on the biology and pathogenicity of certain caliciviruses, such as Norovirus and Sapovirus, is hindered by the lack of easy-to-use cell culture system. Feline calicivirus (FCV), which grows effectively in cell lines, is used as a substitute. At present, there is limited understanding of the genome release mechanism in caliciviruses. Our findings suggest that FCV uses VP2 to pierce the endosome membrane for genome release and provide new insights into the calicivirus gRNA release mechanism.


Subject(s)
Calicivirus, Feline , Capsid Proteins , Endosomes , RNA, Viral , Animals , Cats , Caliciviridae Infections/virology , Caliciviridae Infections/metabolism , Calicivirus, Feline/genetics , Calicivirus, Feline/metabolism , Calicivirus, Feline/physiology , Capsid/metabolism , Capsid Proteins/metabolism , Capsid Proteins/genetics , Cell Line , Endosomes/virology , Endosomes/metabolism , Genome, Viral , Liposomes/metabolism , RNA, Viral/metabolism , RNA, Viral/genetics , Virus Release
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