1
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Strauss A, Gonzalez-Hernandez AJ, Lee J, Abreu N, Selvakumar P, Salas-Estrada L, Kristt M, Arefin A, Huynh K, Marx DC, Gilliland K, Melancon BJ, Filizola M, Meyerson J, Levitz J. Structural basis of positive allosteric modulation of metabotropic glutamate receptor activation and internalization. Nat Commun 2024; 15:6498. [PMID: 39090128 PMCID: PMC11294631 DOI: 10.1038/s41467-024-50548-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric compounds as therapeutics, an understanding of the functional and structural basis of their effects is limited. Here we use multiple approaches to dissect the functional and structural effects of orthosteric versus allosteric ligands. We find, using electrophysiological and live cell imaging assays, that both agonists and positive allosteric modulators (PAMs) can drive activation and internalization of group II and III mGluRs. The effects of PAMs are pleiotropic, boosting the maximal response to orthosteric agonists and serving independently as internalization-biased agonists across mGluR subtypes. Motivated by this and intersubunit FRET analyses, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling.
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Affiliation(s)
- Alexa Strauss
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Chemical Biology, New York, NY, 10065, USA
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nohely Abreu
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Purushotham Selvakumar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melanie Kristt
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Anisul Arefin
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kevin Huynh
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Dagan C Marx
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kristen Gilliland
- Warren Center for Neuroscience Drug Discovery at Vanderbilt University, Vanderbilt University, Nashville, TN, 37232, USA
| | - Bruce J Melancon
- Warren Center for Neuroscience Drug Discovery at Vanderbilt University, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA.
- Tri-Institutional Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA.
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2
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Li H, Teng J, Hibbs RE. Structural switch in acetylcholine receptors in developing muscle. Nature 2024:10.1038/s41586-024-07774-6. [PMID: 39085615 DOI: 10.1038/s41586-024-07774-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
During development, motor neurons originating in the brainstem and spinal cord form elaborate synapses with skeletal muscle fibres1. These neurons release acetylcholine (ACh), which binds to nicotinic ACh receptors (AChRs) on the muscle, initiating contraction. Two types of AChR are present in developing muscle cells, and their differential expression serves as a hallmark of neuromuscular synapse maturation2-4. The structural principles underlying the switch from fetal to adult muscle receptors are unknown. Here, we present high-resolution structures of both fetal and adult muscle nicotinic AChRs, isolated from bovine skeletal muscle in developmental transition. These structures, obtained in the absence and presence of ACh, provide a structural context for understanding how fetal versus adult receptor isoforms are tuned for synapse development versus the all-or-none signalling required for high-fidelity skeletal muscle contraction. We find that ACh affinity differences are driven by binding site access, channel conductance is tuned by widespread surface electrostatics and open duration changes result from intrasubunit interactions and structural flexibility. The structures further reveal pathogenic mechanisms underlying congenital myasthenic syndromes.
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Affiliation(s)
- Huanhuan Li
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jinfeng Teng
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Ryan E Hibbs
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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3
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Hendrix S, Dartigue V, Hall H, Bawaria S, Kingma J, Bajaj B, Zelcer N, Kober DL. SPRING licenses S1P-mediated cleavage of SREBP2 by displacing an inhibitory pro-domain. Nat Commun 2024; 15:5732. [PMID: 38977690 PMCID: PMC11231238 DOI: 10.1038/s41467-024-50068-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
Site-one protease (S1P) conducts the first of two cleavage events in the Golgi to activate Sterol regulatory element binding proteins (SREBPs) and upregulate lipogenic transcription. S1P is also required for a wide array of additional signaling pathways. A zymogen serine protease, S1P matures through autoproteolysis of two pro-domains, with one cleavage event in the endoplasmic reticulum (ER) and the other in the Golgi. We recently identified the SREBP regulating gene, (SPRING), which enhances S1P maturation and is necessary for SREBP signaling. Here, we report the cryo-EM structures of S1P and S1P-SPRING at sub-2.5 Å resolution. SPRING activates S1P by dislodging its inhibitory pro-domain and stabilizing intra-domain contacts. Functionally, SPRING licenses S1P to cleave its cognate substrate, SREBP2. Our findings reveal an activation mechanism for S1P and provide insights into how spatial control of S1P activity underpins cholesterol homeostasis.
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Affiliation(s)
- Sebastian Hendrix
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, the Netherlands
| | - Vincent Dartigue
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hailee Hall
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shrankhla Bawaria
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jenina Kingma
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, the Netherlands
| | - Bilkish Bajaj
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Noam Zelcer
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, the Netherlands.
| | - Daniel L Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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4
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Gan N, Han Y, Zeng W, Jiang Y. TRPML1 gating modulation by allosteric mutations and lipids (Design of allosteric mutations that recapitulate the gating of TRPML1 ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602033. [PMID: 39005349 PMCID: PMC11245044 DOI: 10.1101/2024.07.04.602033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Transient Receptor Potential Mucolipin 1 (TRPML1) is a lysosomal cation channel whose loss-of-function mutations directly cause the lysosomal storage disorder mucolipidosis type IV (MLIV). TRPML1 can be allosterically regulated by various ligands including natural lipids and small synthetic molecules and the channel undergoes a global movement propagated from ligand-induced local conformational changes upon activation. In this study, we identified a functionally critical residue, Tyr404, at the C-terminus of the S4 helix, whose mutations to tryptophan and alanine yield gain- and loss-of-function channels, respectively. These allosteric mutations mimic the ligand activation or inhibition of the TRPML1 channel without interfering with ligand binding and both mutant channels are susceptible to agonist or antagonist modulation, making them better targets for screening potent TRPML1 activators and inhibitors. We also determined the high-resolution structure of TRPML1 in complex with the PI(4,5)P2 inhibitor, revealing the structural basis underlying this lipid inhibition. In addition, an endogenous phospholipid likely from sphingomyelin is identified in the PI(4,5)P2-bound TRPML1 structure at the same hotspot for agonists and antagonists, providing a plausible structural explanation for the inhibitory effect of sphingomyelin on agonist activation.
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Affiliation(s)
- Ninghai Gan
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Weizhong Zeng
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Youxing Jiang
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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5
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Mazzaferro S, Kang G, Natarajan K, Hibbs RE, Sine SM. Structural bases for stoichiometry-selective calcium potentiation of a neuronal nicotinic receptor. Br J Pharmacol 2024; 181:1973-1992. [PMID: 38454578 DOI: 10.1111/bph.16321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND AND PURPOSE α4β2 nicotinic acetylcholine (nACh) receptors assemble in two stoichiometric forms, one of which is potentiated by calcium. The sites of calcium binding that underpin potentiation are not known. EXPERIMENTAL APPROACH To identify calcium binding sites, we applied cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulations to each stoichiometric form of the α4β2 nACh receptor in the presence of calcium ions. To test whether the identified calcium sites are linked to potentiation, we generated mutants of anionic residues at the sites, expressed wild type and mutant receptors in clonal mammalian fibroblasts, and recorded ACh-elicited single-channel currents with or without calcium. KEY RESULTS Both cryo-EM and MD simulations show calcium bound to a site between the extracellular and transmembrane domains of each α4 subunit (ECD-TMD site). Substituting alanine for anionic residues at the ECD-TMD site abolishes stoichiometry-selective calcium potentiation, as monitored by single-channel patch clamp electrophysiology. Additionally, MD simulation reveals calcium association at subunit interfaces within the extracellular domain. Substituting alanine for anionic residues at the ECD sites reduces or abolishes stoichiometry-selective calcium potentiation. CONCLUSIONS AND IMPLICATIONS Stoichiometry-selective calcium potentiation of the α4β2 nACh receptor is achieved by calcium association with topographically distinct sites framed by anionic residues within the α4 subunit and between the α4 and β2 subunits. Stoichiometry-selective calcium potentiation could result from the greater number of calcium sites in the stoichiometric form with three rather than two α4 subunits. The results are relevant to modulation of signalling via α4β2 nACh receptors in physiological and pathophysiological conditions.
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Affiliation(s)
- Simone Mazzaferro
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kathiresan Natarajan
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Neurobiology, University of California San Diego, La Jolla, California, USA
| | - Steven M Sine
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
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6
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Roy-Chowdhury S, Jang S, Abderemane-Ali F, Naughton F, Grabe M, Minor DL. Structure of the human K 2P13.1(THIK-1) channel reveals a novel hydrophilic pore restriction and lipid cofactor site. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600491. [PMID: 38979306 PMCID: PMC11230452 DOI: 10.1101/2024.06.26.600491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The halothane-inhibited K2P leak potassium channel K2P13.1 (THIK-1)1-3 is found in diverse cells1,4 including neurons1,5 and microglia6-8 where it affects surveillance6, synaptic pruning7, phagocytosis7, and inflammasome-mediated interleukin-1β release6,8,9. As with many K2Ps1,5,10-14 and other voltage-gated ion channel (VGIC) superfamily members3,15,16, polyunsaturated fatty acid (PUFA) lipids modulate K2P13.1 (THIK-1)1,5,14,17 via a poorly understood mechanism. Here, we present cryo-electronmicroscopy (cryo-EM) structures of human K2P13.1 (THIK-1) and mutants in lipid nanodiscs and detergent. These reveal that, unlike other K2Ps13,18-24, K2P13.1 (THIK-1) has a two-chamber aqueous inner cavity obstructed by a M4 transmembrane helix tyrosine (Tyr273, the flow restrictor). This hydrophilic barrier can be opened by an activatory mutation, S136P25, at natural break in the M2 transmembrane helix and by intrinsic channel dynamics. The structures also reveal a buried lipid in the P1/M4 intersubunit interface at a location, the PUFA site, that coincides with the TREK subfamily K2P modulator pocket for small molecule agonists18,26,27. This overlap, together with the effects of mutation on K2P13.1 (THIK-1) PUFA responses, indicates that the PUFA site lipids are K2P13.1 (THIK-1) cofactors. Comparison with the PUFA-responsive VGIC Kv7.1 (KCNQ1)28-31 reveals a shared role for the equivalent pore domain intersubunit interface in lipid modulation, providing a framework for dissecting the effects of PUFAs on the VGIC superfamily. Our findings reveal the unique architecture underlying K2P13.1 (THIK-1) function, highlight the importance of the P1/M4 interface in control of K2Ps by both natural and synthetic agents, and should aid development of THIK subfamily modulators for diseases such as neuroinflammation6,32 and autism6.
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Affiliation(s)
- Shatabdi Roy-Chowdhury
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
| | - Seil Jang
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
| | - Fiona Naughton
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California 93858-2330 USA
| | - Daniel L. Minor
- Cardiovascular Research Institute, University of California, San Francisco, California 93858-2330 USA
- Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, California 93858-2330 USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, California 93858-2330 USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California 93858-2330 USA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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7
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Chojnacka W, Teng J, Kim JJ, Jensen AA, Hibbs RE. Structural insights into GABA A receptor potentiation by Quaalude. Nat Commun 2024; 15:5244. [PMID: 38898000 PMCID: PMC11187190 DOI: 10.1038/s41467-024-49471-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Methaqualone, a quinazolinone marketed commercially as Quaalude, is a central nervous system depressant that was used clinically as a sedative-hypnotic, then became a notorious recreational drug in the 1960s-80s. Due to its high abuse potential, medical use of methaqualone was eventually prohibited, yet it persists as a globally abused substance. Methaqualone principally targets GABAA receptors, which are the major inhibitory neurotransmitter-gated ion channels in the brain. The restricted status and limited accessibility of methaqualone have contributed to its pharmacology being understudied. Here, we use cryo-EM to localize the GABAA receptor binding sites of methaqualone and its more potent derivative, PPTQ, to the same intersubunit transmembrane sites targeted by the general anesthetics propofol and etomidate. Both methaqualone and PPTQ insert more deeply into subunit interfaces than the previously-characterized modulators. Binding of quinazolinones to this site results in widening of the extracellular half of the ion-conducting pore, following a trend among positive allosteric modulators in destabilizing the hydrophobic activation gate in the pore as a mechanism for receptor potentiation. These insights shed light on the underexplored pharmacology of quinazolinones and further elucidate the molecular mechanisms of allosteric GABAA receptor modulation through transmembrane binding sites.
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Affiliation(s)
- Weronika Chojnacka
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jinfeng Teng
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jeong Joo Kim
- Protein Structure and Function, Loxo@Lilly, Louisville, CO, USA
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ryan E Hibbs
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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8
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Yen YC, Li Y, Chen CL, Klose T, Watts VJ, Dessauer CW, Tesmer JJG. Structure of adenylyl cyclase 5 in complex with Gβγ offers insights into ADCY5-related dyskinesia. Nat Struct Mol Biol 2024:10.1038/s41594-024-01263-0. [PMID: 38589608 DOI: 10.1038/s41594-024-01263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
The nine different membrane-anchored adenylyl cyclase isoforms (AC1-9) in mammals are stimulated by the heterotrimeric G protein, Gαs, but their response to Gβγ regulation is isoform specific. In the present study, we report cryo-electron microscope structures of ligand-free AC5 in complex with Gβγ and a dimeric form of AC5 that could be involved in its regulation. Gβγ binds to a coiled-coil domain that links the AC transmembrane region to its catalytic core as well as to a region (C1b) that is known to be a hub for isoform-specific regulation. We confirmed the Gβγ interaction with both purified proteins and cell-based assays. Gain-of-function mutations in AC5 associated with human familial dyskinesia are located at the interface of AC5 with Gβγ and show reduced conditional activation by Gβγ, emphasizing the importance of the observed interaction for motor function in humans. We propose a molecular mechanism wherein Gβγ either prevents dimerization of AC5 or allosterically modulates the coiled-coil domain, and hence the catalytic core. As our mechanistic understanding of how individual AC isoforms are uniquely regulated is limited, studies such as this may provide new avenues for isoform-specific drug development.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yong Li
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Thomas Klose
- Purdue Cryo-EM Facility, Hockmeyer Hall for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - John J G Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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9
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Kalienkova V, Dandamudi M, Paulino C, Lynagh T. Structural basis for excitatory neuropeptide signaling. Nat Struct Mol Biol 2024; 31:717-726. [PMID: 38337033 PMCID: PMC11026163 DOI: 10.1038/s41594-023-01198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/05/2023] [Indexed: 02/12/2024]
Abstract
Rapid signaling between neurons is mediated by ligand-gated ion channels, cell-surface proteins with an extracellular ligand-binding domain and a membrane-spanning ion channel domain. The degenerin/epithelial sodium channel (DEG/ENaC) superfamily is diverse in terms of its gating stimuli, with some DEG/ENaCs gated by neuropeptides, and others gated by pH, mechanical force or enzymatic activity. The mechanism by which ligands bind to and activate DEG/ENaCs is poorly understood. Here we dissected the structural basis for neuropeptide-gated activity of a neuropeptide-gated DEG/ENaC, FMRFamide-gated sodium channel 1 (FaNaC1) from the annelid worm Malacoceros fuliginosus, using cryo-electron microscopy. Structures of FaNaC1 in the ligand-free resting state and in several ligand-bound states reveal the ligand-binding site and capture the ligand-induced conformational changes of channel gating, which we verified with complementary mutagenesis experiments. Our results illuminate channel gating in DEG/ENaCs and offer a structural template for experimental dissection of channel pharmacology and ion conduction.
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Affiliation(s)
- Valeria Kalienkova
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Cristina Paulino
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
- Biochemistry Center, Heidelberg University, Heidelberg, Germany.
| | - Timothy Lynagh
- Michael Sars Centre, University of Bergen, Bergen, Norway.
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10
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Wang M, Chen L, He J, Xia W, Ye Z, She J. Structural insights into IL-6 signaling inhibition by therapeutic antibodies. Cell Rep 2024; 43:113819. [PMID: 38393945 DOI: 10.1016/j.celrep.2024.113819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Antibody inhibitors of the interleukin-6 (IL-6) signaling pathway, such as tocilizumab and sarilumab, have been used to treat rheumatoid arthritis, chimeric antigen receptor T cell-induced cytokine storm, and severe COVID-19 pneumonia. Here, we solve the cryogenic electron microscopy structures of sarilumab and tocilizumab in complex with IL-6R to resolutions of 3.2 and 3.3 Å, respectively. These structures reveal that both tocilizumab and sarilumab bind to the D3 domain of IL-6R. The binding surfaces of the two antibodies largely overlap, but the detailed interactions are different. Functional studies of various mutants show results consistent with our structural analysis of the antibodies and IL-6R interactions. Structural comparisons with the IL-6/IL-6R/gp130 complex indicate that sarilumab and tocilizumab probably inhibit IL-6/IL-6R signaling by competing for the IL-6 binding site. In summary, this work reveals the antibody-blocking mechanism of the IL-6 signaling pathway and paves the way for future antibody discovery.
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Affiliation(s)
- Mingxing Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Long Chen
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Jin He
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Wenqiang Xia
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China.
| | - Ji She
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China.
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11
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Wang J, Luo Y, Ye F, Ding ZJ, Zheng SJ, Qiao S, Wang Y, Guo J, Yang W, Su N. Structures and ion transport mechanisms of plant high-affinity potassium transporters. MOLECULAR PLANT 2024; 17:409-422. [PMID: 38335958 DOI: 10.1016/j.molp.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Plant high-affinity K+ transporters (HKTs) mediate Na+ and K+ uptake, maintain Na+/K+ homeostasis, and therefore play crucial roles in plant salt tolerance. In this study, we present cryoelectron microscopy structures of HKTs from two classes, class I HKT1;1 from Arabidopsis thaliana (AtHKT1;1) and class II HKT2;1 from Triticum aestivum (TaHKT2;1), in both Na+- and K+-bound states at 2.6- to 3.0-Å resolutions. Both AtHKT1;1 and TaHKT2;1 function as homodimers. Each HKT subunit consists of four tandem domain units (D1-D4) with a repeated K+-channel-like M-P-M topology. In each subunit, D1-D4 assemble into an ion conduction pore with a pseudo-four-fold symmetry. Although both TaHKT2;1 and AtHKT1;1 have only one putative Na+ ion bound in the selectivity filter with a similar coordination pattern, the two HKTs display different K+ binding modes in the filter. TaHKT2;1 has three K+ ions bound in the selectivity filter, but AtHKT1;1 has only two K+ ions bound in the filter, which has a narrowed external entrance due to the presence of a Ser residue in the first filter motif. These structures, along with computational, mutational, and electrophysiological analyses, enable us to pinpoint key residues that are critical for the ion selectivity of HKTs. The findings provide new insights into the ion selectivity and ion transport mechanisms of plant HKTs and improve our understanding about how HKTs mediate plant salt tolerance and enhance crop growth.
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Affiliation(s)
- Jiangqin Wang
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Yanping Luo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Fan Ye
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zhong Jie Ding
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuai Qiao
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China; Nanhu Brain-computer Interface Institute, Hangzhou, Zhejiang 311100, China.
| | - Wei Yang
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Nannan Su
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China.
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12
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Ma D, Hu M, Yang X, Liu Q, Ye F, Cai W, Wang Y, Xu X, Chang S, Wang R, Yang W, Ye S, Su N, Fan M, Xu H, Guo J. Structural basis for sugar perception by Drosophila gustatory receptors. Science 2024; 383:eadj2609. [PMID: 38305684 DOI: 10.1126/science.adj2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Insects rely on a family of seven transmembrane proteins called gustatory receptors (GRs) to encode different taste modalities, such as sweet and bitter. We report structures of Drosophila sweet taste receptors GR43a and GR64a in the apo and sugar-bound states. Both GRs form tetrameric sugar-gated cation channels composed of one central pore domain (PD) and four peripheral ligand-binding domains (LBDs). Whereas GR43a is specifically activated by the monosaccharide fructose that binds to a narrow pocket in LBDs, disaccharides sucrose and maltose selectively activate GR64a by binding to a larger and flatter pocket in LBDs. Sugar binding to LBDs induces local conformational changes, which are subsequently transferred to the PD to cause channel opening. Our studies reveal a structural basis for sugar recognition and activation of GRs.
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Affiliation(s)
- Demin Ma
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China
| | - Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou 311121, China
| | - Xiaotong Yang
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou 311121, China
| | - Qiang Liu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou 311121, China
| | - Fan Ye
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China
| | - Weijie Cai
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou 311121, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ximing Xu
- Marine Biomedical Institute of Qingdao, School of Pharmacy and Medicine, Ocean University of China, Qingdao, Shandong 266100, China
| | - Shenghai Chang
- Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ruiying Wang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei Yang
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Nannan Su
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Minrui Fan
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310058, China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou 311121, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
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13
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Bihler H, Sivachenko A, Millen L, Bhatt P, Patel AT, Chin J, Bailey V, Musisi I, LaPan A, Allaire NE, Conte J, Simon NR, Magaret AS, Raraigh KS, Cutting GR, Skach WR, Bridges RJ, Thomas PJ, Mense M. In vitro modulator responsiveness of 655 CFTR variants found in people with cystic fibrosis. J Cyst Fibros 2024:S1569-1993(24)00021-3. [PMID: 38388235 DOI: 10.1016/j.jcf.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND In 2017, the US Food and Drug Administration initiated expansion of drug labels for the treatment of cystic fibrosis (CF) to include CF transmembrane conductance regulator (CFTR) gene variants based on in vitro functional studies. This study aims to identify CFTR variants that result in increased chloride (Cl-) transport function by the CFTR protein after treatment with the CFTR modulator combination elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA). These data may benefit people with CF (pwCF) who are not currently eligible for modulator therapies. METHODS Plasmid DNA encoding 655 CFTR variants and wild-type (WT) CFTR were transfected into Fisher Rat Thyroid cells that do not natively express CFTR. After 24 h of incubation with control or TEZ and ELX, and acute addition of IVA, CFTR function was assessed using the transepithelial current clamp conductance assay. Each variant's forskolin/cAMP-induced baseline Cl- transport activity, responsiveness to IVA alone, and responsiveness to the TEZ/ELX/IVA combination were measured in three different laboratories. Western blots were conducted to evaluate CFTR protein maturation and complement the functional data. RESULTS AND CONCLUSIONS 253 variants not currently approved for CFTR modulator therapy showed low baseline activity (<10 % of normal CFTR Cl- transport activity). For 152 of these variants, treatment with ELX/TEZ/IVA improved the Cl- transport activity by ≥10 % of normal CFTR function, which is suggestive of clinical benefit. ELX/TEZ/IVA increased CFTR function by ≥10 percentage points for an additional 140 unapproved variants with ≥10 % but <50 % of normal CFTR function at baseline. These findings significantly expand the number of rare CFTR variants for which ELX/TEZ/IVA treatment should result in clinical benefit.
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Affiliation(s)
- Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | | | - Linda Millen
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Priyanka Bhatt
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | | | - Justin Chin
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - Violaine Bailey
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - Isaac Musisi
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - André LaPan
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | | | - Joshua Conte
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA
| | - Noah R Simon
- University of Washington, Seattle, WA 98195-9300, USA
| | | | - Karen S Raraigh
- Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
| | - Garry R Cutting
- Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
| | | | - Robert J Bridges
- Rosalind Franklin University Medical School, Chicago, IL 60064, USA
| | - Philip J Thomas
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA 02421, USA.
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14
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Kallure GS, Pal K, Zhou Y, Lingle CJ, Chowdhury S. High-resolution structures illuminate key principles underlying voltage and LRRC26 regulation of Slo1 channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572542. [PMID: 38187713 PMCID: PMC10769243 DOI: 10.1101/2023.12.20.572542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Multi-modal regulation of Slo1 channels by membrane voltage, intracellular calcium, and auxiliary subunits enables its pleiotropic physiological functions. Our understanding of how voltage impacts Slo1 conformational dynamics and the mechanisms by which auxiliary subunits, particularly of the LRRC (Leucine Rich Repeat containing) family of proteins, modulate its voltage gating remain unresolved. Here, we used single particle cryo-electron microscopy to determine structures of human Slo1 mutants which functionally stabilize the closed pore (F315A) or the activated voltage-sensor (R207A). Our structures, obtained under calcium-free conditions, reveal that a key step in voltage-sensing by Slo1 involves a rotameric flip of the voltage-sensing charges (R210 and R213) moving them by ∼6 Å across a hydrophobic gasket. Next we obtained reconstructions of a complex of human Slo1 with the human LRRC26 (γ1) subunit in absence of calcium. Together with extensive biochemical tests, we show that the extracellular domains of γ1 form a ring of interlocked dominos that stabilizes the quaternary assembly of the complex and biases Slo1:γ1 assembly towards high stoichiometric complexes. The transmembrane helix of γ1 is kinked and tightly packed against the Slo1 voltage-sensor. We hypothesize that γ1 subunits exert relatively small effects on early steps in voltage-gating but structurally stabilize non-S4 helices of Slo1 voltage-sensor which energetically facilitate conformational rearrangements that occur late in voltage stimulated transitions.
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15
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Cowgill J, Fan C, Haloi N, Tobiasson V, Zhuang Y, Howard RJ, Lindahl E. Structure and dynamics of differential ligand binding in the human ρ-type GABA A receptor. Neuron 2023; 111:3450-3464.e5. [PMID: 37659407 DOI: 10.1016/j.neuron.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/04/2023]
Abstract
The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of ρ-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human ρ1 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.
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Affiliation(s)
- John Cowgill
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Chen Fan
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Nandan Haloi
- Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 17121 Solna, Sweden
| | - Victor Tobiasson
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden.
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, 17121 Solna, Sweden; Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 17121 Solna, Sweden.
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16
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Kalienkova V, Peter MF, Rheinberger J, Paulino C. Structures of a sperm-specific solute carrier gated by voltage and cAMP. Nature 2023; 623:202-209. [PMID: 37880361 PMCID: PMC10620091 DOI: 10.1038/s41586-023-06629-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Abstract
The newly characterized sperm-specific Na+/H+ exchanger stands out by its unique tripartite domain composition1,2. It unites a classical solute carrier unit with regulatory domains usually found in ion channels, namely, a voltage-sensing domain and a cyclic-nucleotide binding domain1,3, which makes it a mechanistic chimera and a secondary-active transporter activated strictly by membrane voltage. Our structures of the sea urchin SpSLC9C1 in the absence and presence of ligands reveal the overall domain arrangement and new structural coupling elements. They allow us to propose a gating model, where movements in the voltage sensor indirectly cause the release of the exchanging unit from a locked state through long-distance allosteric effects transmitted by the newly characterized coupling helices. We further propose that modulation by its ligand cyclic AMP occurs by means of disruption of the cytosolic dimer interface, which lowers the energy barrier for S4 movements in the voltage-sensing domain. As SLC9C1 members have been shown to be essential for male fertility, including in mammals2,4,5, our structure represents a potential new platform for the development of new on-demand contraceptives.
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Affiliation(s)
- Valeria Kalienkova
- Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, The Netherlands
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Martin F Peter
- Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, The Netherlands
- Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Jan Rheinberger
- Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Cristina Paulino
- Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, The Netherlands.
- Biochemistry Center, Heidelberg University, Heidelberg, Germany.
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17
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Xue J, Zeng W, Han Y, John S, Ottolia M, Jiang Y. Structural mechanisms of the human cardiac sodium-calcium exchanger NCX1. Nat Commun 2023; 14:6181. [PMID: 37794011 PMCID: PMC10550945 DOI: 10.1038/s41467-023-41885-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
Abstract
Na+/Ca2+ exchangers (NCX) transport Ca2+ in or out of cells in exchange for Na+. They are ubiquitously expressed and play an essential role in maintaining cytosolic Ca2+ homeostasis. Although extensively studied, little is known about the global structural arrangement of eukaryotic NCXs and the structural mechanisms underlying their regulation by various cellular cues including cytosolic Na+ and Ca2+. Here we present the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange function and its modulation by cytosolic Ca2+ and Na+. We demonstrate that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca2+], a TM-associated four-stranded β-hub mediates a tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange function. Ca2+ binding to the cytosolic second Ca2+-binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the current NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins.
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Affiliation(s)
- Jing Xue
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weizhong Zeng
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Scott John
- Department of Medicine (Cardiology), David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michela Ottolia
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Youxing Jiang
- Howard Hughes Medical Institute and Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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18
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Liu F, Dang Y, Li L, Feng H, Li J, Wang H, Zhang X, Zhang Z, Ye S, Tian Y, Chen Q. Structure and mechanism of a neuropeptide-activated channel in the ENaC/DEG superfamily. Nat Chem Biol 2023; 19:1276-1285. [PMID: 37550431 DOI: 10.1038/s41589-023-01401-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Phe-Met-Arg-Phe-amide (FMRFamide)-activated sodium channels (FaNaCs) are a family of channels activated by the neuropeptide FMRFamide, and, to date, the underlying ligand gating mechanism remains unknown. Here we present the high-resolution cryo-electron microscopy structures of Aplysia californica FaNaC in both apo and FMRFamide-bound states. AcFaNaC forms a chalice-shaped trimer and possesses several notable features, including two FaNaC-specific insertion regions, a distinct finger domain and non-domain-swapped transmembrane helix 2 in the transmembrane domain (TMD). One FMRFamide binds to each subunit in a cleft located in the top-most region of the extracellular domain, with participation of residues from the neighboring subunit. Bound FMRFamide adopts an extended conformation. FMRFamide binds tightly to A. californica FaNaC in an N terminus-in manner, which causes collapse of the binding cleft and induces large local conformational rearrangements. Such conformational changes are propagated downward toward the TMD via the palm domain, possibly resulting in outward movement of the TMD and dilation of the ion conduction pore.
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Affiliation(s)
- Fenglian Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yu Dang
- State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lu Li
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China
| | - Hao Feng
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Jianlin Li
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China
| | - Haowei Wang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China.
| | - Yutao Tian
- Academy of Medical Engineering and Translational Medicine (AMT) and Tianjin Key Laboratory of Brain Science and Neural Engineering, Tianjin University, Tianjin, China.
| | - Qingfeng Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China.
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19
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Balakrishnan S, Adolph M, Tsai MS, Gallagher K, Cortez D, Chazin WJ. Structure of RADX and mechanism for regulation of RAD51 nucleofilaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558089. [PMID: 37786681 PMCID: PMC10541619 DOI: 10.1101/2023.09.19.558089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed ssDNA. To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here we present a structure-based investigation of RADX's mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (EM) from maps in the 2-3 Å range. The structure reveals the molecular basis for RADX oligomerization and binding of ssDNA binding. The binding of RADX to RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the growing end of RAD51 filaments.
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Affiliation(s)
- Swati Balakrishnan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Madison Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Miaw-Sheue Tsai
- Biological Systems and Bioengineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kaitlyn Gallagher
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Walter J. Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Lead contact
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20
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Legesse DH, Fan C, Teng J, Zhuang Y, Howard RJ, Noviello CM, Lindahl E, Hibbs RE. Structural insights into opposing actions of neurosteroids on GABA A receptors. Nat Commun 2023; 14:5091. [PMID: 37607940 PMCID: PMC10444788 DOI: 10.1038/s41467-023-40800-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors mediate fast inhibitory signaling in the brain and are targets of numerous drugs and endogenous neurosteroids. A subset of neurosteroids are GABAA receptor positive allosteric modulators; one of these, allopregnanolone, is the only drug approved specifically for treating postpartum depression. There is a consensus emerging from structural, physiological and photolabeling studies as to where positive modulators bind, but how they potentiate GABA activation remains unclear. Other neurosteroids are negative modulators of GABAA receptors, but their binding sites remain debated. Here we present structures of a synaptic GABAA receptor bound to allopregnanolone and two inhibitory sulfated neurosteroids. Allopregnanolone binds at the receptor-bilayer interface, in the consensus potentiator site. In contrast, inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support a mechanism by which allopregnanolone potentiates channel activity and suggest the dominant mechanism for sulfated neurosteroid inhibition is through pore block.
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Affiliation(s)
| | - Chen Fan
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Jinfeng Teng
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Yuxuan Zhuang
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Colleen M Noviello
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Erik Lindahl
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
| | - Ryan E Hibbs
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
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21
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Strauss A, Gonzalez-Hernandez AJ, Lee J, Abreu N, Selvakumar P, Salas-Estrada L, Kristt M, Marx DC, Gilliland K, Melancon BJ, Filizola M, Meyerson J, Levitz J. Structural basis of allosteric modulation of metabotropic glutamate receptor activation and desensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.552748. [PMID: 37645747 PMCID: PMC10461995 DOI: 10.1101/2023.08.13.552748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted either at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric TMD-targeting compounds as therapeutics, an understanding of the functional and structural basis of their effects on mGluRs is limited. Here we use a battery of approaches to dissect the distinct functional and structural effects of orthosteric versus allosteric ligands. We find using electrophysiological and live cell imaging assays that both agonists and positive allosteric modulators (PAMs) can drive activation and desensitization of mGluRs. The effects of PAMs are pleiotropic, including both the ability to boost the maximal response to orthosteric agonists and to serve independently as desensitization-biased agonists across mGluR subtypes. Conformational sensors reveal PAM-driven inter-subunit re-arrangements at both the LBD and TMD. Motivated by this, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling. Highlights -Agonists and PAMs drive mGluR activation, desensitization, and endocytosis-PAMs are desensitization-biased and synergistic with agonists-Four combinatorial ligand conditions reveal an ensemble of full-length mGluR structures with novel interfaces-Activation and desensitization involve rolling TMD interfaces which are re-shaped by PAM.
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22
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Hernando G, Turani O, Rodriguez Araujo N, Bouzat C. The diverse family of Cys-loop receptors in Caenorhabditis elegans: insights from electrophysiological studies. Biophys Rev 2023; 15:733-750. [PMID: 37681094 PMCID: PMC10480131 DOI: 10.1007/s12551-023-01080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/18/2023] [Indexed: 09/09/2023] Open
Abstract
Cys-loop receptors integrate a large family of pentameric ligand-gated ion channels that mediate fast ionotropic responses in vertebrates and invertebrates. Their vital role in converting neurotransmitter recognition into an electrical impulse makes these receptors essential for a great variety of physiological processes. In vertebrates, the Cys-loop receptor family includes the cation-selective channels, nicotinic acetylcholine and 5-hydroxytryptamine type 3 receptors, and the anion-selective channels, GABAA and glycine receptors, whereas in invertebrates, the repertoire is significantly larger. The free-living nematode Caenorhabditis elegans has the largest known Cys-loop receptor family as well as unique receptors that are absent in vertebrates and constitute attractive targets for anthelmintic drugs. Given the large number and variety of Cys-loop receptor subunits and the multiple possible ways of subunit assembly, C. elegans offers a large diversity of receptors although only a limited number of them have been characterized to date. C. elegans has emerged as a powerful model for the study of the nervous system and human diseases as well as a model for antiparasitic drug discovery. This nematode has also shown promise in the pharmaceutical industry search for new therapeutic compounds. C. elegans is therefore a powerful model organism to explore the biology and pharmacology of Cys-loop receptors and their potential as targets for novel therapeutic interventions. In this review, we provide a comprehensive overview of what is known about the function of C. elegans Cys-loop receptors from an electrophysiological perspective.
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Affiliation(s)
- Guillermina Hernando
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Bioquímicas de Bahía Blanca, Camino La Carrindanga Km 7, 8000 Bahía Blanca, Argentina
| | - Ornella Turani
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Bioquímicas de Bahía Blanca, Camino La Carrindanga Km 7, 8000 Bahía Blanca, Argentina
| | - Noelia Rodriguez Araujo
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Bioquímicas de Bahía Blanca, Camino La Carrindanga Km 7, 8000 Bahía Blanca, Argentina
| | - Cecilia Bouzat
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Bioquímicas de Bahía Blanca, Camino La Carrindanga Km 7, 8000 Bahía Blanca, Argentina
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23
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Zhang J, Zeng W, Han Y, Lee WR, Liou J, Jiang Y. Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel. Mol Cell 2023; 83:2524-2539.e7. [PMID: 37390818 PMCID: PMC10528928 DOI: 10.1016/j.molcel.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/03/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
Maintaining a highly acidic lysosomal pH is central to cellular physiology. Here, we use functional proteomics, single-particle cryo-EM, electrophysiology, and in vivo imaging to unravel a key biological function of human lysosome-associated membrane proteins (LAMP-1 and LAMP-2) in regulating lysosomal pH homeostasis. Despite being widely used as a lysosomal marker, the physiological functions of the LAMP proteins have long been overlooked. We show that LAMP-1 and LAMP-2 directly interact with and inhibit the activity of the lysosomal cation channel TMEM175, a key player in lysosomal pH homeostasis implicated in Parkinson's disease. This LAMP inhibition mitigates the proton conduction of TMEM175 and facilitates lysosomal acidification to a lower pH environment crucial for optimal hydrolase activity. Disrupting the LAMP-TMEM175 interaction alkalinizes the lysosomal pH and compromises the lysosomal hydrolytic function. In light of the ever-increasing importance of lysosomes to cellular physiology and diseases, our data have widespread implications for lysosomal biology.
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Affiliation(s)
- Jiyuan Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute at University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wan-Ru Lee
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jen Liou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute at University of Texas Southwestern Medical Center, Dallas, TX, USA.
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24
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Hu Z, Zheng X, Yang J. Conformational trajectory of allosteric gating of the human cone photoreceptor cyclic nucleotide-gated channel. Nat Commun 2023; 14:4284. [PMID: 37463923 DOI: 10.1038/s41467-023-39971-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide-binding domain (CNBD) to open a gate located 50-60 Å away in the central cavity. Structures of closed and open vertebrate CNG channels have been solved, but the conformational landscape of this allosteric gating remains to be elucidated and enriched. Here, we report structures of the cGMP-activated human cone photoreceptor CNGA3/CNGB3 channel in closed, intermediate, pre-open and open states in detergent or lipid nanodisc, all with fully bound cGMP. The pre-open and open states are obtained only in the lipid nanodisc, suggesting a critical role of lipids in tuning the energetic landscape of CNGA3/CNGB3 activation. The different states exhibit subunit-unique, incremental and distinct conformational rearrangements that originate in the CNBD, propagate through the gating ring to the transmembrane domain, and gradually open the S6 cavity gate. Our work illustrates a spatial conformational-change wave of allosteric gating of a vertebrate CNG channel by its natural ligand and provides an expanded framework for studying CNG properties and channelopathy.
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Affiliation(s)
- Zhengshan Hu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Xiangdong Zheng
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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25
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Yen YC, Li Y, Chen CL, Klose T, Watts VJ, Dessauer CW, Tesmer JJG. Isoform Specific Regulation of Adenylyl Cyclase 5 by Gβγ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539090. [PMID: 37205557 PMCID: PMC10187219 DOI: 10.1101/2023.05.02.539090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The nine different membrane-anchored adenylyl cyclase isoforms (AC1-9) in mammals are stimulated by the heterotrimeric G protein Gαs, but their response to Gβγ regulation is isoform-specific. For example, AC5 is conditionally activated by Gβγ. Here, we report cryo-EM structures of ligand-free AC5 in complex with Gβγ and of a dimeric form of AC5 that could be involved in its regulation. Gβγ binds to a coiled-coil domain that links the AC transmembrane region to its catalytic core as well as to a region (C1b) that is known to be a hub for isoform-specific regulation. We confirmed the Gβγ interaction with both purified proteins and cell-based assays. The interface with Gβγ involves AC5 residues that are subject to gain-of-function mutations in humans with familial dyskinesia, indicating that the observed interaction is important for motor function. A molecular mechanism wherein Gβγ either prevents dimerization of AC5 or allosterically modulates the coiled-coil domain, and hence the catalytic core, is proposed. Because our mechanistic understanding of how individual AC isoforms are uniquely regulated is limited, studies such as this may provide new avenues for isoform-specific drug development.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yong Li
- Department Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Thomas Klose
- Purdue CryoEM Facility, Suite 171, Hockmeyer Hall for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Val J Watts
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Carmen W Dessauer
- Department Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
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26
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Wang L, Hall C, Li J, Choi E, Bai XC. Structural basis of the alkaline pH-dependent activation of insulin receptor-related receptor. Nat Struct Mol Biol 2023; 30:661-669. [PMID: 37055497 PMCID: PMC10465182 DOI: 10.1038/s41594-023-00974-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/20/2023] [Indexed: 04/15/2023]
Abstract
The insulin receptor (IR) family is a subfamily of receptor tyrosine kinases that controls metabolic homeostasis and cell growth. Distinct from IR and insulin-like growth factor 1 receptor, whose activation requires ligand binding, insulin receptor-related receptor (IRR)-the third member of the IR family-is activated by alkaline pH. However, the molecular mechanism underlying alkaline pH-induced IRR activation remains unclear. Here, we present cryo-EM structures of human IRR in both neutral pH inactive and alkaline pH active states. Combined with mutagenesis and cellular assays, we show that, upon pH increase, electrostatic repulsion of the pH-sensitive motifs of IRR disrupts its autoinhibited state and promotes a scissor-like rotation between two protomers, leading to a T-shaped active conformation. Together, our study reveals an unprecedented alkaline pH-dependent activation mechanism of IRR, opening up opportunities to understand the structure-function relationship of this important receptor.
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Affiliation(s)
- Liwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Catherine Hall
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eunhee Choi
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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27
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Saotome K, Dudgeon D, Colotti K, Moore MJ, Jones J, Zhou Y, Rafique A, Yancopoulos GD, Murphy AJ, Lin JC, Olson WC, Franklin MC. Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Nat Commun 2023; 14:2401. [PMID: 37100770 PMCID: PMC10132440 DOI: 10.1038/s41467-023-37532-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023] Open
Abstract
The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.
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Affiliation(s)
- Kei Saotome
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
| | - Drew Dudgeon
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Jennifer Jones
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | | | - John C Lin
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
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28
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Chen H, Qin Y, Chou M, Cyster JG, Li X. Transmembrane protein CD69 acts as an S1PR1 agonist. eLife 2023; 12:e88204. [PMID: 37039481 PMCID: PMC10154026 DOI: 10.7554/elife.88204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 04/12/2023] Open
Abstract
The activation of Sphingosine-1-phosphate receptor 1 (S1PR1) by S1P promotes lymphocyte egress from lymphoid organs, a process critical for immune surveillance and T cell effector activity. Multiple drugs that inhibit S1PR1 function are in use clinically for the treatment of autoimmune diseases. Cluster of Differentiation 69 (CD69) is an endogenous negative regulator of lymphocyte egress that interacts with S1PR1 in cis to facilitate internalization and degradation of the receptor. The mechanism by which CD69 causes S1PR1 internalization has been unclear. Moreover, although there are numerous class A GPCR structures determined with different small molecule agonists bound, it remains unknown whether a transmembrane protein per se can act as a class A GPCR agonist. Here, we present the cryo-EM structure of CD69-bound S1PR1 coupled to the heterotrimeric Gi complex. The transmembrane helix (TM) of one protomer of CD69 homodimer contacts the S1PR1-TM4. This interaction allosterically induces the movement of S1PR1-TMs 5-6, directly activating the receptor to engage the heterotrimeric Gi. Mutations in key residues at the interface affect the interactions between CD69 and S1PR1, as well as reduce the receptor internalization. Thus, our structural findings along with functional analyses demonstrate that CD69 acts in cis as a protein agonist of S1PR1, thereby promoting Gi-dependent S1PR1 internalization, loss of S1P gradient sensing, and inhibition of lymphocyte egress.
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Affiliation(s)
- Hongwen Chen
- Department of Molecular Genetics, The University of Texas Southwestern Medical CenterDallasUnited States
| | - Yu Qin
- Department of Molecular Genetics, The University of Texas Southwestern Medical CenterDallasUnited States
| | - Marissa Chou
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Xiaochun Li
- Department of Molecular Genetics, The University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biophysics, The University of Texas Southwestern Medical CenterDallasUnited States
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29
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Kang G, Allard CAH, Valencia-Montoya WA, van Giesen L, Kim JJ, Kilian PB, Bai X, Bellono NW, Hibbs RE. Sensory specializations drive octopus and squid behaviour. Nature 2023; 616:378-383. [PMID: 37045917 PMCID: PMC10262778 DOI: 10.1038/s41586-023-05808-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
The evolution of new traits enables expansion into new ecological and behavioural niches. Nonetheless, demonstrated connections between divergence in protein structure, function and lineage-specific behaviours remain rare. Here we show that both octopus and squid use cephalopod-specific chemotactile receptors (CRs) to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles. We find that squid express ancient CRs that more closely resemble related nicotinic acetylcholine receptors, whereas octopuses exhibit a more recent expansion in CRs consistent with their elaborated 'taste by touch' sensory system. Using a combination of genetic profiling, physiology and behavioural analyses, we identify the founding member of squid CRs that detects soluble bitter molecules that are relevant in ambush predation. We present the cryo-electron microscopy structure of a squid CR and compare this with octopus CRs1 and nicotinic receptors2. These analyses demonstrate an evolutionary transition from an ancestral aromatic 'cage' that coordinates soluble neurotransmitters or tastants to a more recent octopus CR hydrophobic binding pocket that traps insoluble molecules to mediate contact-dependent chemosensation. Thus, our study provides a foundation for understanding how adaptation of protein structure drives the diversification of organismal traits and behaviour.
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Affiliation(s)
- Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Corey A H Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Lena van Giesen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jeong Joo Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter B Kilian
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xiaochen Bai
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA.
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30
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Allard CAH, Kang G, Kim JJ, Valencia-Montoya WA, Hibbs RE, Bellono NW. Structural basis of sensory receptor evolution in octopus. Nature 2023; 616:373-377. [PMID: 37045920 PMCID: PMC10228259 DOI: 10.1038/s41586-023-05822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/10/2023] [Indexed: 04/14/2023]
Abstract
Chemotactile receptors (CRs) are a cephalopod-specific innovation that allow octopuses to explore the seafloor via 'taste by touch'1. CRs diverged from nicotinic acetylcholine receptors to mediate contact-dependent chemosensation of insoluble molecules that do not readily diffuse in marine environments. Here we exploit octopus CRs to probe the structural basis of sensory receptor evolution. We present the cryo-electron microscopy structure of an octopus CR and compare it with nicotinic receptors to determine features that enable environmental sensation versus neurotransmission. Evolutionary, structural and biophysical analyses show that the channel architecture involved in cation permeation and signal transduction is conserved. By contrast, the orthosteric ligand-binding site is subject to diversifying selection, thereby mediating the detection of new molecules. Serendipitous findings in the cryo-electron microscopy structure reveal that the octopus CR ligand-binding pocket is exceptionally hydrophobic, enabling sensation of greasy compounds versus the small polar molecules detected by canonical neurotransmitter receptors. These discoveries provide a structural framework for understanding connections between evolutionary adaptations at the atomic level and the emergence of new organismal behaviour.
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Affiliation(s)
- Corey A H Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeong Joo Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA.
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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31
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Barrantes FJ. Structure and function meet at the nicotinic acetylcholine receptor-lipid interface. Pharmacol Res 2023; 190:106729. [PMID: 36931540 DOI: 10.1016/j.phrs.2023.106729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
The nicotinic acetylcholine receptor (nAChR) is a transmembrane protein that mediates fast intercellular communication in response to the endogenous neurotransmitter acetylcholine. It is the best characterized and archetypal molecule in the superfamily of pentameric ligand-gated ion channels (pLGICs). As a typical transmembrane macromolecule, it interacts extensively with its vicinal lipid microenvironment. Experimental evidence provides a wealth of information on receptor-lipid crosstalk: the nAChR exerts influence on its immediate membrane environment and conversely, the lipid moiety modulates ligand binding, affinity state transitions and gating of ion translocation functions of the receptor protein. Recent cryogenic electron microscopy (cryo-EM) studies have unveiled the occurrence of sites for phospholipids and cholesterol on the lipid-exposed regions of neuronal and electroplax nAChRs, confirming early spectroscopic and affinity labeling studies demonstrating the close contact of lipid molecules with the receptor transmembrane segments. This new data provides structural support to the postulated "lipid sensor" ability displayed by the outer ring of M4 transmembrane domains and their modulatory role on nAChR function, as we postulated a decade ago. Borrowing from the best characterized nAChR, the electroplax (muscle-type) receptor, and exploiting new structural information on the neuronal nAChR, it is now possible to achieve an improved depiction of these sites. In combination with site-directed mutagenesis, single-channel electrophysiology, and molecular dynamics studies, the new structural information delivers a more comprehensive portrayal of these lipid-sensitive loci, providing mechanistic explanations for their ability to modulate nAChR properties and raising the possibility of targetting them in disease.
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Affiliation(s)
- Francisco J Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research Institute, Faculty of Medical Sciences, Pontifical Catholic University of Argentina (UCA) - Argentine Scientific & Technol. Research Council (CONICET), Av. Alicia Moreau de Justo 1600, C1107AAZ Buenos Aires, Argentina.
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He C, Mansilla-Soto J, Khanra N, Hamieh M, Bustos V, Paquette AJ, Garcia Angus A, Shore DM, Rice WJ, Khelashvili G, Sadelain M, Meyerson JR. CD19 CAR antigen engagement mechanisms and affinity tuning. Sci Immunol 2023; 8:eadf1426. [PMID: 36867678 DOI: 10.1126/sciimmunol.adf1426] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Chimeric antigen receptor (CAR) T cell therapy relies on T cells that are guided by synthetic receptors to target and lyse cancer cells. CARs bind to cell surface antigens through an scFv (binder), the affinity of which is central to determining CAR T cell function and therapeutic success. CAR T cells targeting CD19 were the first to achieve marked clinical responses in patients with relapsed/refractory B cell malignancies and to be approved by the U.S. Food and Drug Administration (FDA). We report cryo-EM structures of CD19 antigen with the binder FMC63, which is used in four FDA-approved CAR T cell therapies (Kymriah, Yescarta, Tecartus, and Breyanzi), and the binder SJ25C1, which has also been used extensively in multiple clinical trials. We used these structures for molecular dynamics simulations, which guided creation of lower- or higher-affinity binders, and ultimately produced CAR T cells endowed with distinct tumor recognition sensitivities. The CAR T cells exhibited different antigen density requirements to trigger cytolysis and differed in their propensity to prompt trogocytosis upon contacting tumor cells. Our work shows how structural information can be applied to tune CAR T cell performance to specific target antigen densities.
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Affiliation(s)
- Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Nandish Khanra
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Mohamad Hamieh
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Victor Bustos
- Fisher Drug Discovery Resource Center, Rockefeller University, New York, NY, USA
| | - Alice J Paquette
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Andreina Garcia Angus
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Derek M Shore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - William J Rice
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joel R Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
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Chen H, Qin Y, Chou M, Cyster JG, Li X. Transmembrane protein CD69 acts as an S1PR1 agonist. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528406. [PMID: 36824756 PMCID: PMC9949048 DOI: 10.1101/2023.02.13.528406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The activation of Sphingosine-1-phosphate receptor 1 (S1PR1) by S1P promotes lymphocyte egress from lymphoid organs, a process critical for immune surveillance and T cell effector activity 1-4 . Multiple drugs that inhibit S1PR1 function are in use clinically for the treatment of autoimmune diseases. Cluster of Differentiation 69 (CD69) is an endogenous negative regulator of lymphocyte egress that interacts with S1PR1 in cis to facilitate internalization and degradation of the receptor 5,6 . The mechanism by which CD69 causes S1PR1 internalization has been unclear. Moreover, although there are numerous class A GPCR structures determined with different small molecule agonists bound, it remains unknown whether a transmembrane protein per se can act as a class A GPCR agonist. Here, we present the cryo-EM structure of CD69-bound S1PR1 coupled to the heterotrimeric G i complex. The transmembrane helix (TM) of one protomer of CD69 homodimer contacts the S1PR1-TM4. This interaction allosterically induces the movement of S1PR1-TMs 5-6, directly activating the receptor to engage the heterotrimeric G i . Mutations in key residues at the interface affect the interactions between CD69 and S1PR1, as well as reduce the receptor internalization. Thus, our structural findings along with functional analyses demonstrate that CD69 acts in cis as a protein agonist of S1PR1, thereby promoting G i -dependent S1PR1 internalization, loss of S1P gradient sensing, and inhibition of lymphocyte egress.
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Affiliation(s)
- Hongwen Chen
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Qin
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marissa Chou
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jason G. Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Miller AN, Houlihan PR, Matamala E, Cabezas-Bratesco D, Lee GY, Cristofori-Armstrong B, Dilan TL, Sanchez-Martinez S, Matthies D, Yan R, Yu Z, Ren D, Brauchi SE, Clapham DE. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. eLife 2023; 12:e84477. [PMID: 36695574 PMCID: PMC9910834 DOI: 10.7554/elife.84477] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 01/26/2023] Open
Abstract
The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as viroporins. Here, we show that neither SARS-CoV-2 nor SARS-CoV-1 Orf3a form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a positively charged aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a's ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
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Affiliation(s)
| | | | - Ella Matamala
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
| | - Deny Cabezas-Bratesco
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
| | - Gi Young Lee
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | | | | | | | | | - Rui Yan
- Janelia Research CampusAshburnUnited States
| | - Zhiheng Yu
- Janelia Research CampusAshburnUnited States
| | - Dejian Ren
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Sebastian E Brauchi
- Janelia Research CampusAshburnUnited States
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
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TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction. Nat Commun 2023; 14:164. [PMID: 36631495 PMCID: PMC9834221 DOI: 10.1038/s41467-023-35844-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Toll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous biochemical and structural studies have revealed that a minimum length of approximately 40-50 base pairs of dsRNA is necessary for TLR3 binding and dimerization. However, efficient TLR3 activation requires longer dsRNA and the molecular mechanism underlying its dsRNA length-dependent activation remains unknown. Here, we report cryo-electron microscopy analyses of TLR3 complexed with longer dsRNA. TLR3 dimers laterally form a higher multimeric complex along dsRNA, providing the basis for cooperative binding and efficient signal transduction.
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36
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Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket. J Biol Chem 2022; 299:102833. [PMID: 36581207 PMCID: PMC9898749 DOI: 10.1016/j.jbc.2022.102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022] Open
Abstract
Nitrate is one of the major nitrogen sources for most plants. Chloride channel (CLC) proteins mediate the transport and vacuole storage of nitrate in plants, but the structural basis of nitrate transport by plant CLC proteins remains unknown. Here, we solved the cryo-EM structure of ATP-bound Arabidopsis thaliana CLCa (AtCLCa) at 2.8 Å resolution. Structural comparison between nitrate-selective AtCLCa and chloride-selective CLC-7 reveals key differences in the central anion-binding site. We observed that the central nitrate is shifted by ∼1.4 Å from chloride, which is likely caused by a weaker interaction between the anion and Pro160; the side chains of aromatic residues around the central binding site are rearranged to accommodate the larger nitrate. Additionally, we identified the ATP-binding pocket of AtCLCa to be located between the cytosolic cystathionine β-synthase domains and the N-terminus. The N-terminus may mediate the ATP inhibition of AtCLCa by interacting with both ATP and the pore-forming transmembrane helix. Together, our studies provide insights into the nitrate selectivity and ATP regulation of plant CLCs.
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37
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Structural basis for gating mechanism of the human sodium-potassium pump. Nat Commun 2022; 13:5293. [PMID: 36075933 PMCID: PMC9458724 DOI: 10.1038/s41467-022-32990-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
P2-type ATPase sodium-potassium pumps (Na+/K+-ATPases) are ion-transporting enzymes that use ATP to transport Na+ and K+ on opposite sides of the lipid bilayer against their electrochemical gradients to maintain ion concentration gradients across the membranes in all animal cells. Despite the available molecular architecture of the Na+/K+-ATPases, a complete molecular mechanism by which the Na+ and K+ ions access into and are released from the pump remains unknown. Here we report five cryo-electron microscopy (cryo-EM) structures of the human alpha3 Na+/K+-ATPase in its cytoplasmic side-open (E1), ATP-bound cytoplasmic side-open (E1•ATP), ADP-AlF4− trapped Na+-occluded (E1•P-ADP), BeF3− trapped exoplasmic side-open (E2P) and MgF42− trapped K+-occluded (E2•Pi) states. Our work reveals the atomically resolved structural detail of the cytoplasmic gating mechanism of the Na+/K+-ATPase. Through cryo-EM analysis, here authors reveal conformational rearrangements that are critical for the gating mechanism of the human alpha3 Na+/K+−ATPase
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38
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Miller AN, Houlihan PR, Matamala E, Cabezas-Bratesco D, Lee GY, Cristofori-Armstrong B, Dilan TL, Sanchez-Martinez S, Matthies D, Yan R, Yu Z, Ren D, Brauchi SE, Clapham DE. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.02.506428. [PMID: 36263072 PMCID: PMC9580380 DOI: 10.1101/2022.09.02.506428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
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39
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Structural and dynamic mechanisms of GABA A receptor modulators with opposing activities. Nat Commun 2022; 13:4582. [PMID: 35933426 PMCID: PMC9357065 DOI: 10.1038/s41467-022-32212-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors are pentameric ligand-gated ion channels abundant in the central nervous system and are prolific drug targets for treating anxiety, sleep disorders and epilepsy. Diverse small molecules exert a spectrum of effects on γ-aminobutyric acid type A (GABAA) receptors by acting at the classical benzodiazepine site. They can potentiate the response to GABA, attenuate channel activity, or counteract modulation by other ligands. Structural mechanisms underlying the actions of these drugs are not fully understood. Here we present two high-resolution structures of GABAA receptors in complex with zolpidem, a positive allosteric modulator and heavily prescribed hypnotic, and DMCM, a negative allosteric modulator with convulsant and anxiogenic properties. These two drugs share the extracellular benzodiazepine site at the α/γ subunit interface and two transmembrane sites at β/α interfaces. Structural analyses reveal a basis for the subtype selectivity of zolpidem that underlies its clinical success. Molecular dynamics simulations provide insight into how DMCM switches from a negative to a positive modulator as a function of binding site occupancy. Together, these findings expand our understanding of how GABAA receptor allosteric modulators acting through a common site can have diverging activities. GABAA receptors are important targets for anxiety, sedation and anesthesia. Here, the authors present structures bound by zolpidem (Ambien), the most prescribed hypnotic in the US, and DMCM, a negative modulator, providing insights into receptor modulation.
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40
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Structure of SARS-CoV-2 membrane protein essential for virus assembly. Nat Commun 2022; 13:4399. [PMID: 35931673 PMCID: PMC9355944 DOI: 10.1038/s41467-022-32019-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022] Open
Abstract
The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein. M protein plays essential roles in virus assembly and morphogenesis. Here, authors reveal two cryo-EM structures of M protein from SARS-CoV-2 that suggest conformational dynamics of M protein and its role in virus assembly.
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41
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Chen H, Qi X, Faulkner RA, Schumacher MM, Donnelly LM, DeBose-Boyd RA, Li X. Regulated degradation of HMG CoA reductase requires conformational changes in sterol-sensing domain. Nat Commun 2022; 13:4273. [PMID: 35879350 PMCID: PMC9314443 DOI: 10.1038/s41467-022-32025-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/12/2022] [Indexed: 01/20/2023] Open
Abstract
3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) is the rate-limiting enzyme in cholesterol synthesis and target of cholesterol-lowering statin drugs. Accumulation of sterols in endoplasmic reticulum (ER) membranes accelerates degradation of HMGCR, slowing the synthesis of cholesterol. Degradation of HMGCR is inhibited by its binding to UBIAD1 (UbiA prenyltransferase domain-containing protein-1). This inhibition contributes to statin-induced accumulation of HMGCR, which limits their cholesterol-lowering effects. Here, we report cryo-electron microscopy structures of the HMGCR-UBIAD1 complex, which is maintained by interactions between transmembrane helix (TM) 7 of HMGCR and TMs 2-4 of UBIAD1. Disrupting this interface by mutagenesis prevents complex formation, enhancing HMGCR degradation. TMs 2-6 of HMGCR contain a 170-amino acid sterol sensing domain (SSD), which exists in two conformations-one of which is essential for degradation. Thus, our data supports a model that rearrangement of the TMs in the SSD permits recruitment of proteins that initate HMGCR degradation, a key reaction in the regulatory system that governs cholesterol synthesis.
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Affiliation(s)
- Hongwen Chen
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofeng Qi
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rebecca A Faulkner
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marc M Schumacher
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Linda M Donnelly
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Russell A DeBose-Boyd
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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42
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Selvakumar P, Fernández-Mariño AI, Khanra N, He C, Paquette AJ, Wang B, Huang R, Smider VV, Rice WJ, Swartz KJ, Meyerson JR. Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators. Nat Commun 2022; 13:3854. [PMID: 35788586 PMCID: PMC9253088 DOI: 10.1038/s41467-022-31285-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
The Kv1.3 potassium channel is expressed abundantly on activated T cells and mediates the cellular immune response. This role has made the channel a target for therapeutic immunomodulation to block its activity and suppress T cell activation. Here, we report structures of human Kv1.3 alone, with a nanobody inhibitor, and with an antibody-toxin fusion blocker. Rather than block the channel directly, four copies of the nanobody bind the tetramer's voltage sensing domains and the pore domain to induce an inactive pore conformation. In contrast, the antibody-toxin fusion docks its toxin domain at the extracellular mouth of the channel to insert a critical lysine into the pore. The lysine stabilizes an active conformation of the pore yet blocks ion permeation. This study visualizes Kv1.3 pore dynamics, defines two distinct mechanisms to suppress Kv1.3 channel activity with exogenous inhibitors, and provides a framework to aid development of emerging T cell immunotherapies.
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Affiliation(s)
- Purushotham Selvakumar
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Ana I Fernández-Mariño
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nandish Khanra
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Alice J Paquette
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, USA
- Minotaur Therapeutics, San Diego, CA, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, USA
- Minotaur Therapeutics, San Diego, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - William J Rice
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel R Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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Ca 2+-mediated higher-order assembly of heterodimers in amino acid transport system b 0,+ biogenesis and cystinuria. Nat Commun 2022; 13:2708. [PMID: 35577790 PMCID: PMC9110406 DOI: 10.1038/s41467-022-30293-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, causing recurrent kidney stones and kidney failure. Mutations of the regulatory glycoprotein rBAT and the amino acid transporter b0,+AT, which constitute system b0,+, are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Here, using electron cryo-microscopy and biochemistry, we discover that Ca2+ mediates higher-order assembly of system b0,+. Ca2+ stabilizes the interface between two rBAT molecules, leading to super-dimerization of b0,+AT-rBAT, which in turn facilitates N-glycan maturation and protein trafficking. A cystinuria mutant T216M and mutations of the Ca2+ site of rBAT cause the loss of higher-order assemblies, resulting in protein trapping at the ER and the loss of function. These results provide the molecular basis of system b0,+ biogenesis and type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and protein-trafficking diseases.
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44
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Lu D, Shang G, Li J, Lu Y, Bai XC, Zhang X. Activation of STING by targeting a pocket in the transmembrane domain. Nature 2022; 604:557-562. [PMID: 35388221 PMCID: PMC9098198 DOI: 10.1038/s41586-022-04559-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/15/2022] [Indexed: 12/14/2022]
Abstract
Stimulator of interferon genes (STING) is an adaptor protein in innate immunity against DNA viruses or bacteria1-5. STING-mediated immunity could be exploited in the development of vaccines or cancer immunotherapies. STING is a transmembrane dimeric protein that is located in the endoplasmic reticulum or in the Golgi apparatus. STING is activated by the binding of its cytoplasmic ligand-binding domain to cyclic dinucleotides that are produced by the DNA sensor cyclic GMP-AMP (cGAMP) synthase or by invading bacteria1,6,7. Cyclic dinucleotides induce a conformational change in the STING ligand-binding domain, which leads to a high-order oligomerization of STING that is essential for triggering the downstream signalling pathways8,9. However, the cGAMP-induced STING oligomers tend to dissociate in solution and have not been resolved to high resolution, which limits our understanding of the activation mechanism. Here we show that a small-molecule agonist, compound 53 (C53)10, promotes the oligomerization and activation of human STING through a mechanism orthogonal to that of cGAMP. We determined a cryo-electron microscopy structure of STING bound to both C53 and cGAMP, revealing a stable oligomer that is formed by side-by-side packing and has a curled overall shape. Notably, C53 binds to a cryptic pocket in the STING transmembrane domain, between the two subunits of the STING dimer. This binding triggers outward shifts of transmembrane helices in the dimer, and induces inter-dimer interactions between these helices to mediate the formation of the high-order oligomer. Our functional analyses show that cGAMP and C53 together induce stronger activation of STING than either ligand alone.
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Affiliation(s)
- Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yong Lu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Miyauchi Y, Kimura A, Sawai M, Fujimoto K, Hirota Y, Tanaka Y, Takechi S, Mackenzie PI, Ishii Y. Use of a Baculovirus-Mammalian Cell Expression-System for Expression of Drug-Metabolizing Enzymes: Optimization of Infection With a Focus on Cytochrome P450 3A4. Front Pharmacol 2022; 13:832931. [PMID: 35295333 PMCID: PMC8919721 DOI: 10.3389/fphar.2022.832931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Heterologous expression systems are important for analyzing the effects of genetic factors including single nucleotide polymorphisms on the functions of drug-metabolizing enzymes. In this study, we focused on a baculovirus-mammalian cell (Bac-Mam) expression system as a safer and more efficient approach for this purpose. The baculovirus-insect cell expression system is widely utilized in large-scale protein expression. Baculovirus has been shown to also infect certain mammalian cells, although the virus only replicates in insect cells. With this knowledge, baculovirus is now being applied in a mammalian expression system called the Bac-Mam system wherein a gene-modified baculovirus is used whose promotor is replaced with one that can function in mammalian cells. We subcloned open-reading frames of cytochrome P450 3A4 (CYP3A4), UDP-glucuronosyltransferase (UGT) 1A1, and UGT2B7 into a transfer plasmid for the Bac-Mam system, and prepared recombinant Bac-Mam virus. The obtained virus was amplified in insect Sf9 cells and used to infect mammalian COS-1 cells. Expression of CYP3A4, UGT1A1, and UGT2B7 in COS-1 cell homogenates were confirmed by immunoblotting. Optimum infection conditions including the amount of Bac-Mam virus, culture days before collection, and concentration of sodium butyrate, an enhancer of viral-transduction were determined by monitoring CYP3A4 expression. Expressed CYP3A4 showed appropriate activity without supplying hemin/5-aminolevulinic acid or co-expressing with NADPH-cytochrome P450 reductase. Further, we compared gene transfer efficiency between the Bac-Mam system and an established method using recombinant plasmid and transfection reagent. Our results indicate that the Bac-Mam system can be applied to introduce drug-metabolizing enzyme genes into mammalian cells that are widely used in drug metabolism research. The expressed enzymes are expected to undergo appropriate post-translational modification as they are in mammalian bodies. The Bac-Mam system may thus accelerate pharmacogenetics and pharmacogenomics research.
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Affiliation(s)
- Yuu Miyauchi
- Laboratory of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan.,Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akane Kimura
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Madoka Sawai
- Laboratory of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Keiko Fujimoto
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuko Hirota
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitaka Tanaka
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinji Takechi
- Laboratory of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Peter I Mackenzie
- Clinical Pharmacology, College of Medicine and Public Health, Flinders Medical Centre and Flinders University, Adelaide, SA, Australia
| | - Yuji Ishii
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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Meyerowitz JG, Robertson MJ, Barros-Álvarez X, Panova O, Nwokonko RM, Gao Y, Skiniotis G. The oxytocin signaling complex reveals a molecular switch for cation dependence. Nat Struct Mol Biol 2022; 29:274-281. [PMID: 35241813 DOI: 10.1038/s41594-022-00728-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
Oxytocin (OT) and vasopressin (AVP) are conserved peptide signaling hormones that are critical for diverse processes including osmotic homeostasis, reproduction, lactation and social interaction. OT acts through the oxytocin receptor (OTR), a magnesium-dependent G protein-coupled receptor that is a therapeutic target for treatment of postpartum hemorrhage, dysfunctional labor and autism. However, the molecular mechanisms that underlie OTR activation by OT and the dependence on magnesium remain unknown. Here we present the wild-type active-state structure of human OTR bound to OT and miniGq/i determined by cryo-EM. The structure reveals a unique activation mechanism adopted by OTR involving both the formation of a Mg2+ coordination complex between OT and the receptor, and disruption of transmembrane helix 7 (TM7) by OT. Our functional assays demonstrate the role of TM7 disruption and provide the mechanism of full agonism by OT and partial agonism by OT analogs. Furthermore, we find that the identity of a single cation-coordinating residue across vasopressin family receptors determines whether the receptor is cation-dependent. Collectively, these results demonstrate how the Mg2+-dependent OTR is activated by OT, provide essential information for structure-based drug discovery efforts and shed light on the molecular determinants of cation dependence of vasopressin family receptors throughout the animal kingdom.
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Affiliation(s)
- Justin G Meyerowitz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ximena Barros-Álvarez
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert M Nwokonko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Gao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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Structural and functional characterization of an achromatopsia-associated mutation in a phototransduction channel. Commun Biol 2022; 5:190. [PMID: 35233102 PMCID: PMC8888761 DOI: 10.1038/s42003-022-03120-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 02/03/2022] [Indexed: 12/30/2022] Open
Abstract
Numerous missense mutations in cyclic nucleotide-gated (CNG) channels cause achromatopsia and retinitis pigmentosa, but the underlying pathogenic mechanisms are often unclear. We investigated the structural basis and molecular/cellular effects of R410W, an achromatopsia-associated, presumed loss-of-function mutation in human CNGA3. Cryo-EM structures of the Caenorhabditis elegans TAX-4 CNG channel carrying the analogous mutation, R421W, show that most apo channels are open. R421, located in the gating ring, interacts with the S4 segment in the closed state. R421W disrupts this interaction, destabilizes the closed state, and stabilizes the open state. CNGA3_R410W/CNGB3 and TAX4_R421W channels are spontaneously active without cGMP and induce cell death, suggesting cone degeneration triggered by spontaneous CNG channel activity as a possible cause of achromatopsia. Our study sheds new light on CNG channel allosteric gating, provides an impetus for a reevaluation of reported loss-of-function CNG channel missense disease mutations, and has implications for mutation-specific treatment of retinopathy. The R410W mutation in the cone photoreceptor CNG channel, linked to achromatopsia and assumed to be a loss-of-function variant, causes the channel to open spontaneously as revealed by cryo-EM, electrophysiology and calcium imaging, and is cytotoxic. This study calls for a multipronged evaluation/reevaluation of other inherited mutations associated with CNG channelopathy.
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Wang EY, Dai Y, Rosen CE, Schmitt MM, Dong MX, Ferré EM, Liu F, Yang Y, González-Hernández JA, Meffre E, Hinchcliff M, Koumpouras F, Lionakis MS, Ring AM. High-throughput identification of autoantibodies that target the human exoproteome. CELL REPORTS METHODS 2022; 2:100172. [PMID: 35360706 PMCID: PMC8967185 DOI: 10.1016/j.crmeth.2022.100172] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
Autoantibodies that recognize extracellular proteins (the exoproteome) exert potent biological effects but are challenging to detect. Here, we developed rapid extracellular antigen profiling (REAP), a high-throughput technique for the comprehensive discovery of exoproteome-targeting autoantibodies. Patient samples are applied to a genetically barcoded yeast surface display library containing 2,688 human extracellular proteins. Antibody-coated yeast are isolated, and sequencing of barcodes is used to identify displayed antigens. To benchmark REAP's performance, we screened 77 patients with autoimmune polyglandular syndrome type 1 (APS-1). REAP sensitively and specifically detected both known and previously unidentified autoantibodies in APS-1. We further screened 106 patients with systemic lupus erythematosus (SLE) and identified numerous autoantibodies, several of which were associated with disease severity or specific clinical manifestations and exerted functional effects on cell signaling ex vivo. These findings demonstrate the utility of REAP to atlas the expansive landscape of exoproteome-targeting autoantibodies and their impacts on patient health outcomes.
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Affiliation(s)
- Eric Y. Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Connor E. Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monica M. Schmitt
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mei X. Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Elise M.N. Ferré
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Eric Meffre
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monique Hinchcliff
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fotios Koumpouras
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA
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He C, Maniyar RR, Avraham Y, Zappasodi R, Rusinova R, Newman W, Heath H, Wolchok JD, Dahan R, Merghoub T, Meyerson JR. Therapeutic antibody activation of the glucocorticoid-induced TNF receptor by a clustering mechanism. SCIENCE ADVANCES 2022; 8:eabm4552. [PMID: 35213218 PMCID: PMC8880771 DOI: 10.1126/sciadv.abm4552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/12/2022] [Indexed: 05/11/2023]
Abstract
GITR is a TNF receptor, and its activation promotes immune responses and drives antitumor activity. The receptor is activated by the GITR ligand (GITRL), which is believed to cluster receptors into a high-order array. Immunotherapeutic agonist antibodies also activate the receptor, but their mechanisms are not well characterized. We solved the structure of full-length mouse GITR bound to Fabs from the antibody DTA-1. The receptor is a dimer, and each subunit binds one Fab in an orientation suggesting that the antibody clusters receptors. Binding experiments with purified proteins show that DTA-1 IgG and GITRL both drive extensive clustering of GITR. Functional data reveal that DTA-1 and the anti-human GITR antibody TRX518 activate GITR in their IgG forms but not as Fabs. Thus, the divalent character of the IgG agonists confers an ability to mimic GITRL and cluster and activate GITR. These findings will inform the clinical development of this class of antibodies for immuno-oncology.
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Affiliation(s)
- Changhao He
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Rachana R. Maniyar
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yahel Avraham
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Roberta Zappasodi
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Radda Rusinova
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Jedd D. Wolchok
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rony Dahan
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel R. Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
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Abstract
Adenylyl cyclase 9 (AC9) is a membrane-bound enzyme that converts ATP into cAMP. The enzyme is weakly activated by forskolin, fully activated by the G protein Gαs subunit and is autoinhibited by the AC9 C-terminus. Although our recent structural studies of the AC9-Gαs complex provided the framework for understanding AC9 autoinhibition, the conformational changes that AC9 undergoes in response to activator binding remains poorly understood. Here, we present the cryo-EM structures of AC9 in several distinct states: (i) AC9 bound to a nucleotide inhibitor MANT-GTP, (ii) bound to an artificial activator (DARPin C4) and MANT-GTP, (iii) bound to DARPin C4 and a nucleotide analogue ATPαS, (iv) bound to Gαs and MANT-GTP. The artificial activator DARPin C4 partially activates AC9 by binding at a site that overlaps with the Gαs binding site. Together with the previously observed occluded and forskolin-bound conformations, structural comparisons of AC9 in the four conformations described here show that secondary structure rearrangements in the region surrounding the forskolin binding site are essential for AC9 activation. Adenylyl cyclases (ACs) generate the second messenger cAMP and play an important role in cellular signaling. Here, the authors use cryo-EM to trace the conformational changes resulting from binding to partial and full activators to one of these enzymes, AC9.
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