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Baxter L, Hopkins S, O'Connor KC, Pham MC, Nowak RJ, Monson NL, Blackburn K, Hibbs RE, Vernino S, Noviello CM. Fluorescence-detection size-exclusion chromatography specifically detects autoantibodies targeting the ganglionic acetylcholine receptor in patients with autoimmune autonomic ganglionopathy. J Neuroimmunol 2024; 396:578454. [PMID: 39277987 DOI: 10.1016/j.jneuroim.2024.578454] [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: 06/17/2024] [Revised: 09/03/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
Autoimmune autonomic ganglionopathy (AAG) is a rare disease wherein autoantibodies target the ganglionic acetylcholine receptor (gAChR). Current diagnosis in the United States depends upon clinical symptoms and positive autoantibody detection using a radioimmunoprecipitation assay (RIA). Here we offer a proof-of-principle study on an alternative method, fluorescence-detection size-exclusion-chromatography (FSEC). We show FSEC can detect autoantibodies against gAChR from patient sera but not healthy controls or samples from other autoimmune diseases. We compare FSEC to RIA and find good correlation. We discuss potential advantages of using FSEC as an alternative or as a first-step diagnostic prior to pursuing existing methodologies.
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Affiliation(s)
- Leah Baxter
- Department of Neurobiology, University of California San Diego, United States
| | - Steven Hopkins
- Department of Neurology, University of Texas Southwestern Medical Center, United States
| | - Kevin C O'Connor
- Department of Neurology, Yale University School of Medicine, United States; Department of Immunobiology, Yale University School of Medicine, United States
| | - Minh C Pham
- Department of Neurology, Yale University School of Medicine, United States
| | - Richard J Nowak
- Department of Immunobiology, Yale University School of Medicine, United States
| | - Nancy L Monson
- Department of Neurology, University of Texas Southwestern Medical Center, United States
| | - Kyle Blackburn
- Department of Neurology, University of Texas Southwestern Medical Center, United States
| | - Ryan E Hibbs
- Department of Neurobiology, University of California San Diego, United States; Department of Pharmacology, University of California San Diego, United States
| | - Steven Vernino
- Department of Neurology, University of Texas Southwestern Medical Center, United States
| | - Colleen M Noviello
- Department of Neurobiology, University of California San Diego, United States.
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2
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Radwan WH, Abdelhafez AAM, Mahgoub AE, Zayed MS. Streptomyces avermitilis MICNEMA2022: a new biorational strain for producing abamectin as an integrated nematode management agent. BMC Microbiol 2024; 24:329. [PMID: 39244577 PMCID: PMC11380338 DOI: 10.1186/s12866-024-03466-3] [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: 01/31/2024] [Accepted: 08/16/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Abamectin (ABA) is considered a powerful insecticidal and anthelmintic agent. It is an intracellular product of Streptomyces avermitilis; is synthesized through complicated pathways and can then be extracted from mycelial by methanol extraction. ABA serves as a biological control substance against the root-knot nematode Meloidogyne incognita. This investigation is intended to reach a new strain of S. avermitilis capable of producing ABA effectively. RESULTS Among the sixty actinobacterial isolates, Streptomyces St.53 isolate was chosen for its superior nematicidal effectiveness. The mycelial-methanol extract of isolate St.53 exhibited a maximum in vitro mortality of 100% in one day. In the greenhouse experiment, the mycelial-methanol extract demonstrated, for the second-stage juveniles (J2s), 75.69% nematode reduction and 0.84 reproduction rate (Rr) while for the second-stage juveniles (J2s), the culture suspension demonstrated 75.38% nematode reduction and 0.80 reproduction rate (Rr). Molecular identification for St.53 was performed using 16 S rRNA gene analysis and recorded in NCBI Genbank as S. avermitilis MICNEMA2022 with accession number (OP108264.1). LC-MS was utilized to detect and identify abamectin in extracts while HPLC analysis was carried out for quantitative determination. Both abamectin B1a and abamectin B1b were produced and detected at retention times of 4.572 and 3.890 min respectively. CONCLUSION Streptomyces avermitilis MICNEMA2022 proved to be an effective source for producing abamectin as a biorational agent for integrated nematode management.
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Affiliation(s)
- Wafaa H Radwan
- Department of Microbiology, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Shoubra El-Kheima, Cairo, 11566, Egypt
| | - Ahmed A M Abdelhafez
- Department of Microbiology, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Shoubra El-Kheima, Cairo, 11566, Egypt
- Faculty of Organic Agriculture, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Ahmed E Mahgoub
- Department of Plant Protection, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Shoubra El- Kheima, Cairo, 11566, Egypt
| | - Mona S Zayed
- Department of Microbiology, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Shoubra El-Kheima, Cairo, 11566, Egypt.
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3
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Cecchini M, Corringer PJ, Changeux JP. The Nicotinic Acetylcholine Receptor and Its Pentameric Homologs: Toward an Allosteric Mechanism of Signal Transduction at the Atomic Level. Annu Rev Biochem 2024; 93:339-366. [PMID: 38346274 DOI: 10.1146/annurev-biochem-030122-033116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The nicotinic acetylcholine receptor has served, since its biochemical identification in the 1970s, as a model of an allosteric ligand-gated ion channel mediating signal transition at the synapse. In recent years, the application of X-ray crystallography and high-resolution cryo-electron microscopy, together with molecular dynamic simulations of nicotinic receptors and homologs, have opened a new era in the understanding of channel gating by the neurotransmitter. They reveal, at atomic resolution, the diversity and flexibility of the multiple ligand-binding sites, including recently discovered allosteric modulatory sites distinct from the neurotransmitter orthosteric site, and the conformational dynamics of the activation process as a molecular switch linking these multiple sites. The model emerging from these studies paves the way for a new pharmacology based, first, upon the occurrence of an original mode of indirect allosteric modulation, distinct from a steric competition for a single and rigid binding site, and second, the design of drugs that specifically interact with privileged conformations of the receptor such as agonists, antagonists, and desensitizers. Research on nicotinic receptors is still at the forefront of understanding the mode of action of drugs on the nervous system.
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Affiliation(s)
- Marco Cecchini
- Institut de Chimie de Strasbourg, CNRS UMR 7177, Université de Strasbourg, Strasbourg, France
| | - Pierre-Jean Corringer
- Channel Receptors Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Paris, France
| | - Jean-Pierre Changeux
- Department of Neuroscience, Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Paris, France;
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4
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Obiol DJ, Amundarain MJ, Zamarreño F, Vietri A, Antollini SS, Costabel MD. Oleic Acid Could Act as a Channel Blocker in the Inhibition of nAChR: Insights from Molecular Dynamics Simulations. J Phys Chem B 2024; 128:2398-2411. [PMID: 38445598 DOI: 10.1021/acs.jpcb.3c07067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The activation of the muscular nicotinic acetylcholine receptor (nAChR) produces the opening of the channel, with the consequent increase in the permeability of cations, triggering an excitatory signal. Free fatty acids (FFA) are known to modulate the activity of the receptor as noncompetitive antagonists, acting at the membrane-AChR interface. We present molecular dynamics simulations of a model of nAChR in a desensitized closed state embedded in a lipid bilayer in which distinct membrane phospholipids were replaced by two different monounsaturated FFA that differ in the position of a double bond. This allowed us to detect and describe that the cis-18:1ω-9 FFA were located at the interface between the transmembrane segments of α2 and γ subunits diffused into the channel lumen with the consequent potential ability to block the channel to the passage of ions.
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Affiliation(s)
- Diego J Obiol
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - María J Amundarain
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
- Department of Chemistry, Organic Chemistry III, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Fernando Zamarreño
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Agustín Vietri
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Silvia S Antollini
- Instituto de Investigaciones Bioquímicas de Bahía Blanca CONICET-UNS, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, B8000FWB Bahía Blanca, Argentina
| | - Marcelo D Costabel
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Avenida Leandro N. Alem 1253, B8000CPB Bahía Blanca, Argentina
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5
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Bergh C, Rovšnik U, Howard R, Lindahl E. Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. eLife 2024; 12:RP86016. [PMID: 38289224 PMCID: PMC10945520 DOI: 10.7554/elife.86016] [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] [Indexed: 02/01/2024] Open
Abstract
Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
| | - Urška Rovšnik
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Rebecca Howard
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Erik Lindahl
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
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6
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Pitman C, Santiago-McRae E, Lohia R, Bassi K, Joseph TT, Hansen MEB, Brannigan G. The blobulator: a webtool for identification and visual exploration of hydrophobic modularity in protein sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575761. [PMID: 38293114 PMCID: PMC10827107 DOI: 10.1101/2024.01.15.575761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Motivation Clusters of hydrophobic residues are known to promote structured protein stability and drive protein aggregation. Recent work has shown that identifying contiguous hydrophobic residue clusters (termed "blobs") has proven useful in both intrinsically disordered protein (IDP) simulation and human genome studies. However, a graphical interface was unavailable. Results Here, we present the blobulator: an interactive and intuitive web interface to detect intrinsic modularity in any protein sequence based on hydrophobicity. We demonstrate three use cases of the blobulator and show how identifying blobs with biologically relevant parameters provides useful information about a globular protein, two orthologous membrane proteins, and an IDP. Other potential applications are discussed, including: predicting protein segments with critical roles in tertiary interactions, providing a definition of local order and disorder with clear edges, and aiding in predicting protein features from sequence. Availability The blobulator GUI can be found at www.blobulator.branniganlab.org, and the source code with pip installable command line tool can be found on GitHub at www.GitHub.com/BranniganLab/blobulator.
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Affiliation(s)
- Connor Pitman
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Ruchi Lohia
- Department of Physiology, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, Ontario, Canada
| | - Kaitlin Bassi
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, JMB 305, 3620 Hamilton Walk, 19104, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, 19104, PA, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
- Department of Physics, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
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7
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Raisch T, Raunser S. The modes of action of ion-channel-targeting neurotoxic insecticides: lessons from structural biology. Nat Struct Mol Biol 2023; 30:1411-1427. [PMID: 37845413 DOI: 10.1038/s41594-023-01113-5] [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: 11/23/2022] [Accepted: 08/31/2023] [Indexed: 10/18/2023]
Abstract
Insecticides are indispensable tools for plant protection in modern agriculture. Despite having highly heterogeneous structures, many neurotoxic insecticides use similar principles to inhibit or deregulate neuronal ion channels. Insecticides targeting pentameric ligand-gated channels are structural mimetics of neurotransmitters or manipulate and deregulate the proteins. Those binding to (pseudo-)tetrameric voltage-gated(-like) channels, on the other hand, are natural or synthetic compounds that directly block the ion-conducting pore or prevent conformational changes in the transmembrane domain necessary for opening and closing the pore. The use of a limited number of inhibition mechanisms can be problematic when resistances arise and become more widespread. Therefore, there is a rising interest in the development of insecticides with novel mechanisms that evade resistance and are pest-insect-specific. During the last decade, most known insecticide targets, many with bound compounds, have been structurally characterized, bringing the rational design of novel classes of agrochemicals within closer reach than ever before.
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Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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8
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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [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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9
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Tribiños F, Cuevas P, Cornejo I, Sepúlveda FV, Cid LP. A new family of glutamate-gated chloride channels in parasitic sea louse Caligus rogercresseyi: A subunit refractory to activation by ivermectin is dominant in heteromeric assemblies. PLoS Pathog 2023; 19:e1011188. [PMID: 36917600 PMCID: PMC10038264 DOI: 10.1371/journal.ppat.1011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 03/24/2023] [Accepted: 02/07/2023] [Indexed: 03/16/2023] Open
Abstract
Sea louse ectoparasitosis is a major threat to fish aquaculture. Avermectins such as ivermectin and emamectin have been effectively used against sea louse infestation, but the emergence of resistance has limited their use. A better understanding of the molecular targets of avermectins is essential to the development of novel treatment strategies or new, more effective drugs. Avermectins are known to act by inhibiting neurotransmission through allosteric activation of glutamate-gated chloride channels (GluCls). We have investigated the GluCl subunit present in Caligus rogercresseyi, a sea louse affecting aquaculture in the Southern hemisphere. We identify four new subunits, CrGluCl-B to CrGluCl-E, and characterise them functionally. CrGluCl-A (previously reported as CrGluClα), CrGluCl-B and CrGluCl-C all function as glutamate channel receptors with different sensitivities to the agonist, but in contrast to subunit -A and -C, CrGluCl-B is not activated by ivermectin but is rather antagonised by the drug. CrGluCl-D channel appears active in the absence of any stimulation by glutamate or ivermectin and CrGluCl-E does not exhibit any activity. Notably, the expression of CrGluCl-B with either -A or -C subunits gives rise to receptors unresponsive to ivermectin and showing altered response to glutamate, suggesting that coexpression has led to the preferential formation of heteromers to which the presence of CrGluCl-B confers the property of ivermectin-activation refractoriness. Furthermore, there was evidence for heteromer formation with novel properties only when coexpressing pairs E/C and D/B CrGluCl subtypes. Site-directed mutagenesis shows that three transmembrane domain residues contribute to the lack of activation by ivermectin, most crucially Gln 15' in M2, with mutation Q15'T (the residue present in ivermectin-activated subunits A and C) conferring ivermectin activation to CrGluCl-B. The differential response to avermectin of these Caligus rogercresseyi GluClsubunits, which are highly conserved in the Northern hemisphere sea louse Lepeophtheirus salmonis, could have an influence on the response of these parasites to treatment with macrocyclic lactones. They could serve as molecular markers to assess susceptibility to existing treatments and might be useful molecular targets in the search for novel antiparasitic drugs.
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Affiliation(s)
| | | | - Isabel Cornejo
- Centro de Estudios Científicos (CECs), Valdivia, Chile
- Facultad de Ciencias para el Cuidado de la Salud, Universidad San Sebastián, Valdivia, Chile
| | - Francisco V Sepúlveda
- Centro de Estudios Científicos (CECs), Valdivia, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
| | - L Pablo Cid
- Centro de Estudios Científicos (CECs), Valdivia, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile
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10
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Hernandez CC, Shen Y, Hu N, Shen W, Narayanan V, Ramsey K, He W, Zou L, Macdonald RL. GABRG2 Variants Associated with Febrile Seizures. Biomolecules 2023; 13:414. [PMID: 36979350 PMCID: PMC10046037 DOI: 10.3390/biom13030414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Febrile seizures (FS) are the most common form of epilepsy in children between six months and five years of age. FS is a self-limited type of fever-related seizure. However, complicated prolonged FS can lead to complex partial epilepsy. We found that among the GABAA receptor subunit (GABR) genes, most variants associated with FS are harbored in the γ2 subunit (GABRG2). Here, we characterized the effects of eight variants in the GABAA receptor γ2 subunit on receptor biogenesis and channel function. Two-thirds of the GABRG2 variants followed the expected autosomal dominant inheritance in FS and occurred as missense and nonsense variants. The remaining one-third appeared as de novo in the affected probands and occurred only as missense variants. The loss of GABAA receptor function and dominant negative effect on GABAA receptor biogenesis likely caused the FS phenotype. In general, variants in the GABRG2 result in a broad spectrum of phenotypic severity, ranging from asymptomatic, FS, genetic epilepsy with febrile seizures plus (GEFS+), and Dravet syndrome individuals. The data presented here support the link between FS, epilepsy, and GABRG2 variants, shedding light on the relationship between the variant topological occurrence and disease severity.
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Affiliation(s)
- Ciria C. Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanwen Shen
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Wen He
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Liping Zou
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Robert L. Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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11
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Cryo-EM structure supports a role of AQP7 as a junction protein. Nat Commun 2023; 14:600. [PMID: 36737436 PMCID: PMC9898259 DOI: 10.1038/s41467-023-36272-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Aquaglyceroporin 7 (AQP7) facilitates glycerol flux across the plasma membrane with a critical physiological role linked to metabolism, obesity, and associated diseases. Here, we present the single-particle cryo-EM structure of AQP7 determined at 2.55 Å resolution adopting two adhering tetramers, stabilized by extracellularly exposed loops, in a configuration like that of the well-characterized interaction of AQP0 tetramers. The central pore, in-between the four monomers, displays well-defined densities restricted by two leucine filters. Gas chromatography mass spectrometry (GC/MS) results show that the AQP7 sample contains glycerol 3-phosphate (Gro3P), which is compatible with the identified features in the central pore. AQP7 is shown to be highly expressed in human pancreatic α- and β- cells suggesting that the identified AQP7 octamer assembly, in addition to its function as glycerol channel, may serve as junction proteins within the endocrine pancreas.
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12
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Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, Trent Moreland K, Deng Z, Rau M, Fitzpatrick JAJ, Yuan P, Joseph TT, Hénin J, Brannigan G, Cheng WWL. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nat Commun 2022; 13:7017. [PMID: 36385237 PMCID: PMC9668969 DOI: 10.1038/s41467-022-34813-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site.
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Affiliation(s)
- John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Brett Deng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maya S Washington
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Lawrence J Chen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - K Trent Moreland
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, MO, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Cité, CNRS UPR 9080, Paris, France
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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13
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Gallagher CI, Ha DA, Harvey RJ, Vandenberg RJ. Positive Allosteric Modulators of Glycine Receptors and Their Potential Use in Pain Therapies. Pharmacol Rev 2022; 74:933-961. [PMID: 36779343 PMCID: PMC9553105 DOI: 10.1124/pharmrev.122.000583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/26/2022] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Glycine receptors are ligand-gated ion channels that mediate synaptic inhibition throughout the mammalian spinal cord, brainstem, and higher brain regions. They have recently emerged as promising targets for novel pain therapies due to their ability to produce antinociception by inhibiting nociceptive signals within the dorsal horn of the spinal cord. This has greatly enhanced the interest in developing positive allosteric modulators of glycine receptors. Several pharmaceutical companies and research facilities have attempted to identify new therapeutic leads by conducting large-scale screens of compound libraries, screening new derivatives from natural sources, or synthesizing novel compounds that mimic endogenous compounds with antinociceptive activity. Advances in structural techniques have also led to the publication of multiple high-resolution structures of the receptor, highlighting novel allosteric binding sites and providing additional information for previously identified binding sites. This has greatly enhanced our understanding of the functional properties of glycine receptors and expanded the structure activity relationships of novel pharmacophores. Despite this, glycine receptors are yet to be used as drug targets due to the difficulties in obtaining potent, selective modulators with favorable pharmacokinetic profiles that are devoid of side effects. This review presents a summary of the structural basis for how current compounds cause positive allosteric modulation of glycine receptors and discusses their therapeutic potential as analgesics. SIGNIFICANCE STATEMENT: Chronic pain is a major cause of disability, and in Western societies, this will only increase as the population ages. Despite the high level of prevalence and enormous socioeconomic burden incurred, treatment of chronic pain remains limited as it is often refractory to current analgesics, such as opioids. The National Institute for Drug Abuse has set finding effective, safe, nonaddictive strategies to manage chronic pain as their top priority. Positive allosteric modulators of glycine receptors may provide a therapeutic option.
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Affiliation(s)
- Casey I Gallagher
- Molecular Biomedicine, School of Medical Sciences, University of Sydney, Sydney, Australia (C.I.G., D.A.H., R.J.V.) and Biomedical Science, School of Health and Behavioural Sciences and Sunshine Coast Health Institute, University of the Sunshine Coast, Maroochydore, Australia (R.J.H.)
| | - Damien A Ha
- Molecular Biomedicine, School of Medical Sciences, University of Sydney, Sydney, Australia (C.I.G., D.A.H., R.J.V.) and Biomedical Science, School of Health and Behavioural Sciences and Sunshine Coast Health Institute, University of the Sunshine Coast, Maroochydore, Australia (R.J.H.)
| | - Robert J Harvey
- Molecular Biomedicine, School of Medical Sciences, University of Sydney, Sydney, Australia (C.I.G., D.A.H., R.J.V.) and Biomedical Science, School of Health and Behavioural Sciences and Sunshine Coast Health Institute, University of the Sunshine Coast, Maroochydore, Australia (R.J.H.)
| | - Robert J Vandenberg
- Molecular Biomedicine, School of Medical Sciences, University of Sydney, Sydney, Australia (C.I.G., D.A.H., R.J.V.) and Biomedical Science, School of Health and Behavioural Sciences and Sunshine Coast Health Institute, University of the Sunshine Coast, Maroochydore, Australia (R.J.H.)
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14
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Speculation on How RIC-3 and Other Chaperones Facilitate α7 Nicotinic Receptor Folding and Assembly. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144527. [PMID: 35889400 PMCID: PMC9318448 DOI: 10.3390/molecules27144527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022]
Abstract
The process of how multimeric transmembrane proteins fold and assemble in the endoplasmic reticulum is not well understood. The alpha7 nicotinic receptor (α7 nAChR) is a good model for multimeric protein assembly since it has at least two independent and specialized chaperones: Resistance to Inhibitors of Cholinesterase 3 (RIC-3) and Nicotinic Acetylcholine Receptor Regulator (NACHO). Recent cryo-EM and NMR data revealed structural features of α7 nAChRs. A ser-ala-pro (SAP) motif precedes a structurally important but unique "latch" helix in α7 nAChRs. A sampling of α7 sequences suggests the SAP motif is conserved from C. elegans to humans, but the latch sequence is only conserved in vertebrates. How RIC-3 and NACHO facilitate receptor subunits folding into their final pentameric configuration is not known. The artificial intelligence program AlphaFold2 recently predicted structures for NACHO and RIC-3. NACHO is highly conserved in sequence and structure across species, but RIC-3 is not. This review ponders how different intrinsically disordered RIC-3 isoforms from C. elegans to humans interact with α7 nAChR subunits despite having little sequence homology across RIC-3 species. Two models from the literature about how RIC-3 assists α7 nAChR assembly are evaluated considering recent structural information about the receptor and its chaperones.
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15
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Molecular encoding and synaptic decoding of context during salt chemotaxis in C. elegans. Nat Commun 2022; 13:2928. [PMID: 35624091 PMCID: PMC9142520 DOI: 10.1038/s41467-022-30279-7] [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: 10/07/2021] [Accepted: 04/25/2022] [Indexed: 01/21/2023] Open
Abstract
Animals navigate toward favorable locations using various environmental cues. However, the mechanism of how the goal information is encoded and decoded to generate migration toward the appropriate direction has not been clarified. Here, we describe the mechanism of migration towards a learned concentration of NaCl in Caenorhabditis elegans. In the salt-sensing neuron ASER, the difference between the experienced and currently perceived NaCl concentration is encoded as phosphorylation at Ser65 of UNC-64/Syntaxin 1 A through the protein kinase C(PKC-1) signaling pathway. The phosphorylation affects basal glutamate transmission from ASER, inducing the reversal of the postsynaptic response of reorientation-initiating neurons (i.e., from inhibitory to excitatory), guiding the animals toward the experienced concentration. This process, the decoding of the context, is achieved through the differential sensitivity of postsynaptic excitatory and inhibitory receptors. Our results reveal the mechanism of migration based on the synaptic plasticity that conceptually differs from the classical ones. The nematode C. elegans moves around to find an optimal environment. This work demonstrates how it can detect and move towards a previously learned salinity using the salt-sensing neuron ASER.
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16
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Mesoy SM, Bridgland-Taylor M, Lummis SCR. Mutations of the nACh Receptor M4 Helix Reveal Different Phenotypes in Different Expression Systems: Could Lipids be Responsible? Front Physiol 2022; 13:850782. [PMID: 35600303 PMCID: PMC9116227 DOI: 10.3389/fphys.2022.850782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
The role of the outermost helix (M4) in the pentameric ligand-gated ion channel (pLGIC) family is currently not fully understood. It is known that M4 is important for receptor assembly, possibly via interactions with neighboring M1 and M3 helices. M4 can also transmit information on the lipid content of the membrane to the gating mechanism, and it may form a link to the extracellular domain via the Cys-loop. Our previous study examining the α4β2 nACh receptor M4 helix using HEK cells indicated M4 here is more sensitive to change than those of other pLGIC. Many of these other studies, however, were performed in Xenopus oocytes. Here we examine the nine previously identified nonfunctional α4β2 nACh receptor M4 mutant receptors using this system. The data reveal that seven of these mutant receptors do function when expressed in oocytes, with only 2, the conserved Asp at the intracellular end of M4 and a Phe in the center, having a similar phenotype (nonfunctional) in both HEK cells and oocytes. The oocyte data are more consistent with studies in other pLGIC and demonstrate the importance of the expression system used. Of the many differences between these two expression systems, we suggest that the different lipid content of the plasma membrane is a possible candidate for explaining these discrepancies.
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Affiliation(s)
- Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Bridgland-Taylor
- Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Sarah C. R. Lummis,
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17
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O’Halloran DM. Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification. G3 GENES|GENOMES|GENETICS 2022; 12:6472361. [PMID: 35100348 PMCID: PMC9210312 DOI: 10.1093/g3journal/jkab438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/23/2022]
Abstract
Glutamate-gated chloride channels belong to the Cys-loop receptor superfamily. Glutamate-gated chloride channels are activated by glutamate and form substrates for the antiparasitic drugs from the avermectin family. Glutamate-gated chloride channels are pentameric, and each subunit contains an N-terminal extracellular domain that binds glutamate and 4 helical transmembrane domains, which contain binding sites for avermectin drugs. In order to provide more insight into phylum-wide patterns of glutamate-gated chloride subunit gene expansion and sequence diversity across nematodes, we have developed a database of predicted glutamate-gated chloride subunit genes from 125 nematode species. Our analysis into this dataset described assorted patterns of species-specific glutamate-gated chloride gene counts across different nematodes as well as sequence diversity in key residues thought to be involved in avermectin binding.
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Affiliation(s)
- Damien M O’Halloran
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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18
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Kono M, Ozoe F, Asahi M, Ozoe Y. State-dependent inhibition of GABA receptor channels by the ectoparasiticide fluralaner. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 181:105008. [PMID: 35082031 DOI: 10.1016/j.pestbp.2021.105008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
γ-Aminobutyric acid (GABA) receptors (GABARs) are ligand-gated Cl- channels, which cause an influx of Cl- that inhibits excitation in postsynaptic cells upon activation. GABARs are important targets for drugs and pest control chemicals. We previously reported that the isoxazoline ectoparasiticide fluralaner inhibits GABA-induced currents in housefly (Musca domestica) GABARs by binding to the putative binding site in the transmembrane subunit interface. In the present study, we investigated whether fluralaner inhibits the GABA response in the GABAR activated state, the resting state, or both, using two-electrode voltage clamp electrophysiology protocols. We found that inhibition progresses over time to steady-state levels by repeated short applications of GABA during fluralaner perfusion. The GABA response was not impaired by fluralaner treatment in the GABAR resting state. However, once inhibited, the GABA response was not restored by repeated applications of GABA. These findings suggest that fluralaner might reach the binding site of the activated conformation of GABARs in a stepwise fashion and tightly bind to it.
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Affiliation(s)
- Miku Kono
- Faculty of Life and Environmental Sciences, Shimane University, Matsue, Shimane 690-8504, Japan
| | - Fumiyo Ozoe
- Interdisciplinary Institute for Science Research, Organization for Research and Academic Information, Shimane University, Matsue, Shimane 690-8504, Japan
| | - Miho Asahi
- Biological Research Laboratories, Nissan Chemical Corporation, Shiraoka, Saitama 349-0294, Japan
| | - Yoshihisa Ozoe
- Faculty of Life and Environmental Sciences, Shimane University, Matsue, Shimane 690-8504, Japan; Interdisciplinary Institute for Science Research, Organization for Research and Academic Information, Shimane University, Matsue, Shimane 690-8504, Japan.
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19
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Cheng WWL, Arcario MJ, Petroff JT. Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels. Front Physiol 2022; 12:798102. [PMID: 35069257 PMCID: PMC8777383 DOI: 10.3389/fphys.2021.798102] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.
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Affiliation(s)
- Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - Mark J Arcario
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
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20
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Felsztyna I, Villarreal MA, García DA, Miguel V. Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels. ACS OMEGA 2022; 7:1988-2001. [PMID: 35071887 PMCID: PMC8771969 DOI: 10.1021/acsomega.1c05465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The RDL receptor is one of the most relevant protein targets for insecticide molecules. It belongs to the pentameric ligand-gated ion channel (pLGIC) family. Given that the experimental structures of pLGICs are difficult to obtain, homology modeling has been extensively used for these proteins, particularly for the RDL receptor. However, no detailed assessments of the usefulness of homology models for virtual screening (VS) have been carried out for pLGICs. The aim of this study was to evaluate which are the determinant factors for a good VS performance using RDL homology models, specially analyzing the impact of the template conformational state. Fifteen RDL homology models were obtained based on different pLGIC templates representing the closed, open, and desensitized states. A retrospective VS process was performed on each model, and their performance in the prioritization of active ligands was assessed. In addition, the three best-performing models among each of the conformations were subjected to molecular dynamics simulations (MDS) in complex with a representative active ligand. The models showed variations in their VS performance parameters that were related to the structural properties of the binding site. VS performance tended to improve in more constricted binding cavities. The best performance was obtained with a model based on a template in the closed conformation. MDS confirmed that the closed model was the one that best represented the interactions with an active ligand. These results imply that different templates should be evaluated and the structural variations between their channel conformational states should be specially examined, providing guidelines for the application of homology modeling for VS in other proteins of the pLGIC family.
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Affiliation(s)
- Iván Felsztyna
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Marcos A. Villarreal
- Facultad
de Ciencias Químicas, Departamento de Química Teórica
y Computacional, Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones en Físico-Química de Córdoba
(INFIQC), CONICET-Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
| | - Daniel A. García
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Virginia Miguel
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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21
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Lipovsek M, Marcovich I, Elgoyhen AB. The Hair Cell α9α10 Nicotinic Acetylcholine Receptor: Odd Cousin in an Old Family. Front Cell Neurosci 2021; 15:785265. [PMID: 34867208 PMCID: PMC8634148 DOI: 10.3389/fncel.2021.785265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are a subfamily of pentameric ligand-gated ion channels with members identified in most eumetazoan clades. In vertebrates, they are divided into three subgroups, according to their main tissue of expression: neuronal, muscle and hair cell nAChRs. Each receptor subtype is composed of different subunits, encoded by paralogous genes. The latest to be identified are the α9 and α10 subunits, expressed in the mechanosensory hair cells of the inner ear and the lateral line, where they mediate efferent modulation. α9α10 nAChRs are the most divergent amongst all nicotinic receptors, showing marked differences in their degree of sequence conservation, their expression pattern, their subunit co-assembly rules and, most importantly, their functional properties. Here, we review recent advances in the understanding of the structure and evolution of nAChRs. We discuss the functional consequences of sequence divergence and conservation, with special emphasis on the hair cell α9α10 receptor, a seemingly distant cousin of neuronal and muscle nicotinic receptors. Finally, we highlight potential links between the evolution of the octavolateral system and the extreme divergence of vertebrate α9α10 receptors.
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Affiliation(s)
- Marcela Lipovsek
- Ear Institute, Faculty of Brain Sciences, University College London, London, United Kingdom
| | - Irina Marcovich
- Departments of Otolaryngology & Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Ana Belén Elgoyhen
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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22
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Trampari S, Neumann C, Hjorth-Jensen SJ, Shahsavar A, Quistgaard EM, Nissen P. Insights into the mechanism of high lipid–detergent crystallization of membrane proteins. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721010669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Obtaining well diffracting crystals of membrane proteins is often challenging, but chances can be improved by crystallizing them in lipidic conditions that mimic their natural membrane environments. One approach is the high lipid–detergent (HiLiDe) method, which works by mixing the target protein with high concentrations of lipid and detergent prior to crystallization. Although this approach is convenient and flexible, understanding the effects of systematically varying lipid/detergent ratios and a characterization of the lipid phases that form during crystallization would be useful. Here, a HiLiDe phase diagram is reported for the model membrane protein MhsT, which tracks the precipitation and crystallization zones as a function of lipid and detergent concentrations, and is augmented with data on crystal sizes and diffraction properties. Additionally, the crystallization of SERCA1a solubilized directly with native lipids is characterized as a function of detergent concentration. Finally, HiLiDe crystallization drops are analysed with transmission electron microscopy, which among other features reveals liposomes, stacked lamellae that may represent crystal precursors, and mature crystals with clearly discernible packing arrangements. The results emphasize the significance of optimizing lipid/detergent ratios over broad ranges and provide insights into the mechanism of HiLiDe crystallization.
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23
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Lefebvre SN, Taly A, Menny A, Medjebeur K, Corringer PJ. Mutational analysis to explore long-range allosteric couplings involved in a pentameric channel receptor pre-activation and activation. eLife 2021; 10:60682. [PMID: 34590583 PMCID: PMC8504973 DOI: 10.7554/elife.60682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using simultaneous steady-state fluorescence and electrophysiological measurements over a broad pH range. Our data, fitted to a three-state Monod-Wyman-Changeux model, show that mutations at the subunit interface in the extracellular domain (ECD) principally alter pre-activation, while mutations in the lower ECD and in the transmembrane domain principally alter activation. We also show that propofol alters both transitions. Data are discussed in the framework of transition pathways generated by normal mode analysis (iModFit). It further supports that pre-activation involves major quaternary compaction of the ECD, and suggests that activation involves principally a reorganization of a ‘central gating region’ involving a contraction of the ECD β-sandwich and the tilt of the channel lining M2 helix.
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Affiliation(s)
- Solène N Lefebvre
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Antoine Taly
- Institut de Biologie Physico-chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.,Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
| | - Anaïs Menny
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Karima Medjebeur
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
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24
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Sridhar A, Lummis SCR, Pasini D, Mehregan A, Brams M, Kambara K, Bertrand D, Lindahl E, Howard RJ, Ulens C. Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding site. J Biol Chem 2021; 297:100899. [PMID: 34157288 PMCID: PMC8327344 DOI: 10.1016/j.jbc.2021.100899] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 02/08/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are crucial mediators of electrochemical signal transduction in various organisms from bacteria to humans. Lipids play an important role in regulating pLGIC function, yet the structural bases for specific pLGIC-lipid interactions remain poorly understood. The bacterial channel ELIC recapitulates several properties of eukaryotic pLGICs, including activation by the neurotransmitter GABA and binding and modulation by lipids, offering a simplified model system for structure-function relationship studies. In this study, functional effects of noncanonical amino acid substitution of a potential lipid-interacting residue (W206) at the top of the M1-helix, combined with detergent interactions observed in recent X-ray structures, are consistent with this region being the location of a lipid-binding site on the outward face of the ELIC transmembrane domain. Coarse-grained and atomistic molecular dynamics simulations revealed preferential binding of lipids containing a positive charge, particularly involving interactions with residue W206, consistent with cation-π binding. Polar contacts from other regions of the protein, particularly M3 residue Q264, further support lipid binding via headgroup ester linkages. Aromatic residues were identified at analogous sites in a handful of eukaryotic family members, including the human GABAA receptor ε subunit, suggesting conservation of relevant interactions in other evolutionary branches. Further mutagenesis experiments indicated that mutations at this site in ε-containing GABAA receptors can change the apparent affinity of the agonist response to GABA, suggesting a potential role of this site in channel gating. In conclusion, this work details type-specific lipid interactions, which adds to our growing understanding of how lipids modulate pLGICs.
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Affiliation(s)
- Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah C R Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Diletta Pasini
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Aujan Mehregan
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Marijke Brams
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | | | | | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.
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Tong G, Baker MA, Shenvi RA. Change the channel: CysLoop receptor antagonists from nature. PEST MANAGEMENT SCIENCE 2021; 77:3650-3662. [PMID: 33135373 PMCID: PMC8087819 DOI: 10.1002/ps.6166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 05/04/2023]
Abstract
Vertebrate and invertebrate ligand-gated ion channels (LGICs) exhibit significant structural homology and often share ligands. As a result, ligands with activity against one class can be brought to bear against another, including for development as insecticides. Receptor selectivity, metabolism and distribution must then be optimized using chemical synthesis. Here we review natural products (NPs) that ligate and inhibit the Cys-loop family of LGICs, which benefit from the unique physicochemical properties of natural product space but often present a high synthetic burden. Recent advances in chemical synthesis, however, have opened practical entries into these complex structures, several of which are highlighted. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Guanghu Tong
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Meghan A Baker
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Ryan A Shenvi
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
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Nakao T, Banba S. Important amino acids for function of the insect Rdl GABA receptor. PEST MANAGEMENT SCIENCE 2021; 77:3753-3762. [PMID: 33002317 DOI: 10.1002/ps.6121] [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: 07/24/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Insect Rdl GABA receptor is an important insecticide target. To design a novel insecticide, studies on the structures of homologous pentameric ligand-gated ion channels provide information about important amino acids that are necessary for the function of insect Rdl GABA receptors. RESULTS L9'A, T12'A, T13'A, T13'S, M15'S, and M15'N mutations in the Drosophila Rdl GABA receptor subunit caused the protein to spontaneously adopt the open state conformation. In contrast, the S16'A, S16'T, S17'A, and S17'H mutant homomers showed the same levels of agonist and antagonist sensitivity as the wild-type receptor. The G336M mutation in the Drosophila Rdl GABA receptor abolished the agonist activities of ivermectin and milbemectin, but the F339M mutation did not. Additionally, the F339M mutation caused spontaneous opening of the receptor. In the Drosophila Rdl model, the hydrophobic girdle plays an important role in stabilization of the closed state. Mutations which decrease hydrophobic interactions resulted in spontaneous opening, supporting the importance of the hydrophobic girdle for keeping the channel closed. Through a mutational study of transmembrane 3 (TM3) cytoplasmic domain and Rdl GABA receptor modeling, hydrophobic interactions between TM3 and TM4 and intersubunit interaction were demonstrated to be important for channel gating. Alternatively, the intrasubunit interaction between TM2 and TM3 domains were less important for channel gating in case of Drosophila Rdl GABA receptor. CONCLUSION This study demonstrates important amino acids critical to the function of the Drosophila Rdl GABA receptor based on the mutational studies and Drosophila Rdl GABA receptor modeling approach. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Toshifumi Nakao
- Organic Chemistry G, Agrochemicals Research Center, Mitsui Chemicals Agro, Inc., Chiba, Japan
| | - Shinichi Banba
- Organic Chemistry G, Agrochemicals Research Center, Mitsui Chemicals Agro, Inc., Chiba, Japan
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Noack S, Harrington J, Carithers DS, Kaminsky R, Selzer PM. Heartworm disease - Overview, intervention, and industry perspective. Int J Parasitol Drugs Drug Resist 2021; 16:65-89. [PMID: 34030109 PMCID: PMC8163879 DOI: 10.1016/j.ijpddr.2021.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Dirofilaria immitis, also known as heartworm, is a major parasitic threat for dogs and cats around the world. Because of its impact on the health and welfare of companion animals, heartworm disease is of huge veterinary and economic importance especially in North America, Europe, Asia and Australia. Within the animal health market many different heartworm preventive products are available, all of which contain active components of the same drug class, the macrocyclic lactones. In addition to compliance issues, such as under-dosing or irregular treatment intervals, the occurrence of drug-resistant heartworms within the populations in the Mississippi River areas adds to the failure of preventive treatments. The objective of this review is to provide an overview of the disease, summarize the current disease control measures and highlight potential new avenues and best practices for treatment and prevention.
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Affiliation(s)
- Sandra Noack
- Boehringer Ingelheim Animal Health, Binger Str. 173, 55216, Ingelheim am Rhein, Germany
| | - John Harrington
- Boehringer Ingelheim Animal Health, 1730 Olympic Drive, 30601, Athens, GA, USA
| | - Douglas S Carithers
- Boehringer Ingelheim Animal Health, 3239 Satellite Blvd, 30096, Duluth, GA, USA
| | - Ronald Kaminsky
- paraC Consulting, Altenstein 13, 79685, Häg-Ehrsberg, Germany
| | - Paul M Selzer
- Boehringer Ingelheim Animal Health, Binger Str. 173, 55216, Ingelheim am Rhein, Germany.
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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models. J Mol Biol 2021; 433:167128. [PMID: 34224751 DOI: 10.1016/j.jmb.2021.167128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.
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Sharifi-Rad J, Quispe C, Herrera-Bravo J, Martorell M, Sharopov F, Tumer TB, Kurt B, Lankatillake C, Docea AO, Moreira AC, Dias DA, Mahomoodally MF, Lobine D, Cruz-Martins N, Kumar M, Calina D. A Pharmacological Perspective on Plant-derived Bioactive Molecules for Epilepsy. Neurochem Res 2021; 46:2205-2225. [PMID: 34120291 DOI: 10.1007/s11064-021-03376-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022]
Abstract
Epilepsy is a related chronic neurological condition of a predisposition for recurrent epileptic seizures, with various manifestations and causes. Although there are antiepileptic drugs, complementary natural therapies are widely used. The purpose of this systematic review was to analyze the antiepileptic/anticonvulsant pharmacological properties of plant-food derived bioactive molecules. In this regard, a systematic review of the PubMed database was made based on the inclusion criteria. Natural compounds/herbs with scientifically proven antiepileptic properties were selected. Experimental pharmacological studies in vitro and in vivo have shown that flavonoids, alkaloids and terpenoids may have anticonvulsant mechanisms similar to the new generation antiepileptic drugs. The relationships of structure-anticonvulsant effect, pharmacological models, seizure-inducing factors and response, effective dose were also analyzed and discussed. The results of in vitro and in vivo pharmacological studies analyzed in this systematic review support the clinical importance of plant-food-derived bioactive molecules for the complementary treatment of epilepsy. Thus, are opened new perspectives to develop new natural anticonvulsant drugs.
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Affiliation(s)
- Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Facultad de Medicina, Universidad del Azuay, Cuenca, Ecuador.
| | - Cristina Quispe
- Facultad de Ciencias de La Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique, Chile
| | - Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Santiago, Chile.,Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, 4811230, Temuco, Chile
| | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, University of Concepcion, 4070386, Concepcion, Chile.,Universidad de Concepción, Unidad de Desarrollo Tecnológico, UDT, 4070386, Concepcion, Chile
| | - Farukh Sharopov
- Department of Pharmaceutical Technology, Avicenna Tajik State Medical University, Rudaki 139, Dushanbe, 734003, Tajikistan
| | - Tugba Boyunegmez Tumer
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Canakkale Onsekiz Mart University, Canakkale, 17020, Turkey
| | - Begum Kurt
- Graduate Program of Biomolecular Sciences, Institute of Natural and Applied Sciences, Canakkale Onsekiz Mart University, Canakkale, 17020, Turkey
| | - Chintha Lankatillake
- School of Health and Biomedical Sciences, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania
| | - Ana Catarina Moreira
- Pulmonology Department, Hospital Garcia de Orta, EPE Almada, 2801-951, Lisboa, Portugal
| | - Daniel A Dias
- School of Health and Biomedical Sciences, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
| | | | - Devina Lobine
- Department of Health Sciences, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal. .,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal. .,Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, 4200-135, Porto, Portugal.
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR - Central Institute for Research on Cotton Echnology, Mumbai, 400019, India
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
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30
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Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A 2021; 118:2100164118. [PMID: 34083441 DOI: 10.1073/pnas.2100164118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although it has long been proposed that membrane proteins may contain tightly bound lipids, their identity, the structure of their binding sites, and their functional and structural relevance have remained elusive. To some extent, this is because tightly bound lipids are often located at the periphery of proteins, where the quality of density maps is usually poorer, and because they may be outcompeted by detergent molecules used during standard purification procedures. As a step toward characterizing natively bound lipids in the superfamily of pentameric ligand-gated ion channels (pLGICs), we applied single-particle cryogenic electron microscopy to fragments of native membrane obtained in the complete absence of detergent-solubilization steps. Because of the heterogeneous lipid composition of membranes in the secretory pathway of eukaryotic cells, we chose to study a bacterial pLGIC (ELIC) expressed in Escherichia coli's inner membrane. We obtained a three-dimensional reconstruction of unliganded ELIC (2.5-Å resolution) that shows clear evidence for two types of tightly bound lipid at the protein-bulk-membrane interface. One of them was consistent with a "regular" diacylated phospholipid, in the cytoplasmic leaflet, whereas the other one was consistent with the tetra-acylated structure of cardiolipin, in the periplasmic leaflet. Upon reconstitution in E. coli polar-lipid bilayers, ELIC retained the functional properties characteristic of members of this superfamily, and thus, the fitted atomic model is expected to represent the (long-debated) unliganded-closed, "resting" conformation of this ion channel. Notably, the addition of cardiolipin to phosphatidylcholine membranes restored the ion-channel activity that is largely lost in phosphatidylcholine-only bilayers.
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Lenz KD, Klosterman KE, Mukundan H, Kubicek-Sutherland JZ. Macrolides: From Toxins to Therapeutics. Toxins (Basel) 2021; 13:347. [PMID: 34065929 PMCID: PMC8150546 DOI: 10.3390/toxins13050347] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/17/2022] Open
Abstract
Macrolides are a diverse class of hydrophobic compounds characterized by a macrocyclic lactone ring and distinguished by variable side chains/groups. Some of the most well characterized macrolides are toxins produced by marine bacteria, sea sponges, and other species. Many marine macrolide toxins act as biomimetic molecules to natural actin-binding proteins, affecting actin polymerization, while other toxins act on different cytoskeletal components. The disruption of natural cytoskeletal processes affects cell motility and cytokinesis, and can result in cellular death. While many macrolides are toxic in nature, others have been shown to display therapeutic properties. Indeed, some of the most well known antibiotic compounds, including erythromycin, are macrolides. In addition to antibiotic properties, macrolides have been shown to display antiviral, antiparasitic, antifungal, and immunosuppressive actions. Here, we review each functional class of macrolides for their common structures, mechanisms of action, pharmacology, and human cellular targets.
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Affiliation(s)
| | | | | | - Jessica Z. Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.D.L.); (K.E.K.); (H.M.)
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32
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Crnjar A, Mesoy SM, Lummis SCR, Molteni C. A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism. Front Mol Biosci 2021; 8:644720. [PMID: 33996899 PMCID: PMC8119899 DOI: 10.3389/fmolb.2021.644720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast synaptic transmission and are crucial drug targets. Their gating mechanism is triggered by ligand binding in the extracellular domain that culminates in the opening of a hydrophobic gate in the transmembrane domain. This domain is made of four α-helices (M1 to M4). Recently the outer lipid-facing helix (M4) has been shown to be key to receptor function, however its role in channel opening is still poorly understood. It could act through its neighboring helices (M1/M3), or via the M4 tip interacting with the pivotal Cys-loop in the extracellular domain. Mutation of a single M4 tyrosine (Y441) to alanine renders one pLGIC-the 5-HT3A receptor-unable to function despite robust ligand binding. Using Y441A as a proxy for M4 function, we here predict likely paths of Y441 action using molecular dynamics, and test these predictions with functional assays of mutant receptors in HEK cells and Xenopus oocytes using fluorescent membrane potential sensitive dye and two-electrode voltage clamp respectively. We show that Y441 does not act via the M4 tip or Cys-loop, but instead connects radially through M1 to a residue near the ion channel hydrophobic gate on the pore-lining helix M2. This demonstrates the active role of the M4 helix in channel opening.
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Affiliation(s)
| | - Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Carla Molteni
- Physics Department, King's College London, London, United Kingdom
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33
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Brafa Musicoro V, Sortino V, Pecora G, Tosto M, Lo Bianco M, Soma R, Romano C, Falsaperla R, Praticò AD. Gamma-Aminobutyric Acid Type A Receptor Genes and Their Related Epilepsies. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractGamma-aminobutyric acid type A (GABA-A) receptor subunit gene mutations, which include GABRA1, GABRB3, GABRD, and GABRG2, are often involved in several genetic epilepsy syndromes and other neuropsychiatric diseases like autism spectrum disorder, schizophrenia, and anxiety. GABA-A are ligand-gated ionic channels, and are involved firstly in the fast inhibitory synaptic transmission of the central nervous system. The GABA receptors include the ionotropic GABA-A and GABA-C receptors and the metabotropic GABA-B receptors. According to the site in which mutations occur, they cause disorders in channel opening, “lock-and-pull” receptor system functioning, and capable of causing a specific epilepsy phenotype. The aim of this article is to summarize the most recent literature findings, considering genetic mutations, clinical features, genotype/phenotype correlation, and therapy about neurodevelopment diseases correlated to GABA receptors dysfunction, in particular epilepsy. According to our findings, we conclude that further mutation analysis could permit genotype–phenotype correlation and give more information about the best efficient treatment, even if—at present—more clinical and genetic studies are necessary.
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Affiliation(s)
- Viviana Brafa Musicoro
- Pediatric Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Vincenzo Sortino
- Pediatric Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Giulia Pecora
- Pediatric Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Monica Tosto
- Pediatric Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Manuela Lo Bianco
- Pediatric Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Rachele Soma
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | | | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco”, Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco”, Catania, Italy
| | - Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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Yu J, Zhu H, Lape R, Greiner T, Du J, Lü W, Sivilotti L, Gouaux E. Mechanism of gating and partial agonist action in the glycine receptor. Cell 2021; 184:957-968.e21. [PMID: 33567265 PMCID: PMC8115384 DOI: 10.1016/j.cell.2021.01.026] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.
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Affiliation(s)
- Jie Yu
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Remigijus Lape
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK
| | - Timo Greiner
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK
| | - Juan Du
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Wei Lü
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lucia Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK.
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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Asymmetric opening of the homopentameric 5-HT 3A serotonin receptor in lipid bilayers. Nat Commun 2021; 12:1074. [PMID: 33594077 PMCID: PMC7887223 DOI: 10.1038/s41467-021-21016-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT3A serotonin receptor (5HT3R) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HT3R conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, ‘coupled’ state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HT3R by the membrane environment, and a model for asymmetric activation of the receptor. Pentameric ligand-gated ion channels (pLGICs) are key players in neurotransmission and have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. Here, the authors report structures of the pLGIC 5-HT3A serotonin receptor reconstituted into lipid bilayer discs and reveal lipid–protein interactions as well as asymmetric activation of the homopentameric receptor.
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36
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Dämgen MA, Biggin PC. State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. PLoS Comput Biol 2021; 17:e1007856. [PMID: 33571182 PMCID: PMC7904231 DOI: 10.1371/journal.pcbi.1007856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/24/2021] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are receptor proteins that are sensitive to their membrane environment, but the mechanism for how lipids modulate function under physiological conditions in a state dependent manner is not known. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. Using a realistic model of a neuronal membrane coupled with coarse-grained molecular dynamics simulations, we demonstrate that some key lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor's conformational dynamics. Comparison with existing structural data confirms known lipid binding sites, but we also predict further protein-lipid interactions including a site at the communication interface between the extracellular and transmembrane domain. Moreover, in the active state, cholesterol can bind to the binding site of the positive allosteric modulator ivermectin. These protein-lipid interaction sites could in future be exploited for the rational design of lipid-like allosteric drugs.
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Affiliation(s)
- Marc A. Dämgen
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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37
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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38
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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Nixon SA, Welz C, Woods DJ, Costa-Junior L, Zamanian M, Martin RJ. Where are all the anthelmintics? Challenges and opportunities on the path to new anthelmintics. Int J Parasitol Drugs Drug Resist 2020; 14:8-16. [PMID: 32814269 PMCID: PMC7452592 DOI: 10.1016/j.ijpddr.2020.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 01/03/2023]
Abstract
Control of helminth parasites is a key challenge for human and veterinary medicine. In the absence of effective vaccines and adequate sanitation, prophylaxis and treatment commonly rely upon anthelmintics. There are concerns about the development of drug resistance, side-effects, lack of efficacy and cost-effectiveness that drive the need for new classes of anthelmintics. Despite this need, only three new drug classes have reached the animal market since 2000 and no new classes of anthelmintic have been approved for human use. So where are all the anthelmintics? What are the barriers to anthelmintic discovery, and what emerging opportunities can be used to address this? This was a discussion group focus at the 2019 8th Consortium for Anthelmintic Resistance and Susceptibility (CARS) in Wisconsin, USA. Here we report the findings of the group in the broader context of the human and veterinary anthelmintic discovery pipeline, highlighting challenges unique to antiparasitic drug discovery. We comment on why the development of novel anthelmintics has been so rare. Further, we discuss potential opportunities for drug development moving into the 21st Century.
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Affiliation(s)
- Samantha A Nixon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia; CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Australia
| | | | - Debra J Woods
- Zoetis, Veterinary Medicine Research and Development, Kalamazoo, MI, USA
| | - Livio Costa-Junior
- Federal University of Maranhão, Pathology Department, São Luís, Maranhão, Brazil
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
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Interaction between GABA A receptor α 1 and β 2 subunits at the N-terminal peripheral regions is crucial for receptor binding and gating. Biochem Pharmacol 2020; 183:114338. [PMID: 33189674 DOI: 10.1016/j.bcp.2020.114338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Pentameric ligand gated ion channels (pLGICs) are crucial in electrochemical signaling but exact molecular mechanisms of their activation remain elusive. So far, major effort focused on the top-down molecular pathway between the ligand binding site and the channel gate. However, recent studies revealed that pLGIC activation is associated with coordinated subunit twisting in the membrane plane. This suggests a key role of intersubunit interactions but the underlying mechanisms remain largely unknown. Herein, we investigated a "peripheral" subunit interface region of GABAA receptor where structural modeling indicated interaction between N-terminal α1F14 and β2F31 residues. Our experiments underscored a crucial role of this interaction in ligand binding and gating, especially preactivation and opening, showing that the intersubunit cross-talk taking place outside (above) the top-down pathway can be strongly involved in receptor activation. Thus, described here intersubunit interaction appears to operate across a particularly long distance, affecting vast portions of the macromolecule.
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41
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Han L, Shan Q. Pair of Residue Substitutions at the Outer Mouth of the Channel Pore Act as Inputs for a Boolean Logic "OR" Gate Based on the Glycine Receptor. ACS Chem Neurosci 2020; 11:3409-3417. [PMID: 32970400 DOI: 10.1021/acschemneuro.0c00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The glycine receptor (GlyR) is a ligand-activated chloride channel, whose mutations are the major cause of hereditary hyperekplexia. The hyperekplexia-causing R271Q mutation, which is located at the extracellular outer mouth of the channel pore, dramatically impairs the GlyR function manifesting a reduced sensitivity toward glycine. This study reports that a second mutation, S273D, rescues the function of the R271Q GlyR to that of the wild-type (WT) GlyR. Surprisingly, the S273D mutation, when introduced to the WT GlyR, does not further increase the receptor function. In other words, the compromised function of the 271Q 273S GlyR (i.e., the R271Q GlyR) can be rescued to WT levels by the introduction of either, or both, of the Q271R and S273D substitutions. From the perspective of Boolean logic gates, the Q271R and S273D substitutions act as inputs for an OR gate based on the GlyR. Further experiments revealed that the negative-charge carried by the 273 residue is essential for the expression of the OR gate and that the expression of the OR gate is residue-position-specific. In addition, mechanistic investigation implied that the 273 residue influences the 271 residue, which might underpin the unique nonadditive OR gate relationship between these two residues. Such an ion-channel-based OR gate, expressing output in the form of electrical current, could potentially be developed to digitally manipulate neuronal activity.
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Affiliation(s)
- Lu Han
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Qiang Shan
- Laboratory for Synaptic Plasticity, Shantou University Medical College, Shantou, Guangdong 515041, China
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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Thompson MJ, Baenziger JE. Structural basis for the modulation of pentameric ligand-gated ion channel function by lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183304. [DOI: 10.1016/j.bbamem.2020.183304] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 04/05/2020] [Indexed: 10/24/2022]
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Cottone G, Chiodo L, Maragliano L. Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. J Chem Inf Model 2020; 60:5045-5056. [PMID: 32803965 PMCID: PMC8011927 DOI: 10.1021/acs.jcim.0c00549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Molecular
studies of human pentameric ligand-gated ion channels
(LGICs) expressed in neurons and at neuromuscular junctions are of
utmost importance in the development of therapeutic strategies for
neurological disorders. We focus here on the nicotinic acetylcholine
receptor nAChR-α7, a homopentameric channel widely expressed
in the human brain, with a proven role in a wide spectrum of disorders
including schizophrenia and Alzheimer’s disease. By exploiting
an all-atom structural model of the full (transmembrane and extracellular)
protein in the open, agonist-bound conformation we recently developed,
we evaluate the free energy and the mean first passage time of single-ion
permeation using molecular dynamics simulations and the milestoning
method with Voronoi tessellation. The results for the wild-type channel
provide the first available mapping of the potential of mean force
in the full-length α7 nAChR, reveal its expected cationic nature,
and are in good agreement with simulation data for other channels
of the LGIC family and with experimental data on nAChRs. We then investigate
the role of a specific mutation directly related to ion selectivity
in LGICs, the E-1′ → A-1′ substitution at the
cytoplasmatic selectivity filter. We find that the mutation strongly
affects sodium and chloride permeation in opposite directions, leading
to a complete inversion of selectivity, at variance with the limited
experimental results available that classify this mutant as cationic.
We thus provide structural determinants for the observed cationic-to-anionic
inversion, revealing a key role of the protonation state of residue
rings far from the mutation, in the proximity of the hydrophobic channel
gate.
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Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, Campus Bio-Medico University of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132 Genova, Italy
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Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat Commun 2020; 11:3752. [PMID: 32719334 PMCID: PMC7385131 DOI: 10.1038/s41467-020-17364-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022] Open
Abstract
Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment. Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Here, authors present cryo-EM structures of the full-length glycine receptors (GlyRs) reconstituted into lipid nanodiscs in the unliganded, glycine-bound and allosteric modulator-bound conformations and reveal global conformational changes underlying GlyR channel gating and modulation.
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45
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Identification of N-acyl amino acids that are positive allosteric modulators of glycine receptors. Biochem Pharmacol 2020; 180:114117. [PMID: 32579961 DOI: 10.1016/j.bcp.2020.114117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/31/2023]
Abstract
Glycine receptors (GlyRs) mediate inhibitory neurotransmission within the spinal cord and play a crucial role in nociceptive signalling. This makes them primary targets for the development of novel chronic pain therapies. Endogenous lipids have previously been shown to modulate glycine receptors and produce analgesia in pain models, however little is known about what chemical features mediate these effects. In this study, we characterised lipid modulation of GlyRs by screening a library of N-acyl amino acids across all receptor subtypes and determined chemical features crucial for their activity. Acyl-glycine's with a C18 carbon tail were found to produce the greatest potentiation, and require a cis double bond within the central region of the carbon tail (ω6 - ω9) to be active. At 1 µM, C18 ω6,9 glycine potentiated glycine induced currents in α3 and α3β receptors by over 50%, and α1, α2, α1β and α2β receptors by over 100%. C18 ω9 glycine (N-oleoyl glycine) significantly enhance glycine induced peak currents and cause a dose-dependent shift in the glycine concentration response. In the presence of 3 µM C18 ω9 glycine, the EC5o of glycine at the α1 receptor was reduced from 17 µM to 10 µM. This study has identified several acyl-amino acids which are positive allosteric modulators of GlyRs and make promising lead compounds for the development of novel chronic pain therapies.
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46
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Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A 2020; 117:13437-13446. [PMID: 32482881 DOI: 10.1073/pnas.1922701117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the animal nervous system through the opening of an ion pore upon binding of neurotransmitters. Orthologs have been found and characterized in prokaryotes and they display highly similar structure-function relationships to eukaryotic pLGICs; however, they often encode greater architectural diversity involving additional amino-terminal domains (NTDs). Here we report structural, functional, and normal-mode analysis of two conformational states of a multidomain pLGIC, called DeCLIC, from a Desulfofustis deltaproteobacterium, including a periplasmic NTD fused to the conventional ligand-binding domain (LBD). X-ray structure determination revealed an NTD consisting of two jelly-roll domains interacting across each subunit interface. Binding of Ca2+ at the LBD subunit interface was associated with a closed transmembrane pore, with resolved monovalent cations intracellular to the hydrophobic gate. Accordingly, DeCLIC-injected oocytes conducted currents only upon depletion of extracellular Ca2+; these were insensitive to quaternary ammonium block. Furthermore, DeCLIC crystallized in the absence of Ca2+ with a wide-open pore and remodeled periplasmic domains, including increased contacts between the NTD and classic LBD agonist-binding sites. Functional, structural, and dynamical properties of DeCLIC paralleled those of sTeLIC, a pLGIC from another symbiotic prokaryote. Based on these DeCLIC structures, we would reclassify the previous structure of bacterial ELIC (the first high-resolution structure of a pLGIC) as a "locally closed" conformation. Taken together, structures of DeCLIC in multiple conformations illustrate dramatic conformational state transitions and diverse regulatory mechanisms available to ion channels in pLGICs, particularly involving Ca2+ modulation and periplasmic NTDs.
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47
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Rahman MM, Teng J, Worrell BT, Noviello CM, Lee M, Karlin A, Stowell MHB, Hibbs RE. Structure of the Native Muscle-type Nicotinic Receptor and Inhibition by Snake Venom Toxins. Neuron 2020; 106:952-962.e5. [PMID: 32275860 DOI: 10.1016/j.neuron.2020.03.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/13/2020] [Accepted: 03/15/2020] [Indexed: 12/28/2022]
Abstract
The nicotinic acetylcholine receptor, a pentameric ligand-gated ion channel, converts the free energy of binding of the neurotransmitter acetylcholine into opening of its central pore. Here we present the first high-resolution structure of the receptor type found in muscle-endplate membrane and in the muscle-derived electric tissues of fish. The native receptor was purified from Torpedo electric tissue and functionally reconstituted in lipids optimal for cryo-electron microscopy. The receptor was stabilized in a closed state by the binding of α-bungarotoxin. The structure reveals the binding of a toxin molecule at each of two subunit interfaces in a manner that would block the binding of acetylcholine. It also reveals a closed gate in the ion-conducting pore, formed by hydrophobic amino acid side chains, located ∼60 Å from the toxin binding sites. The structure provides a framework for understanding gating in ligand-gated channels and how mutations in the acetylcholine receptor cause congenital myasthenic syndromes.
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Affiliation(s)
- Md Mahfuzur Rahman
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jinfeng Teng
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brady T Worrell
- Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Colleen M Noviello
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Myeongseon Lee
- Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Arthur Karlin
- Center for Molecular Recognition & Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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48
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Progress in nicotinic receptor structural biology. Neuropharmacology 2020; 171:108086. [PMID: 32272141 DOI: 10.1016/j.neuropharm.2020.108086] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023]
Abstract
Here we begin by briefly reviewing landmark structural studies on the nicotinic acetylcholine receptor. We highlight challenges that had to be overcome to push through resolution barriers, then focus on what has been gleaned in the past few years from crystallographic and single particle cryo-EM studies of different nicotinic receptor subunit assemblies and ligand complexes. We discuss insights into ligand recognition, ion permeation, and allosteric gating. We then highlight some foundational aspects of nicotinic receptor structural biology that remain unresolved and are areas ripe for future exploration. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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49
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Brodzki M, Michałowski MA, Gos M, Mozrzymas JW. Mutations of α 1F45 residue of GABA A receptor loop G reveal its involvement in agonist binding and channel opening/closing transitions. Biochem Pharmacol 2020; 177:113917. [PMID: 32194055 DOI: 10.1016/j.bcp.2020.113917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
GABAA receptors (GABAARs) mediate inhibitory neurotransmission in the mammalian brain. Recently, numerous GABAAR static structures have been published, but the molecular mechanisms of receptor activation remain elusive. Loop G is a rigid β-strand belonging to an extensive β-sheet that spans the regions involved in GABA binding and the interdomain interface which is important in receptor gating. It has been reported that loop G participates in ligand binding and gating of GABAARs, however, it remains unclear which specific gating transitions are controlled by this loop. Analysis of macroscopic responses revealed that mutation at the α1F45 residue (loop G midpoint) resulted in slower macroscopic desensitization and accelerated deactivation. Single-channel analysis revealed that these mutations also affected open and closed times distributions and reduced open probability. Kinetic modeling demonstrated that mutations affected primarily channel opening/closing and ligand binding with a minor effect on preactivation. Thus, α1F45 residue, in spite of its localization close to binding site, affects late gating transitions. In silico structural analysis suggested an important role of α1F45 residue in loop G stability and rigidity as well as in general structure of the binding site. We propose that the rigid β-sheet comprising loop G is well suited for long range communication within GABAAR but this mechanism becomes impaired when α1F45 is mutated. In conclusion, we demonstrate that loop G is crucial in controlling both binding and gating of GABAARs. These data shed new light on GABAAR activation mechanism and may also be helpful in designing clinically relevant modulators.
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Affiliation(s)
- Marek Brodzki
- University of Wrocław, Department of Molecular Physiology and Neurobiology, ul. Sienkiewicza 21, 50-335 Wrocław, Poland; Wrocław Medical University, Department of Biophysics, Laboratory of Neuroscience, ul. Chałubińskiego 3A, 50-368 Wrocław, Poland.
| | - Michał A Michałowski
- University of Wrocław, Department of Molecular Physiology and Neurobiology, ul. Sienkiewicza 21, 50-335 Wrocław, Poland; Wrocław Medical University, Department of Biophysics, Laboratory of Neuroscience, ul. Chałubińskiego 3A, 50-368 Wrocław, Poland.
| | - Michalina Gos
- University of Wrocław, Department of Molecular Physiology and Neurobiology, ul. Sienkiewicza 21, 50-335 Wrocław, Poland; Wrocław Medical University, Department of Biophysics, Laboratory of Neuroscience, ul. Chałubińskiego 3A, 50-368 Wrocław, Poland
| | - Jerzy W Mozrzymas
- Wrocław Medical University, Department of Biophysics, Laboratory of Neuroscience, ul. Chałubińskiego 3A, 50-368 Wrocław, Poland.
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50
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Lev B, Allen TW. Simulating ion channel activation mechanisms using swarms of trajectories. J Comput Chem 2020; 41:387-401. [PMID: 31743478 DOI: 10.1002/jcc.26102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's "swarms of trajectories" approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
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