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Akbar S, Mozumder S, Sengupta J. Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. J Chem Inf Model 2020; 60:2448-2457. [DOI: 10.1021/acs.jcim.9b01015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirin Akbar
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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52
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Tillman TS, Choi Z, Xu Y, Tang P. Functional Tolerance to Cysteine Mutations in Human α7 Nicotinic Acetylcholine Receptors. ACS Chem Neurosci 2020; 11:242-247. [PMID: 31951367 DOI: 10.1021/acschemneuro.9b00647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (α7 nAChR) is involved in various intracellular signaling pathways that mediate addiction, chronic pain, and other diseases, but its intracellular domain structures remain undetermined. The presence of 17 native cysteines in α7 nAChR provides opportunities for extracting structural information through site-directed labeling of chemical probes in strategic locations, but it also creates uncertainties in channel function when those native cysteines must be mutated. Using site-directed mutagenesis and two-electrode voltage clamp electrophysiology measurements, we found that α7 nAChR's function was well tolerated for mutations of all 13 cysteines as long as two pairs of disulfide-bond cysteines remained in the extracellular domain. Furthermore, surface plasmon resonance measurements showed that the cysteine mutations did not affect α7 nAChR binding to the intracellular protein PICK1. The study suggests that a high native cysteine content does not necessarily preclude the use of single cysteine labeling for acquiring structural information on functional proteins.
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Affiliation(s)
- Tommy S. Tillman
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zachary Choi
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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53
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Guros NB, Balijepalli A, Klauda JB. Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT 3A serotonin receptor. Proc Natl Acad Sci U S A 2020; 117:405-414. [PMID: 31871207 PMCID: PMC6955379 DOI: 10.1073/pnas.1908848117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aided by efforts to improve their speed and efficiency, molecular dynamics (MD) simulations provide an increasingly powerful tool to study the structure-function relationship of pentameric ligand-gated ion channels (pLGICs). However, accurate reporting of the channel state and observation of allosteric regulation by agonist binding with MD remains difficult due to the timescales necessary to equilibrate pLGICs from their artificial and crystalized conformation to a more native, membrane-bound conformation in silico. Here, we perform multiple all-atom MD simulations of the homomeric 5-hydroxytryptamine 3A (5-HT3A) serotonin receptor for 15 to 20 μs to demonstrate that such timescales are critical to observe the equilibration of a pLGIC from its crystalized conformation to a membrane-bound conformation. These timescales, which are an order of magnitude longer than any previous simulation of 5-HT3A, allow us to observe the dynamic binding and unbinding of 5-hydroxytryptamine (5-HT) (i.e., serotonin) to the binding pocket located on the extracellular domain (ECD) and allosteric regulation of the transmembrane domain (TMD) from synergistic 5-HT binding. While these timescales are not long enough to observe complete activation of 5-HT3A, the allosteric regulation of ion gating elements by 5-HT binding is indicative of a preactive state, which provides insight into molecular mechanisms that regulate channel activation from a resting state. This mechanistic insight, enabled by microsecond-timescale MD simulations, will allow a careful examination of the regulation of pLGICs at a molecular level, expanding our understanding of their function and elucidating key structural motifs that can be targeted for therapeutic regulation.
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Affiliation(s)
- Nicholas B Guros
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Balijepalli
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742;
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54
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Montano MM, Yeh IJ, Chen Y, Hernandez C, Kiselar JG, de la Fuente M, Lawes AM, Nieman MT, Kiser PD, Jacobberger J, Exner AA, Lawes MC. Inhibition of the histone demethylase, KDM5B, directly induces re-expression of tumor suppressor protein HEXIM1 in cancer cells. Breast Cancer Res 2019; 21:138. [PMID: 31805991 PMCID: PMC6896798 DOI: 10.1186/s13058-019-1228-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/14/2019] [Indexed: 01/07/2023] Open
Abstract
Background The tumor suppressor actions of hexamethylene bis-acetamide (HMBA)-inducible protein 1 (HEXIM1) in the breast, prostate, melanomas, and AML have been reported by our group and others. Increased HEXIM1 expression caused differentiation and inhibited proliferation and metastasis of cancer cells. Historically, HEXIM1 has been experimentally induced with the hybrid polar compound HMBA, but HMBA is a poor clinical candidate due to lack of a known target, poor pharmacological properties, and unfavorable ADMETox characteristics. Thus, HEXIM1 induction is an intriguing therapeutic approach to cancer treatment, but requires better chemical tools than HMBA. Methods We identified and verified KDM5B as a target of HEXIM1 inducers using a chemical proteomics approach, biotin–NeutrAvidin pull-down assays, surface plasmon resonance, and molecular docking. The regulation of HEXIM1 by KDM5B and KDM5B inhibitors was assessed using chromatin immunoprecipitation assays, RT-PCR, western blotting, and depletion of KDM5B with shRNAs. The regulation of breast cancer cell phenotype by KDM5B inhibitors was assessed using western blots, differentiation assays, proliferation assays, and a mouse model of breast cancer metastasis. The relative role of HEXIM1 in the action of KDM5B inhibitors was determined by depleting HEXIM1 using shRNAs followed by western blots, differentiation assays, and proliferation assays. Results We have identified a highly druggable target, KDM5B, which is inhibited by small molecule inducers of HEXIM1. RNAi knockdown of KDM5B induced HEXIM1 expression, thus validating the specific negative regulation of tumor suppressor HEXIM1 by the H3K4me3/2 demethylase KDM5B. Known inhibitors of KDM5B were also able to induce HEXIM1 expression, inhibit cell proliferation, induce differentiation, potentiate sensitivity to cancer chemotherapy, and inhibit breast tumor metastasis. Conclusion HMBA and 4a1 induce HEXIM1 expression by inhibiting KDM5B. Upregulation of HEXIM1 expression levels plays a critical role in the inhibition of proliferation of breast cancer cells using KDM5B inhibitors. Based on the novel molecular scaffolds that we identified which more potently induced HEXIM1 expression and data in support that KDM5B is a target of these compounds, we have opened up new lead discovery and optimization directions.
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Affiliation(s)
- Monica M Montano
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA. .,Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA.
| | - I-Ju Yeh
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Yinghua Chen
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Chris Hernandez
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Janna G Kiselar
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Maria de la Fuente
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Adriane M Lawes
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Marvin T Nieman
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Philip D Kiser
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - James Jacobberger
- General Medical Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Agata A Exner
- Department of Radiology, and Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Matthew C Lawes
- Oncostatyx, 11000 Cedar Avenue Suite 26, Cleveland, OH, 44106, USA
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55
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Pirayesh E, Stuebler AG, Pandhare A, Jansen M. Delineating the Site of Interaction of the 5-HT 3A Receptor with the Chaperone Protein RIC-3. Biophys J 2019; 118:934-943. [PMID: 31870537 DOI: 10.1016/j.bpj.2019.11.3380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
The serotonin type 3A (5-HT3A) receptor is a homopentameric cation-selective member of the pentameric ligand-gated ion channel (pLGIC) superfamily. Members of this superfamily assemble from five subunits, each of which consists of three domains: extracellular (ECD), transmembrane (TMD), and intracellular domain (ICD). Previously, we have demonstrated that the 5-HT3A-ICD is required for the interaction between 5-HT3A and the chaperone protein resistance to inhibitors of choline esterase (RIC-3). Additionally, we have shown that 5-HT3A-ICD fused to maltose-binding protein (MBP) directly interacts with RIC-3, without the involvement of other protein(s). To elucidate the molecular determinants of this interaction, we developed different MBP-fused 5-HT3A-ICD constructs by deleting large segments of its amino acid sequence. We expressed seven engineered ICDs in Escherichia coli and purified them to homogeneity. Using a RIC-3 affinity pull-down assay, the interaction between MBP-5HT3A-ICD constructs and RIC-3 was investigated. In summary, we identify a 24-amino-acid-long segment of the 5-HT3A-ICD as a molecular determinant for the interaction between the 5-HT3A-ICD and RIC-3.
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Affiliation(s)
- Elham Pirayesh
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Antonia G Stuebler
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Akash Pandhare
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas.
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56
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Munro L, Ladefoged LK, Padmanathan V, Andersen S, Schiøtt B, Kristensen AS. Conformational Changes in the 5-HT 3A Receptor Extracellular Domain Measured by Voltage-Clamp Fluorometry. Mol Pharmacol 2019; 96:720-734. [PMID: 31582575 DOI: 10.1124/mol.119.116657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 09/28/2019] [Indexed: 01/13/2023] Open
Abstract
The 5-hydroxytryptamine (5-HT) type 3 receptor is a member of the cysteine (Cys)-loop receptor super family of ligand-gated ion channels in the nervous system and is a clinical target in a range of diseases. The 5-HT3 receptor mediates fast serotonergic neurotransmission by undergoing a series of conformational changes initiated by ligand binding that lead to the rapid opening of an intrinsic cation-selective channel. However, despite the availability of high-resolution structures of a mouse 5-HT3 receptor, many important aspects of the mechanistic basis of 5-HT3 receptor function and modulation by drugs remain poorly understood. In particular, there is little direct evidence for the specific conformational changes predicted to occur during ligand-gated channel activation and desensitization. In the present study, we used voltage-clamp fluorometry (VCF) to measure conformational changes in regions surrounding the orthosteric binding site of the human 5-HT3A (h5-HT3A) receptor during binding of 5-HT and different classes of 5-HT3 receptor ligands. VCF utilizes parallel measurements of receptor currents with photon emission from fluorescent reporter groups covalently attached to specific positions in the receptor structure. Reporter groups that are highly sensitive to the local molecular environment can, in real time, report conformational changes as changes in fluorescence that can be correlated with changes in receptor currents reporting the functional states of the channel. Within the loop C, D, and E regions that surround the orthosteric binding site in the h5-HT3A receptor, we identify positions that are amenable to tagging with an environmentally sensitive reporter group that reports robust fluorescence changes upon 5-HT binding and receptor activation. We use these reporter positions to characterize the effect of ligand binding on the local structure of the orthosteric binding site by agonists, competitive antagonists, and allosterically acting channel activators. We observed that loop C appears to show distinct fluorescence changes for ligands of the same class, while loop D reports similar fluorescence changes for all ligands binding at the orthosteric site. In contrast, the loop E reporter position shows distinct changes for agonists, antagonists, and allosteric compounds, suggesting the conformational changes in this region are specific to ligand function. Interpretation of these results within the framework of current models of 5-HT3 and Cys-loop mechanisms are used to expand the understanding of how ligand binding in Cys-loop receptors relates to channel gating. SIGNIFICANCE STATEMENT: The 5-HT3 receptor is an important ligand-gated ion channel and drug target in the central and peripheral nervous system. Determining how ligand binding induced conformational changes in the receptor is central for understanding the structural mechanisms underlying 5-HT3 receptor function. Here, we employ voltage-gated fluorometry to characterize conformational changes in the extracellular domain of the human 5-HT3 receptor to identify intrareceptor motions during binding of a range of 5-HT3 receptor agonists and antagonists.
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Affiliation(s)
- Lachlan Munro
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
| | - Lucy Kate Ladefoged
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
| | - Vithushan Padmanathan
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
| | - Signe Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
| | - Birgit Schiøtt
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (L.M., V.P., S.A., A.S.K.); and Department of Chemistry (L.K.L., B.S.) and Interdisciplinary Nanoscience Center (B.S.), Aarhus University, Aarhus, Denmark
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57
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Gharpure A, Teng J, Zhuang Y, Noviello CM, Walsh RM, Cabuco R, Howard RJ, Zaveri NT, Lindahl E, Hibbs RE. Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor. Neuron 2019; 104:501-511.e6. [PMID: 31488329 DOI: 10.1016/j.neuron.2019.07.030] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022]
Abstract
Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.
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Affiliation(s)
- Anant Gharpure
- 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
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden
| | - Colleen M Noviello
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Richard M Walsh
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rico Cabuco
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden
| | | | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden; Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna 17121, Sweden
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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58
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Pandhare A, Pirayesh E, Stuebler AG, Jansen M. Triple arginines as molecular determinants for pentameric assembly of the intracellular domain of 5-HT 3A receptors. J Gen Physiol 2019; 151:1135-1145. [PMID: 31409663 PMCID: PMC6719409 DOI: 10.1085/jgp.201912421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/15/2019] [Indexed: 11/20/2022] Open
Abstract
Serotonin type 3A receptors are homopentameric ligand-gated ion channels that are thought to assemble via interactions involving the subunits’ extracellular and transmembrane domains. Pandhare et al. reveal that channel assembly is also determined by three arginine residues in the receptor’s intracellular domain. Serotonin type 3 receptors (5-HT3Rs) are cation-conducting pentameric ligand-gated ion channels and members of the Cys-loop superfamily in eukaryotes. 5-HT3Rs are found in the peripheral and central nervous system, and they are targets for drugs used to treat anxiety, drug dependence, and schizophrenia, as well as chemotherapy-induced and postoperative nausea and emesis. Decades of research of Cys-loop receptors have identified motifs in both the extracellular and transmembrane domains that mediate pentameric assembly. Those efforts have largely ignored the most diverse domain of these channels, the intracellular domain (ICD). Here we identify molecular determinants within the ICD of serotonin type 3A (5-HT3A) subunits for pentameric assembly by first identifying the segments contributing to pentamerization using deletion constructs of, and finally by making defined amino acid substitutions within, an isolated soluble ICD. Our work provides direct experimental evidence for the contribution of three intracellular arginines, previously implicated in governing the low conductance of 5-HT3ARs, in structural features such as pentameric assembly.
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Affiliation(s)
- Akash Pandhare
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Elham Pirayesh
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Antonia G Stuebler
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
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59
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Basak S, Gicheru Y, Kapoor A, Mayer ML, Filizola M, Chakrapani S. Molecular mechanism of setron-mediated inhibition of full-length 5-HT 3A receptor. Nat Commun 2019; 10:3225. [PMID: 31324772 PMCID: PMC6642186 DOI: 10.1038/s41467-019-11142-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/23/2019] [Indexed: 12/27/2022] Open
Abstract
Serotonin receptor (5-HT3AR) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of competitive antagonists, cause functional inhibition of 5-HT3AR in the gastrointestinal tract and brainstem, acting as effective anti-emetic agents. Despite their prevalent use, the molecular mechanisms underlying setron binding and inhibition of 5-HT3AR are not fully understood. Here, we present the structure of granisetron-bound full-length 5-HT3AR solved by single-particle cryo-electron microscopy to 2.92 Å resolution. The reconstruction reveals the orientation of granisetron in the orthosteric site with unambiguous density for interacting sidechains. Molecular dynamics simulations and electrophysiology confirm the granisetron binding orientation and the residues central for ligand recognition. Comparison of granisetron-bound 5-HT3AR with the apo and serotonin-bound structures, reveals key insights into the mechanism underlying 5-HT3AR inhibition.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Yvonne Gicheru
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan L Mayer
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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60
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Mosesso R, Dougherty DA, Lummis SCR. Proline Residues in the Transmembrane/Extracellular Domain Interface Loops Have Different Behaviors in 5-HT 3 and nACh Receptors. ACS Chem Neurosci 2019; 10:3327-3333. [PMID: 31273982 DOI: 10.1021/acschemneuro.9b00315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cys-loop receptors are important drug targets that are involved in signaling in the nervous system. The binding of neurotransmitters in the extracellular region of these receptors triggers an allosteric activation mechanism, the full details of which remain elusive, although structurally flexible loops in the interface between the extracellular region of Cys-loop receptors and the pore-forming transmembrane domain are known to play an important role. Here we explore the roles of three largely conserved Pro residues in two of these loops, the Cys-loop and M2-M3 loop, in 5-HT3A and α7 nACh receptors. The data from natural and noncanonical amino acid mutagenesis suggest that in both proteins a Pro is essential in the Cys-loop, probably because of its enhanced ability to form a cis peptide bond, although other factors are also involved. The important characteristics of Pros in the M2-M3 loop, however, differ in these two receptors: in the 5-HT3 receptor, the Pros can be replaced by some charged amino acids resulting in EC50s similar to those of wild-type receptors, while such substitutions in the nACh receptor ablate function. Ala substitution at one of these Pros also has different effects in the two receptors. Thus, our data show that even highly conserved residues can have distinct behaviors in related Cys-loop receptors.
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Affiliation(s)
- Richard Mosesso
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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61
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Oliveira ASF, Shoemark DK, Campello HR, Wonnacott S, Gallagher T, Sessions RB, Mulholland AJ. Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations. Structure 2019; 27:1171-1183.e3. [PMID: 31130483 DOI: 10.1016/j.str.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 02/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous system. These receptors have emerged as therapeutic targets in drug discovery for treating several conditions, including Alzheimer's disease, pain, and nicotine addiction. In this in silico study, we use a combination of equilibrium and nonequilibrium molecular dynamics simulations to map dynamic and structural changes induced by nicotine in the human α4β2 nAChR. They reveal a striking pattern of communication between the extracellular binding pockets and the transmembrane domains (TMDs) and show the sequence of conformational changes associated with the initial steps in this process. We propose a general mechanism for signal transduction for Cys-loop receptors: the mechanistic steps for communication proceed firstly through loop C in the principal subunit, and are subsequently transmitted, gradually and cumulatively, to loop F of the complementary subunit, and then to the TMDs through the M2-M3 linker.
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Affiliation(s)
- A Sofia F Oliveira
- School of Biochemistry, University of Bristol, Bristol BS8 1DT, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Hugo Rego Campello
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Susan Wonnacott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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62
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Crnjar A, Comitani F, Melis C, Molteni C. Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution. Interface Focus 2019; 9:20180067. [PMID: 31065340 PMCID: PMC6501341 DOI: 10.1098/rsfs.2018.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
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Affiliation(s)
- Alessandro Crnjar
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudio Melis
- Universitá degli Studi di Cagliari, Complesso Universitario di Monserrato, Dipartimento di Fisica, S.P. Monserrato-Sestu Km 0,700, Monserrato (CA) 09042, Italy
| | - Carla Molteni
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
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63
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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64
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Abdelkhalek AS, Alley GS, Alwassil OI, Khatri S, Mosier PD, Nyce HL, White MM, Schulte MK, Dukat M. "Methylene Bridge" to 5-HT 3 Receptor Antagonists: Conformationally Constrained Phenylguanidines. ACS Chem Neurosci 2019; 10:1380-1389. [PMID: 30375852 DOI: 10.1021/acschemneuro.8b00431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Arylguanidines, depending upon their aromatic substitution pattern, display varying actions at 5-HT3 receptors (e.g., partial agonist, agonist, superagonist). Here, we demonstrate that conformational constraint of these agents as dihydroquinazolines (such as A6CDQ; 1) results in their conversion to 5-HT3 receptor antagonists. We examined the structure-activity relationships of 1. Replacement/removal of any of the guanidinium nitrogen atoms of 1 resulted in decreased affinity. All three nitrogen atoms of 1 are necessary for optimal binding affinity at 5-HT3 receptors. Introduction of substituents as small as an N2-methyl group abolishes affinity. The results are consistent with homology modeling/docking studies and binding data from site-directed mutagenesis studies. Introducing a "methylene bridge" to the arylguanidine structure, regardless of its functional activity, results in a 5-HT3 receptor antagonist.
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Affiliation(s)
- Ahmed S. Abdelkhalek
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Genevieve S. Alley
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Osama I. Alwassil
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Shailesh Khatri
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Philip D. Mosier
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Heather L. Nyce
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania 19102, United States
| | - Michael M. White
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania 19102, United States
| | - Marvin K. Schulte
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Małgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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65
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Crnjar A, Comitani F, Hester W, Molteni C. Trans- Cis Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment. J Phys Chem Lett 2019; 10:694-700. [PMID: 30668119 DOI: 10.1021/acs.jpclett.8b03431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to their complexity and limited structural information available. Here we focus on a potential molecular switch in a prototypical pLGIC, the serotonin-activated 5-HT3 receptor, consisting of the trans- cis isomerization of a proline at the interface between the extracellular and transmembrane domain. Mutagenesis electrophysiology experiments previously showed that if such isomerization could not take place, the channel would not open, but the hypothetical role of this mechanism as key to channel gating is still debated. We investigate this switch within the receptor with molecular dynamics and enhanced sampling simulations. We analyze how the isomerization free energy landscape is affected by the receptor environment in comparison to simplified models. Moreover, we reveal how the isomerization, in turn, affects the structural and electrostatic properties of the receptor at the extracellular-transmembrane domain interface, e.g., by tuning the ion selectivity filter.
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Affiliation(s)
- Alessandro Crnjar
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Federico Comitani
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
- Chemistry Department , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - William Hester
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
| | - Carla Molteni
- Physics Department , King's College London , Strand, London WC2R 2LS , United Kingdom
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66
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Jack T, Leuenberger M, Ruepp MD, Vernekar SKV, Thompson AJ, Braga-Lagache S, Heller M, Lochner M. Mapping the Orthosteric Binding Site of the Human 5-HT 3 Receptor Using Photo-cross-linking Antagonists. ACS Chem Neurosci 2019; 10:438-450. [PMID: 30149702 DOI: 10.1021/acschemneuro.8b00327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The serotonin-gated 5-HT3 receptor is a ligand-gated ion channel. Its location at the synapse in the central and peripheral nervous system has rendered it a prime pharmacological target, for example, for antiemetic drugs that bind with high affinity to the neurotransmitter binding site and prevent the opening of the channel. Advances in structural biology techniques have led to a surge of disclosed three-dimensional receptor structures; however, solving ligand-bound high-resolution 5-HT3 receptor structures has not been achieved to date. Ligand binding poses in the orthosteric binding site have been largely predicted from mutagenesis and docking studies. We report the synthesis of a series of photo-cross-linking compounds whose structures are based on the clinically used antiemetic drug granisetron (Kytril). These displaced [3H]granisetron from the orthosteric binding site with low nanomolar affinities and showed specific photo-cross-linking with the human 5-HT3 receptor. Detailed analysis by protein-MS/MS identified a residue (Met-228) near the tip of binding loop C as the covalent modification site.
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Affiliation(s)
- Thomas Jack
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Michele Leuenberger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | | - Andrew J. Thompson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Sophie Braga-Lagache
- Department of BioMedical Research, Mass Spectrometry and Proteomics Laboratory, University of Bern, Inselspital, 3010 Bern, Switzerland
| | - Manfred Heller
- Department of BioMedical Research, Mass Spectrometry and Proteomics Laboratory, University of Bern, Inselspital, 3010 Bern, Switzerland
| | - Martin Lochner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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67
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68
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Wang X, O Reilly AO, Williamson MS, Puinean AM, Yang Y, Wu S, Wu Y. Function and pharmacology of glutamate-gated chloride channel exon 9 splice variants from the diamondback moth Plutella xylostella. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 104:58-64. [PMID: 30550974 DOI: 10.1016/j.ibmb.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Glutamate-gated chloride channels (GluCls) are found only in invertebrates and mediate fast inhibitory neurotransmission. The structural and functional diversity of GluCls are produced through assembly of multiple subunits and via posttranscriptional alternations. Alternative splicing is the most common way to achieve this in insect GluCls and splicing occurs primarily at exons 3 and 9. As expression pattern and pharmacological properties of exon 9 alternative splices in invertebrate GluCls remain poorly understood, the cDNAs encoding three alternative splice variants (9a, 9b and 9c) of the PxGluCl gene from the diamondback moth Plutella xylostella were constructed and their pharmacological characterizations were examined using electrophysiological studies. Alternative splicing of exon 9 had little to no impact on PxGluCl sensitivity towards the agonist glutamate when subunits were singly or co-expressed in Xenopus oocytes. In contrast, the allosteric modulator abamectin and the chloride channel blocker fipronil had differing effects on PxGluCl splice variants. PxGluCl9c channels were more resistant to abamectin and PxGluCl9b channels were more sensitive to fipronil than other homomeric channels. In addition, heteromeric channels containing different splice variants showed similar sensitivity to abamectin (except for 9c) and reduced sensitivity to fipronil than homomeric channels. These findings suggest that functionally indistinguishable but pharmacologically distinct GluCls could be formed in P. xylostella and that the upregulated constitutive expression of the specific variants may contribute to the evolution of insecticide resistance in P. xylostella and other arthropods.
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Affiliation(s)
- Xingliang Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
| | - Andrias O O Reilly
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
| | - Martin S Williamson
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, UK.
| | - Alin M Puinean
- Oxitec Limited, 71 Innovation Drive, Abingdon, Oxfordshire, UK.
| | - Yihua Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
| | - Shuwen Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
| | - Yidong Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
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69
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Structural biology and structure–function relationships of membrane proteins. Biochem Soc Trans 2018; 47:47-61. [DOI: 10.1042/bst20180269] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 01/02/2023]
Abstract
Abstract
The study of structure–function relationships of membrane proteins (MPs) has been one of the major goals in the field of structural biology. Many Noble Prizes regarding remarkable accomplishments in MP structure determination and biochemistry have been awarded over the last few decades. Mutations or improper folding of these proteins are associated with numerous serious illnesses. Therefore, as important drug targets, the study of their primary sequence and three-dimensional fold, combined with cell-based assays, provides vital information about their structure–function relationships. Today, this information is vital to drug discovery and medicine. In the last two decades, many have been the technical advances and breakthroughs in the field of MP structural biology that have contributed to an exponential growth in the number of unique MP structures in the Protein Data Bank. Nevertheless, given the medical importance and many unanswered questions, it will never be an excess of MP structures, regardless of the method used. Owing to the extension of the field, in this brief review, we will only focus on structure–function relationships of the three most significant pharmaceutical classes: G protein-coupled receptors, ion channels and transporters.
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70
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Wang QQ, Wang CM, Cheng BH, Yang CQ, Bai B, Chen J. Signaling transduction regulated by 5-hydroxytryptamine 1A receptor and orexin receptor 2 heterodimers. Cell Signal 2018; 54:46-58. [PMID: 30481562 DOI: 10.1016/j.cellsig.2018.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/08/2018] [Accepted: 11/15/2018] [Indexed: 12/09/2022]
Abstract
As G-protein-coupled receptors (GPCRs), 5-hydroxytryptamine 1A receptor (5-HT1AR) and orexin receptor 2 (OX2R) regulate the levels of the cellular downstream molecules. The heterodimers of different GPCRs play important roles in various of neurological diseases. Moreover, 5-HT1AR and OX2R are involved in the pathogenesis of neurological diseases such as depression with deficiency of hippocampus plasticity. However, the direct interaction of the two receptors remains elusive. In the present study, we firstly demonstrated the heterodimer formation of 5-HT1AR and OX2R. Exchange protein directly activated by cAMP (Epac) cAMP bioluminescence resonance energy transfer (BRET) biosensor analysis revealed that the expression levels of cellular cAMP significantly increased in HEK293T cells transfected with the two receptors compared with the 5-HT1AR group. Additionally, the cellular level of calcium was upregulated robustly in HEK293T cells co-transfected with 5-HT1AR and OX2R group after agonist treatment. Furthermore, western blotting data showed that 5-HT1AR and OX2R heterodimer decreased the levels of phosphorylation of extracellular signal-regulated kinase (ERK) and cAMP-response element-binding protein (CREB). These results not only unraveled the formation of 5-HT1AR and OX2R heterodimer but also suggested that the heterodimer affected the downstream signaling pathway, which will provide new insights into the function of the two receptors in the brain.
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Affiliation(s)
- Qin-Qin Wang
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China
| | - Chun-Mei Wang
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China
| | - Bao-Hua Cheng
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China
| | - Chun-Qing Yang
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China
| | - Bo Bai
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China.
| | - Jing Chen
- Neurobiology Key Laboratory, Jining Medical University, Colleges of Shandong, Jining 272067, PR China; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
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71
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Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT 3A receptor. Nature 2018; 563:270-274. [PMID: 30401837 PMCID: PMC6237196 DOI: 10.1038/s41586-018-0660-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/30/2018] [Indexed: 12/19/2022]
Abstract
Serotonin receptor (5-HT3AR)1, a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies2. Upon binding, serotonin induces a global conformational change encompassing the ligand-binding extracellular domain (ECD), the transmembrane domain (TMD), and the intracellular domain (ICD), the molecular details of which are unclear. Here, we present two serotonin-bound structures of the full-length 5-HT3AR in distinct conformations at 3.32 Å and 3.89 Å resolutions that reveal the mechanism underlying channel activation. When compared to Apo-5-HT3AR, serotonin-bound states underwent a large twisting motion in the ECD and TMD leading to the opening of a 165 Å long permeation pathway. Notably, this motion results in creation of lateral portals for ion permeation at the interface of the TMD and ICD. Combined with molecular dynamics simulations, these structures provide novel insights into conformational coupling across domains and functional modulation.
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72
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Polovinkin L, Hassaine G, Perot J, Neumann E, Jensen AA, Lefebvre SN, Corringer PJ, Neyton J, Chipot C, Dehez F, Schoehn G, Nury H. Conformational transitions of the serotonin 5-HT 3 receptor. Nature 2018; 563:275-279. [PMID: 30401839 DOI: 10.1038/s41586-018-0672-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
Abstract
The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
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Affiliation(s)
| | | | - Jonathan Perot
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | | | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Solène N Lefebvre
- Channel Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France
| | | | - Jacques Neyton
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Guy Schoehn
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
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73
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Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity. Proc Natl Acad Sci U S A 2018; 115:10672-10677. [PMID: 30275330 PMCID: PMC6196478 DOI: 10.1073/pnas.1809650115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theories of general anesthesia have shifted in focus from bulk lipid effects to specific interactions with membrane proteins. Target receptors include several subtypes of pentameric ligand-gated ion channels; however, structures of physiologically relevant proteins in this family have yet to define anesthetic binding at high resolution. Recent cocrystal structures of the bacterial protein GLIC provide snapshots of state-dependent binding sites for the common surgical agent propofol (PFL), offering a detailed model system for anesthetic modulation. Here, we combine molecular dynamics and oocyte electrophysiology to reveal differential motion and modulation upon modification of a transmembrane binding site within each GLIC subunit. WT channels exhibited net inhibition by PFL, and a contraction of the cavity away from the pore-lining M2 helix in the absence of drug. Conversely, in GLIC variants exhibiting net PFL potentiation, the cavity was persistently expanded and proximal to M2. Mutations designed to favor this deepened site enabled sensitivity even to subclinical concentrations of PFL, and a uniquely prolonged mode of potentiation evident up to ∼30 min after washout. Dependence of these prolonged effects on exposure time implicated the membrane as a reservoir for a lipid-accessible binding site. However, at the highest measured concentrations, potentiation appeared to be masked by an acute inhibitory effect, consistent with the presence of a discrete, water-accessible site of inhibition. These results support a multisite model of transmembrane allosteric modulation, including a possible link between lipid- and receptor-based theories that could inform the development of new anesthetics.
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74
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Structural basis of neurosteroid anesthetic action on GABA A receptors. Nat Commun 2018; 9:3972. [PMID: 30266951 PMCID: PMC6162318 DOI: 10.1038/s41467-018-06361-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/28/2018] [Indexed: 12/05/2022] Open
Abstract
Type A γ-aminobutyric acid receptors (GABAARs) are inhibitory pentameric ligand-gated ion channels in the brain. Many anesthetics and neurosteroids act through binding to the GABAAR transmembrane domain (TMD), but the structural basis of their actions is not well understood and no resting-state GABAAR structure has been determined. Here, we report crystal structures of apo and the neurosteroid anesthetic alphaxalone-bound desensitized chimeric α1GABAAR (ELIC-α1GABAAR). The chimera retains the functional and pharmacological properties of GABAARs, including potentiation, activation and desensitization by alphaxalone. The apo-state structure reveals an unconventional activation gate at the intracellular end of the pore. The desensitized structure illustrates molecular determinants for alphaxalone binding to an inter-subunit TMD site. These structures suggest a plausible signaling pathway from alphaxalone binding at the bottom of the TMD to the channel gate in the pore-lining TM2 through the TM1–TM2 linker. The study provides a framework to discover new GABAAR modulators with therapeutic potential. The anesthetic alphaxalone binds γ-aminobutyric acid type A receptors (GABAARs) that play an important role in regulating sensory processes. Here the authors present the structures of a α1GABAAR chimera in the resting state and in an alphaxalone-bound desensitized state, which might facilitate the development of new GABAAR modulators.
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75
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Ladefoged LK, Munro L, Pedersen AJ, Lummis SCR, Bang-Andersen B, Balle T, Schiøtt B, Kristensen AS. Modeling and Mutational Analysis of the Binding Mode for the Multimodal Antidepressant Drug Vortioxetine to the Human 5-HT3A Receptor. Mol Pharmacol 2018; 94:1421-1434. [DOI: 10.1124/mol.118.113530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022] Open
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76
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Phulera S, Zhu H, Yu J, Claxton DP, Yoder N, Yoshioka C, Gouaux E. Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2S tri-heteromeric GABA A receptor in complex with GABA. eLife 2018; 7:39383. [PMID: 30044221 PMCID: PMC6086659 DOI: 10.7554/elife.39383] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABAA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsant agents, with mutant forms of GABAA receptors implicated in multiple neurological diseases. Despite the profound importance of heteromeric GABAA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of a tri-heteromeric α1β1γ2SEM GABAA receptor in complex with GABA, determined by single particle cryo-EM at 3.1–3.8 Å resolution, elucidating molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the α1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABAA receptors and a framework for rational design of novel therapeutic agents.
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Affiliation(s)
- Swastik Phulera
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jie Yu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Derek P Claxton
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Nate Yoder
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Craig Yoshioka
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, United States.,Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
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