1
|
Nayak SR, Joseph D, Höfner G, Dakua A, Athreya A, Wanner KT, Kanner BI, Penmatsa A. Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism. Nat Struct Mol Biol 2023; 30:1023-1032. [PMID: 37400654 PMCID: PMC10352132 DOI: 10.1038/s41594-023-01011-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/04/2023] [Indexed: 07/05/2023]
Abstract
The inhibitory neurotransmitter γ-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic signaling at the synapse and is a strategy to treat certain forms of epilepsy. In this study, we present the cryo-electron microscopy structure of Rattus norvegicus GABA transporter 1 (rGAT1) at a resolution of 3.1 Å. The structure elucidation was facilitated by epitope transfer of a fragment-antigen binding (Fab) interaction site from the Drosophila dopamine transporter (dDAT) to rGAT1. The structure reveals rGAT1 in a cytosol-facing conformation, with a linear density in the primary binding site that accommodates a molecule of GABA, a displaced ion density proximal to Na site 1 and a bound chloride ion. A unique insertion in TM10 aids the formation of a compact, closed extracellular gate. Besides yielding mechanistic insights into ion and substrate recognition, our study will enable the rational design of specific antiepileptics.
Collapse
Affiliation(s)
| | - Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Georg Höfner
- Department of Pharmacy, Center for Drug Research, Ludwig Maximilians University of Munich, Munich, Germany
| | - Archishman Dakua
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Biophysics Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Klaus T Wanner
- Department of Pharmacy, Center for Drug Research, Ludwig Maximilians University of Munich, Munich, Germany
| | - Baruch I Kanner
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
| |
Collapse
|
2
|
Saenz J, Yao O, Khezerlou E, Aggarwal M, Zhou X, Barker DJ, DiCicco-Bloom E, Pan PY. Cocaine-regulated trafficking of dopamine transporters in cultured neurons revealed by a pH sensitive reporter. iScience 2023; 26:105782. [PMID: 36594015 PMCID: PMC9804146 DOI: 10.1016/j.isci.2022.105782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cocaine acts by inhibiting plasma membrane dopamine transporter (DAT) function and altering its surface expression. The precise manner and mechanism by which cocaine regulates DAT trafficking, especially at neuronal processes, are poorly understood. In this study, we engineered and validated the use of DAT-pHluorin for studying DAT localization and its dynamic trafficking at neuronal processes of cultured mouse midbrain neurons. We demonstrate that unlike neuronal soma and dendrites, which contain a majority of the DATs in weakly acidic intracellular compartments, axonal DATs at both shafts and boutons are primarily (75%) localized to the plasma membrane, whereas large varicosities contain abundant intracellular DAT within acidic intracellular structures. We also demonstrate that cocaine exposure leads to a Synaptojanin1-sensitive DAT internalization process followed by membrane reinsertion that lasts for days. Thus, our study reveals the previously unknown dynamics and molecular regulation for cocaine-regulated DAT trafficking in neuronal processes.
Collapse
Affiliation(s)
- Jacqueline Saenz
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Piscataway, NJ 08854, USA
- Rutgers Graduate School of Biomedical Sciences, Molecular Biosciences Graduate Program, Piscataway, NJ 08854, USA
| | - Oscar Yao
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Elnaz Khezerlou
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Meha Aggarwal
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Xiaofeng Zhou
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 683 Hoes Lane West, Piscataway, NJ 08854, USA
| | - David J. Barker
- Rutgers, The State University of New Jersey, Department of Psychology, 152 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Emanuel DiCicco-Bloom
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 683 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Ping-Yue Pan
- Rutgers University Robert Wood Johnson Medical School, Department of Neuroscience and Cell Biology, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| |
Collapse
|
3
|
Abstract
Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological importance. Several presently used therapeutic compounds elucidate their effects by targeting membrane transporter proteins, including anti-arrhythmic, anesthetic, antidepressant, anxiolytic and diuretic drugs. The lack of three-dimensional structures of human transporters hampers experimental studies and drug discovery. In this chapter, the use of homology modeling for generating structural models of membrane transporter proteins is reviewed. The increasing number of atomic resolution structures available as templates, together with improvements in methods and algorithms for sequence alignments, secondary structure predictions, and model generation, in addition to the increase in computational power have increased the applicability of homology modeling for generating structural models of transporter proteins. Different pitfalls and hints for template selection, multiple-sequence alignments, generation and optimization, validation of the models, and the use of transporter homology models for structure-based virtual ligand screening are discussed.
Collapse
Affiliation(s)
- Ingebrigt Sylte
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Mari Gabrielsen
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kurt Kristiansen
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
4
|
Joseph D, Nayak SR, Penmatsa A. Structural insights into GABA transport inhibition using an engineered neurotransmitter transporter. EMBO J 2022; 41:e110735. [PMID: 35796008 PMCID: PMC9340486 DOI: 10.15252/embj.2022110735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 01/14/2023] Open
Abstract
γ-aminobutyric acid (GABA) is the major inhibitory neurotransmitter, and its levels in the synaptic space are controlled by the GABA transporter isoforms (GATs). GATs are structurally related to biogenic amine transporters but display interactions with distinct inhibitors used as anti-epileptics. In this study, we engineer the binding pocket of Drosophila melanogaster dopamine transporter to resemble GAT1 and determine high-resolution X-ray structures of the modified transporter in the substrate-free state and in complex with GAT1 inhibitors NO711 and SKF89976a that are analogs of tiagabine, a medication prescribed for the treatment of partial seizures. We observe that the primary binding site undergoes substantial shifts in subsite architecture in the modified transporter to accommodate the two GAT1 inhibitors. We also observe that SKF89976a additionally interacts at an allosteric site in the extracellular vestibule, yielding an occluded conformation. Interchanging SKF89976a interacting residue in the extracellular loop 4 between GAT1 and dDAT suggests a role for this motif in the selective control of neurotransmitter uptake. Our findings, therefore, provide vital insights into the organizational principles dictating GAT1 activity and inhibition.
Collapse
Affiliation(s)
- Deepthi Joseph
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | | | - Aravind Penmatsa
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| |
Collapse
|
5
|
Sijben HJ, van den Berg JJE, Broekhuis JD, IJzerman AP, Heitman LH. A study of the dopamine transporter using the TRACT assay, a novel in vitro tool for solute carrier drug discovery. Sci Rep 2021; 11:1312. [PMID: 33446713 PMCID: PMC7809260 DOI: 10.1038/s41598-020-79218-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Members of the solute carrier (SLC) transporter protein family are increasingly recognized as therapeutic drug targets. The majority of drug screening assays for SLCs are based on the uptake of radiolabeled or fluorescent substrates. Thus, these approaches often have limitations that compromise on throughput or the physiological environment of the SLC. In this study, we report a novel application of an impedance-based biosensor, xCELLigence, to investigate dopamine transporter (DAT) activity via substrate-induced activation of G protein-coupled receptors (GPCRs). The resulting assay, which is coined the 'transporter activity through receptor activation' (TRACT) assay, is based on the hypothesis that DAT-mediated removal of extracellular dopamine directly affects the ability of dopamine to activate cognate membrane-bound GPCRs. In two human cell lines with heterologous DAT expression, dopamine-induced GPCR signaling was attenuated. Pharmacological inhibition or the absence of DAT restored the apparent potency of dopamine for GPCR activation. The inhibitory potencies for DAT inhibitors GBR12909 (pIC50 = 6.2, 6.6) and cocaine (pIC50 = 6.3) were in line with values from reported orthogonal transport assays. Conclusively, this study demonstrates the novel use of label-free whole-cell biosensors to investigate DAT activity using GPCR activation as a readout. This holds promise for other SLCs that share their substrate with a GPCR.
Collapse
Affiliation(s)
- Hubert J Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, P.O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Julie J E van den Berg
- Division of Drug Discovery and Safety, LACDR, Leiden University, P.O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Jeremy D Broekhuis
- Division of Drug Discovery and Safety, LACDR, Leiden University, P.O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, P.O. Box 9502, 2300RA, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, P.O. Box 9502, 2300RA, Leiden, The Netherlands.
- Oncode Institute, Leiden, The Netherlands.
| |
Collapse
|
6
|
Aggarwal S, Liu X, Rice C, Menell P, Clark PJ, Paparoidamis N, Xiao YC, Salvino JM, Fontana ACK, España RA, Kortagere S, Mortensen OV. Identification of a Novel Allosteric Modulator of the Human Dopamine Transporter. ACS Chem Neurosci 2019; 10:3718-3730. [PMID: 31184115 PMCID: PMC6703927 DOI: 10.1021/acschemneuro.9b00262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The dopamine transporter (DAT) serves a pivotal role in controlling dopamine (DA)-mediated neurotransmission by clearing DA from synaptic and perisynaptic spaces and controlling its action at postsynaptic DA receptors. Major drugs of abuse such as amphetamine and cocaine interact with DAT to mediate their effects by enhancing extracellular DA concentrations. We previously identified a novel allosteric site in the related human serotonin transporter that lies outside the central substrate and inhibitor binding pocket. We used the hybrid structure based (HSB) method to screen for allosteric modulator molecules that target a similar site in DAT. We identified a compound, KM822, that was found to be a selective, noncompetitive inhibitor of DAT. We confirmed the structural determinants of KM822 allosteric binding within the allosteric site by structure/function and substituted cysteine scanning accessibility biotinylation experiments. In the in vitro cell-based assay and ex vivo in both rat striatal synaptosomal and slice preparations, KM822 was found to decrease the affinity of cocaine for DAT. The in vivo effects of KM822 on cocaine were tested on psychostimulant-associated behaviors in a planarian model where KM822 specifically inhibited the locomotion elicited by DAT-interacting stimulants amphetamine and cocaine. Overall, KM822 provides a unique opportunity as a molecular probe to examine allosteric modulation of DAT function.
Collapse
Affiliation(s)
- Shaili Aggarwal
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Xiaonan Liu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Caitlyn Rice
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Paul Menell
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Philip J. Clark
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, United States
| | | | - You-cai Xiao
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joseph M. Salvino
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Andréia C. K. Fontana
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Rodrigo A. España
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, United States
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, United States
| | - Ole V. Mortensen
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| |
Collapse
|