1
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Deng S, Zhang H, Gou R, Luo D, Liu Z, Zhu F, Xue W. Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J Chem Inf Model 2023. [PMID: 37410882 DOI: 10.1021/acs.jcim.3c00477] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Human dopamine transporter (hDAT) regulates the reuptake of extracellular dopamine (DA) and is an essential therapeutic target for central nervous system (CNS) diseases. The allosteric modulation of hDAT has been identified for decades. However, the molecular mechanism underlying the transportation is still elusive, which hinders the rational design of allosteric modulators against hDAT. Here, a systematic structure-based method was performed to explore allosteric sites on hDAT in inward-open (IO) conformation and to screen compounds with allosteric affinity. First, the model of the hDAT structure was constructed based on the recently reported Cryo-EM structure of the human serotonin transporter (hSERT) and Gaussian-accelerated molecular dynamics (GaMD) simulation was further utilized for the identification of intermediate energetic stable states of the transporter. Then, with the potential druggable allosteric site on hDAT in IO conformation, virtual screening of seven enamine chemical libraries (∼440,000 compounds) was processed, resulting in 10 compounds being purchased for in vitro assay and with Z1078601926 discovered to allosterically inhibit hDAT (IC50 = 0.527 [0.284; 0.988] μM) when nomifensine was introduced as an orthosteric ligand. Finally, the synergistic effect underlying the allosteric inhibition of hDAT by Z1078601926 and nomifensine was explored using additional GaMD simulation and postbinding free energy analysis. The hit compound discovered in this work not only provides a good starting point for lead optimization but also demonstrates the usability of the method for the structure-based discovery of novel allosteric modulators of other therapeutic targets.
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Affiliation(s)
- Shengzhe Deng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Haiwei Zhang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Department of Pathology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical Co., Ltd., Luzhou 646000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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2
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Bhatt M, Gauthier-Manuel L, Lazzarin E, Zerlotti R, Ziegler C, Bazzone A, Stockner T, Bossi E. A comparative review on the well-studied GAT1 and the understudied BGT-1 in the brain. Front Physiol 2023; 14:1145973. [PMID: 37123280 PMCID: PMC10137170 DOI: 10.3389/fphys.2023.1145973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
γ-aminobutyric acid (GABA) is the primary inhibitory neurotransmitter in the central nervous system (CNS). Its homeostasis is maintained by neuronal and glial GABA transporters (GATs). The four GATs identified in humans are GAT1 (SLC6A1), GAT2 (SLC6A13), GAT3 (SLC6A11), and betaine/GABA transporter-1 BGT-1 (SLC6A12) which are all members of the solute carrier 6 (SLC6) family of sodium-dependent transporters. While GAT1 has been investigated extensively, the other GABA transporters are less studied and their role in CNS is not clearly defined. Altered GABAergic neurotransmission is involved in different diseases, but the importance of the different transporters remained understudied and limits drug targeting. In this review, the well-studied GABA transporter GAT1 is compared with the less-studied BGT-1 with the aim to leverage the knowledge on GAT1 to shed new light on the open questions concerning BGT-1. The most recent knowledge on transporter structure, functions, expression, and localization is discussed along with their specific role as drug targets for neurological and neurodegenerative disorders. We review and discuss data on the binding sites for Na+, Cl-, substrates, and inhibitors by building on the recent cryo-EM structure of GAT1 to highlight specific molecular determinants of transporter functions. The role of the two proteins in GABA homeostasis is investigated by looking at the transport coupling mechanism, as well as structural and kinetic transport models. Furthermore, we review information on selective inhibitors together with the pharmacophore hypothesis of transporter substrates.
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Affiliation(s)
- Manan Bhatt
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Centre for Neuroscience—University of Insubria, Varese, Italy
| | - Laure Gauthier-Manuel
- Department of Biophysics II/Structural Biology, University of Regensburg, Regensburg, Germany
| | - Erika Lazzarin
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr, Vienna
| | - Rocco Zerlotti
- Department of Biophysics II/Structural Biology, University of Regensburg, Regensburg, Germany
- Nanion Technologies GmbH, Munich, Germany
| | - Christine Ziegler
- Department of Biophysics II/Structural Biology, University of Regensburg, Regensburg, Germany
| | | | - Thomas Stockner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Waehringerstr, Vienna
- *Correspondence: Thomas Stockner, ; Elena Bossi,
| | - Elena Bossi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Centre for Neuroscience—University of Insubria, Varese, Italy
- *Correspondence: Thomas Stockner, ; Elena Bossi,
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3
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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4
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Yang D, Gouaux E. Illumination of serotonin transporter mechanism and role of the allosteric site. SCIENCE ADVANCES 2021; 7:eabl3857. [PMID: 34851672 PMCID: PMC8635421 DOI: 10.1126/sciadv.abl3857] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/14/2021] [Indexed: 05/10/2023]
Abstract
The serotonin transporter (SERT) terminates serotonin signaling by using sodium and chloride gradients to drive reuptake of serotonin into presynaptic neurons and is the target of widely used medications to treat neuropsychiatric disorders. Despite decades of study, the molecular mechanism of serotonin transport, the coupling to ion gradients, and the role of the allosteric site have remained elusive. Here, we present cryo–electron microscopy structures of SERT in serotonin-bound and serotonin-free states, in the presence of sodium or potassium, resolving all fundamental states of the transport cycle. From the SERT-serotonin complex, we localize the substrate-bound allosteric site, formed by an aromatic pocket positioned in the scaffold domain in the extracellular vestibule, connected to the central site via a short tunnel. Together with elucidation of multiple apo state conformations, we provide previously unseen structural understanding of allosteric modulation, demonstrating how SERT binds serotonin from synaptic volumes and promotes unbinding into the presynaptic neurons.
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Affiliation(s)
- Dongxue Yang
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
- Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR 97239, USA
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5
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Frangos ZJ, Cantwell Chater RP, Vandenberg RJ. Glycine Transporter 2: Mechanism and Allosteric Modulation. Front Mol Biosci 2021; 8:734427. [PMID: 34805268 PMCID: PMC8602798 DOI: 10.3389/fmolb.2021.734427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023] Open
Abstract
Neurotransmitter sodium symporters (NSS) are a subfamily of SLC6 transporters responsible for regulating neurotransmitter signalling. They are a major target for psychoactive substances including antidepressants and drugs of abuse, prompting substantial research into their modulation and structure-function dynamics. Recently, a series of allosteric transport inhibitors have been identified, which may reduce side effect profiles, compared to orthosteric inhibitors. Allosteric inhibitors are also likely to provide different clearance kinetics compared to competitive inhibitors and potentially better clinical outcomes. Crystal structures and homology models have identified several allosteric modulatory sites on NSS including the vestibule allosteric site (VAS), lipid allosteric site (LAS) and cholesterol binding site (CHOL1). Whilst the architecture of eukaryotic NSS is generally well conserved there are differences in regions that form the VAS, LAS, and CHOL1. Here, we describe ligand-protein interactions that stabilize binding in each allosteric site and explore how differences between transporters could be exploited to generate NSS specific compounds with an emphasis on GlyT2 modulation.
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Affiliation(s)
- Zachary J Frangos
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ryan P Cantwell Chater
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Robert J Vandenberg
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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6
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Thomas NE, Feng W, Henzler-Wildman KA. A solid-supported membrane electrophysiology assay for efficient characterization of ion-coupled transport. J Biol Chem 2021; 297:101220. [PMID: 34562455 PMCID: PMC8517846 DOI: 10.1016/j.jbc.2021.101220] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 12/03/2022] Open
Abstract
Transport stoichiometry determination can provide great insight into the mechanism and function of ion-coupled transporters. Traditional reversal potential assays are a reliable, general method for determining the transport stoichiometry of ion-coupled transporters, but the time and material costs of this technique hinder investigations of transporter behavior under multiple experimental conditions. Solid-supported membrane electrophysiology (SSME) allows multiple recordings of liposomal or membrane samples adsorbed onto a sensor and is sensitive enough to detect transport currents from moderate-flux transporters that are inaccessible to traditional electrophysiology techniques. Here, we use SSME to develop a new method for measuring transport stoichiometry with greatly improved throughput. Using this technique, we were able to verify the recent report of a fixed 2:1 stoichiometry for the proton:guanidinium antiporter Gdx, reproduce the 1H+:2Cl- antiport stoichiometry of CLC-ec1, and confirm loose proton:nitrate coupling for CLC-ec1. Furthermore, we were able to demonstrate quantitative exchange of internal contents of liposomes adsorbed onto SSME sensors to allow multiple experimental conditions to be tested on a single sample. Our SSME method provides a fast, easy, general method for measuring transport stoichiometry, which will facilitate future mechanistic and functional studies of ion-coupled transporters.
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Affiliation(s)
- Nathan E Thomas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wei Feng
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
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7
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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8
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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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9
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Xu L, Chen LY. Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. J Chem Inf Model 2020; 60:3958-3968. [PMID: 32649824 PMCID: PMC7484383 DOI: 10.1021/acs.jcim.0c00346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dopamine (DA) transporter (DAT) is a major target for psychostimulant drugs of abuse such as cocaine that competitively binds to DAT, inhibits DA reuptake, and consequently increases synaptic DA levels. In addition to the central binding site inside DAT, the available experimental evidence suggests the existence of alternative binding sites on DAT, but detection and characterization of these sites are challenging by experiments alone. Here, we integrate multiple computational approaches to probe the potential binding sites on the wild-type Drosophila melanogaster DAT and identify a new allosteric site that displays high affinity for cocaine. This site is located on the surface of DAT, and binding of cocaine is primarily dominated by interactions with hydrophobic residues surrounding the site. We show that cocaine binding to this new site allosterically reduces the binding of DA/cocaine to the central binding pocket, and simultaneous binding of two cocaine molecules to a single DAT seems infeasible. Furthermore, we find that binding of cocaine to this site stabilizes the conformation of DAT but alters the conformational population and thereby reduces the accessibility by DA, providing molecular insights into the inhibitory mechanism of cocaine. In addition, our results indicate that the conformations induced by cocaine binding to this site may be relevant to the oligomerization of DAT, highlighting a potential role of this new site in modulating the function of DAT.
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Affiliation(s)
- Liang Xu
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Liao Y Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
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10
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Xue W, Fu T, Zheng G, Tu G, Zhang Y, Yang F, Tao L, Yao L, Zhu F. Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters. Curr Med Chem 2020; 27:3830-3876. [DOI: 10.2174/0929867325666181009123218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023]
Abstract
Background:
The human Monoamine Transporters (hMATs), primarily including hSERT,
hNET and hDAT, are important targets for the treatment of depression and other behavioral disorders
with more than the availability of 30 approved drugs.
Objective:
This paper is to review the recent progress in the binding mode and inhibitory mechanism of
hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor
design and discovery. The Structure-Activity Relationship (SAR) and the selectivity for hit/lead compounds
to hMATs that are evaluated by in vitro and in vivo experiments will be highlighted.
Methods:
PubMed and Web of Science databases were searched for protein-ligand interaction, novel
inhibitors design and synthesis studies related to hMATs.
Results:
Literature data indicate that since the first crystal structure determinations of the homologous
bacterial Leucine Transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental
structures or computational models has been accumulated that now defines a substantial degree
of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs
inhibitors have been discovered by medicinal chemistry with significant help from computational models.
Conclusion:
The reported new compounds act on hMATs as well as the structures of the transporters
complexed with diverse ligands by either experiment or computational modeling have shed light on the
poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies
will greatly promote the Structure-Based Drug Design (SBDD) of structurally novel scaffolds with high
activity and selectivity for hMATs.
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Affiliation(s)
- Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Guoxun Zheng
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Yang Zhang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Lixia Yao
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, United States
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
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11
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Khan JA, Sohail A, Jayaraman K, Szöllősi D, Sandtner W, Sitte HH, Stockner T. The Amino Terminus of LeuT Changes Conformation in an Environment Sensitive Manner. Neurochem Res 2020; 45:1387-1398. [PMID: 31858375 PMCID: PMC7260283 DOI: 10.1007/s11064-019-02928-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/21/2022]
Abstract
Neurotransmitter:sodium symporters are highly expressed in the human brain and catalyze the uptake of substrate through the plasma membrane by using the electrochemical gradient of sodium as the energy source. The bacterial homolog LeuT, a small amino acid transporter isolated from the bacteria Aquifex aeolicus, is the founding member of the family and has been crystallized in three conformations. The N-terminus is structurally well defined and strongly interacts with the transporter core in the outward-facing conformations. However, it could not be resolved in the inward-facing conformation, which indicates enhanced mobility. Here we investigate conformations and dynamics of the N-terminus, by combining molecular dynamics simulations with experimental verification using distance measurements and accessibility studies. We found strongly increased dynamics of the N-terminus, but also that helix TM1A is subject to enhanced mobility. TM1A moves towards the transporter core in the membrane environment, reaching a conformation that is closer to the structure of LeuT with wild type sequence, indicating that the mutation introduced to create the inward-facing structure might have altered the position of helix TM1A. The mobile N-terminus avoids entering the open vestibule of the inward-facing state, as accessibility studies do not show any reduction of quenching by iodide of a fluorophore attached to the N-terminus.
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Affiliation(s)
- Jawad A Khan
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Azmat Sohail
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Kumaresan Jayaraman
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Harald H Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria.
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12
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Joseph D, Pidathala S, Mallela AK, Penmatsa A. Structure and Gating Dynamics of Na +/Cl - Coupled Neurotransmitter Transporters. Front Mol Biosci 2019; 6:80. [PMID: 31555663 PMCID: PMC6742698 DOI: 10.3389/fmolb.2019.00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022] Open
Abstract
Neurotransmitters released at the neural synapse through vesicle exocytosis are spatiotemporally controlled by the action of neurotransmitter transporters. Integral membrane proteins of the solute carrier 6 (SLC6) family are involved in the sodium and chloride coupled uptake of biogenic amine neurotransmitters including dopamine, serotonin, noradrenaline and inhibitory neurotransmitters including glycine and γ-amino butyric acid. This ion-coupled symport works through a well-orchestrated gating of substrate through alternating-access, which is mediated through movements of helices that resemble a rocking-bundle. A large array of commercially prescribed drugs and psychostimulants selectively target neurotransmitter transporters thereby modulating their levels in the synaptic space. Drug-induced changes in the synaptic neurotransmitter levels can be used to treat depression or neuropathic pain whereas in some instances prolonged usage can lead to habituation. Earlier structural studies of bacterial neurotransmitter transporter homolog LeuT and recent structure elucidation of the Drosophila dopamine transporter (dDAT) and human serotonin transporter (hSERT) have yielded a wealth of information in understanding the transport and inhibition mechanism of neurotransmitter transporters. Computational studies based on the structures of dDAT and hSERT have shed light on the dynamics of varied components of these molecular gates in affecting the uphill transport of neurotransmitters. This review seeks to address structural dynamics of neurotransmitter transporters at the extracellular and intracellular gates and the effect of inhibitors on the ligand-binding pocket. We also delve into the effect of additional factors including lipids and cytosolic domains that influence the translocation of neurotransmitters across the membrane.
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Affiliation(s)
- Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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13
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Niello M, Cintulova D, Hellsberg E, Jäntsch K, Holy M, Ayatollahi LH, Cozzi NV, Freissmuth M, Sandtner W, Ecker GF, Mihovilovic MD, Sitte HH. para-Trifluoromethyl-methcathinone is an allosteric modulator of the serotonin transporter. Neuropharmacology 2019; 161:107615. [PMID: 31028773 DOI: 10.1016/j.neuropharm.2019.04.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 11/15/2022]
Abstract
The transporters for dopamine (DAT) and serotonin (SERT) are important targets in the treatment of psychiatric disorders including major depression, anxiety and attention-deficit hyperactivity disorder. Drugs acting at these transporters can act as inhibitors or as releasers. In addition, it has been recently appreciated that some compounds are less efficacious releasers than amphetamine. Thus, they are classified as partial releasers. Compounds can act on both SERT and DAT or display exquisite selectivity for either SERT or DAT, but the structural basis for selectivity is poorly understood. The trifluoromethyl-substitution of methcathinone in the para-position has been shown to dramatically shift the selectivity of methcathinone (MCAT) towards SERT. Here, we examined MCAT, para-trifluoromethyl-methcathinone (pCF3MCAT) and other analogues to understand (i) the determinants of selectivity and (ii) the effects of the para-CF3-substitution of MCAT on the transport cycle. We systematically tested different para-substituted MCATs by biochemical, computational and electrophysiological approaches: addition of the pCF3group, but not of other substituents with larger van der Waal's volume, lipophilicity or polarity, converted the DAT-selective MCAT into a SERT-selective partial releaser. Electrophysiological and superfusion experiments, together with kinetic modelling, showed that pCF3MCAT, but not MCAT, trapped a fraction of SERTs in an inactive state by occupying the S2-site. These findings define a new mechanism of action for partial releasers, which is distinct from the other two known binding modes underlying partial release. Our observations highlight the fact that the substrate permeation pathway of monoamine transporters supports multiple binding modes, which can be exploited for drug design. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Marco Niello
- Institute of Pharmacology, Medical University, Vienna, Austria
| | | | - Eva Hellsberg
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Kathrin Jäntsch
- Institute of Pharmacology, Medical University, Vienna, Austria
| | - Marion Holy
- Institute of Pharmacology, Medical University, Vienna, Austria
| | | | - Nicholas V Cozzi
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | | | - Walter Sandtner
- Institute of Pharmacology, Medical University, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | | | - Harald H Sitte
- Institute of Pharmacology, Medical University, Vienna, Austria.
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14
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Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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15
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Mikelman SR, Guptaroy B, Schmitt KC, Jones KT, Zhen J, Reith MEA, Gnegy ME. Tamoxifen Directly Interacts with the Dopamine Transporter. J Pharmacol Exp Ther 2018; 367:119-128. [PMID: 30108161 PMCID: PMC7250473 DOI: 10.1124/jpet.118.248179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/26/2018] [Indexed: 11/22/2022] Open
Abstract
The selective estrogen receptor modulator tamoxifen increases extracellular dopamine in vivo and acts as a neuroprotectant in models of dopamine neurotoxicity. We investigated the effect of tamoxifen on dopamine transporter (DAT)-mediated dopamine uptake, dopamine efflux, and [3H]WIN 35,428 [(-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane] binding in rat striatal tissue. Tamoxifen dose-dependently blocked dopamine uptake (54% reduction at 10 μM) and amphetamine-stimulated efflux (59% reduction at 10 μM) in synaptosomes. It also produced a small but significant reduction in [3H]WIN 35,428 binding in striatal membranes, indicating a weak interaction with the substrate binding site in the DAT. Biotinylation and cysteine accessibility studies indicated that tamoxifen stabilizes the outward-facing conformation of the DAT in a cocaine-like manner and does not affect surface expression of the DAT. Additional studies with mutant DAT constructs D476A and I159A suggested a direct interaction between tamoxifen and a secondary substrate binding site of the transporter. Locomotor studies revealed that tamoxifen attenuates amphetamine-stimulated hyperactivity in rats but has no depressant or stimulant activity in the absence of amphetamine. These results suggest a complex mechanism of action for tamoxifen as a regulator of the DAT. Due to its effectiveness against amphetamine actions and its central nervous system permeant activity, the tamoxifen structure represents an excellent starting point for a structure-based drug-design program to develop a pharmacological therapeutic for psychostimulant abuse.
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Affiliation(s)
- Sarah R Mikelman
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Bipasha Guptaroy
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Kyle C Schmitt
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Kymry T Jones
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Juan Zhen
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Maarten E A Reith
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
| | - Margaret E Gnegy
- Gnegy Laboratory, Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan (S.R.M., B.G., M.E.G.); and Reith Laboratory, Department of Psychiatry, University of New York School of Medicine, New York, New York (K.C.S., K.T.J., J.Z., M.E.A.R.)
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16
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Yarravarapu N, Geffert L, Surratt CK, Cascio M, Lapinsky DJ. Clickable photoaffinity ligands for the human serotonin transporter based on the selective serotonin reuptake inhibitor (S)-citalopram. Bioorg Med Chem Lett 2018; 28:3431-3435. [PMID: 30266542 DOI: 10.1016/j.bmcl.2018.09.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 12/16/2022]
Abstract
To date, the development of photoaffinity ligands targeting the human serotonin transporter (hSERT), a key protein involved in disease states such as depression and anxiety, have been radioisotope-based (i.e., 3H or 125I). This letter instead highlights three derivatives of the selective serotonin reuptake inhibitor (SSRI) (S)-citalopram that were rationally designed and synthesized to contain a photoreactive benzophenone or an aryl azide for protein target capture via photoaffinity labeling and a terminal alkyne or an aliphatic azide for click chemistry-based proteomics. Specifically, clickable benzophenone-based (S)-citalopram photoprobe 6 (hSERT Ki = 0.16 nM) displayed 11-fold higher binding affinity at hSERT when compared to (S)-citalopram (hSERT Ki = 1.77 nM), and was subsequently shown to successfully undergo tandem photoaffinity labeling-biorthogonal conjugation using purified hSERT. Given clickable photoprobes can be used for various applications depending on which reporter is attached by click chemistry subsequent to photoaffinity labeling, photoprobe 6 is expected to find value in structure-function studies and other research applications involving hSERT (e.g., imaging).
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Affiliation(s)
- Nageswari Yarravarapu
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Laura Geffert
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Christopher K Surratt
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Michael Cascio
- Bayer School of Natural and Environmental Sciences, Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - David J Lapinsky
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States.
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17
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Structural elements required for coupling ion and substrate transport in the neurotransmitter transporter homolog LeuT. Proc Natl Acad Sci U S A 2018; 115:E8854-E8862. [PMID: 30181291 DOI: 10.1073/pnas.1716870115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The coupled transport of ions and substrates allows transporters to accumulate substrates using the energy of transmembrane ion gradients and electrical potentials. During transport, conformational changes that switch accessibility of substrate and ion binding sites from one side of the membrane to the other must be controlled so as to prevent uncoupled movement of ions or substrates. In the neurotransmitter:sodium symporter (NSS) family, Na+ stabilizes the transporter in an outward-open state, thus decreasing the likelihood of uncoupled Na+ transport. Substrate binding, in a step essential for coupled transport, must overcome the effect of Na+, allowing intracellular substrate and Na+ release from an inward-open state. However, the specific elements of the protein that mediate this conformational response to substrate binding are unknown. Previously, we showed that in the prokaryotic NSS transporter LeuT, the effect of Na+ on conformation requires the Na2 site, where it influences conformation by fostering interaction between two domains of the protein. Here, we used cysteine accessibility to measure conformational changes of LeuT in Escherichia coli membranes. We identified a conserved tyrosine residue in the substrate binding site required for substrate to convert LeuT to inward-open states by establishing an interaction between the two transporter domains. We further identify additional required interactions between the two transporter domains in the extracellular pathway. Together with our previous work on the conformational effect of Na+, these results identify mechanistic components underlying ion-substrate coupling in NSS transporters.
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18
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The LeuT-fold neurotransmitter:sodium symporter MhsT has two substrate sites. Proc Natl Acad Sci U S A 2018; 115:E7924-E7931. [PMID: 30082383 DOI: 10.1073/pnas.1717444115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Crystal structures of the neurotransmitter:sodium symporter MhsT revealed occluded inward-facing states with one substrate (Trp) bound in the primary substrate (S1) site and a collapsed extracellular vestibule, which in LeuT contains the second substrate (S2) site. In n-dodecyl-β-d-maltoside, the detergent used to prepare MhsT for crystallization, the substrate-to-protein binding stoichiometry was determined by using scintillation proximity to be 1 Trp:MhsT. Here, using the same experimental approach, as well as equilibrium dialysis, we report that in n-decyl-β-d-maltoside, or after reconstitution in lipid, MhsT, like LeuT, can simultaneously bind two Trp substrate molecules. Trp binding to the S2 site sterically blocks access to a substituted Cys at position 33 in the S2 site, as well as access to the deeper S1 site. Mutation of either the S1 or S2 site disrupts transport, consistent with previous studies in LeuT showing that substrate binding to the S2 site is an essential component of the transport mechanism.
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19
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Yuan Y, Zhu J, Zhan CG. Flipped Phenyl Ring Orientations of Dopamine Binding with Human and Drosophila Dopamine Transporters: Remarkable Role of Three Nonconserved Residues. ACS Chem Neurosci 2018; 9:1426-1431. [PMID: 29494767 DOI: 10.1021/acschemneuro.8b00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Molecular modeling and molecular dynamics simulations were performed in the present study to examine the modes of dopamine binding with human and Drosophila dopamine transporters (hDAT and dDAT). The computational data revealed flipped binding orientations of dopamine in hDAT and dDAT due to the major differences in three key residues (S149, G153, and A423 of hDAT vs A117, D121, and S422 of dDAT) in the binding pocket. These three residues dictate the binding orientation of dopamine in the binding pocket, as the aromatic ring of dopamine tends to take an orientation with both the para- and meta-hydroxyl groups being close to polar residues and away from nonpolar residues of the protein. The flipped binding orientations of dopamine in hDAT and dDAT clearly demonstrate a generally valuable insight concerning how the species difference could drastically affect the protein-ligand binding modes, demonstrating that the species difference, which is a factor rarely considered in early drug design stage, must be accounted for throughout the ligand/drug design and discovery processes in general.
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Affiliation(s)
- Yaxia Yuan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | - Jun Zhu
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, 715 Sumter Street, Columbia, South Carolina 29208, United States
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
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20
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Merkle PS, Gotfryd K, Cuendet MA, Leth-Espensen KZ, Gether U, Loland CJ, Rand KD. Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT. SCIENCE ADVANCES 2018; 4:eaar6179. [PMID: 29756037 PMCID: PMC5947982 DOI: 10.1126/sciadv.aar6179] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na+- and K+-dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.
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Affiliation(s)
- Patrick S. Merkle
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Kamil Gotfryd
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Michel A. Cuendet
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Katrine Z. Leth-Espensen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Ulrik Gether
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
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21
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Carland JE, Thomas M, Mostyn SN, Subramanian N, O’Mara ML, Ryan RM, Vandenberg RJ. Molecular Determinants for Substrate Interactions with the Glycine Transporter GlyT2. ACS Chem Neurosci 2018; 9:603-614. [PMID: 29120604 DOI: 10.1021/acschemneuro.7b00407] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Transporters in the SLC6 family play key roles in regulating neurotransmission and are the targets for a wide range of therapeutics. Important insights into the transport mechanisms and the specificity of drug interactions of SLC6 transporters have been obtained from the crystal structures of a bacterial homologue of the family, LeuTAa, and more recently the Drosophila dopamine transporter and the human serotonin transporter. However, there is disputed evidence that the bacterial leucine transporter, LeuTAa, contains two substrate binding sites that work cooperatively in the mechanism of transport, with the binding of a second substrate being required for the release of the substrate from the primary site. An alternate proposal is that there may be low affinity binding sites that serve to direct the flow of substrates to the primary site. We have used a combination of molecular dynamics simulations of substrate interactions with a homology model of GlyT2, together with radiolabeled amino acid uptake assays and electrophysiological analysis of wild-type and mutant transporters, to provide evidence that substrate selectivity of GlyT2 is determined entirely by the primary substrate binding site and, furthermore, if a secondary site exists then it is a low affinity nonselective amino acid binding site.
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Affiliation(s)
- Jane E. Carland
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Thomas
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Shannon N. Mostyn
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Nandhitha Subramanian
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Renae M. Ryan
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Robert J. Vandenberg
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
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22
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Zhu R, Gruber HJ, Hinterdorfer P. Two Ligand Binding Sites in Serotonin Transporter Revealed by Nanopharmacological Force Sensing. Methods Mol Biol 2018; 1814:19-33. [PMID: 29956224 DOI: 10.1007/978-1-4939-8591-3_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The number of ligand binding sites in neurotransmitter-sodium symporters has been determined by crystal structure analysis and molecular pharmacology with controversial results. Here, we designed molecular tools to measure the interaction forces between the serotonin transporter (SERT) and S-citalopram on the single-molecule level by means of atomic force microscopy. Force spectroscopy allows for the extraction of dynamic information under physiological conditions which is inaccessible via X-ray crystallography. Two populations of distinctly different binding strength between S-citalopram and SERT were demonstrated in Na+-containing buffer. In Li+-containing buffer, SERT showed merely low-force interactions, whereas the vestibular mutant SERT-G402H only displayed the high force population. These observations provide physical evidence for the existence of two different binding sites in SERT when tested under near-physiological conditions.
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Affiliation(s)
- Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Hermann J Gruber
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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23
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Abstract
Isothermal titration calorimetry (ITC) is an emerging, label-free technology used to measure ligand binding to membrane proteins. This technology utilizes a titration calorimeter to measure the heat exchange upon ligands binding to proteins, the magnitude of which is based on the overall enthalpy of the reaction. In this protocol, the steps we and others use to measure ion binding to ion transport proteins are described.
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Affiliation(s)
- Shian Liu
- Department of Biology, Texas A&M University, 3474 TAMU, College Station, TX, 77843-3474, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20148, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, 3474 TAMU, College Station, TX, 77843-3474, USA.
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24
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Reith MEA, Jones KT, Zhen J, Topiol S. Latch and trigger role for R445 in DAT transport explains molecular basis of DTDS. Bioorg Med Chem Lett 2017; 28:470-475. [PMID: 29258773 DOI: 10.1016/j.bmcl.2017.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 01/12/2023]
Abstract
A recent study reports on five different mutations as sources of dopamine transporter (DAT) deficiency syndrome (DTDS). One of these mutations, R445C, is believed to be located on the intracellular side of DAT distal to the primary (S1) or secondary (S2) sites to which substrate binding is understood to occur. Thus, the molecular mechanism by which the R445C mutation results in DAT transport deficiency has eluded explanation. However, the recently reported X-ray structures of the endogenous amine transporters for dDAT and hSERT revealed the presence of a putative salt bridge between R445 and E428 suggesting a possible mechanism. To evaluate whether the R445C effect is a result of a salt bridge interaction, the mutants R445E, E428R, and the double mutant E428R/R445E were generated. The single mutants R445E and E428R displayed loss of binding and transport properties of the substrate [3H]DA and inhibitor [3H]CFT at the cell surface while the double mutant E428R/R445E, although nonfunctional, restored [3H]DA and [3H]CFT binding affinity to that of WT. Structure based analyses of these results led to a model wherein R445 plays a dual role in normal DAT function. R445 acts as a component of a latch in its formation of a salt bridge with E428 which holds the primary substrate binding site (S1) in place and helps enforce the inward closed protein state. When this salt bridge is broken, R445 acts as a trigger which disrupts a local polar network and leads to the release of the N-terminus from its position inducing the inward closed state to one allowing the inward open state. In this manner, both the loss of binding and transport properties of the R445C variant are explained.
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Affiliation(s)
- Maarten E A Reith
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA; Department Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Kymry T Jones
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Juan Zhen
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Sid Topiol
- 3D-2drug, LLC, P.O. Box 184, Fair Lawn, NJ, USA.
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25
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Wyant GA, Abu-Remaileh M, Wolfson RL, Chen WW, Freinkman E, Danai LV, Vander Heiden MG, Sabatini DM. mTORC1 Activator SLC38A9 Is Required to Efflux Essential Amino Acids from Lysosomes and Use Protein as a Nutrient. Cell 2017; 171:642-654.e12. [PMID: 29053970 DOI: 10.1016/j.cell.2017.09.046] [Citation(s) in RCA: 302] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
The mTORC1 kinase is a master growth regulator that senses many environmental cues, including amino acids. Activation of mTORC1 by arginine requires SLC38A9, a poorly understood lysosomal membrane protein with homology to amino acid transporters. Here, we validate that SLC38A9 is an arginine sensor for the mTORC1 pathway, and we uncover an unexpectedly central role for SLC38A9 in amino acid homeostasis. SLC38A9 mediates the transport, in an arginine-regulated fashion, of many essential amino acids out of lysosomes, including leucine, which mTORC1 senses through the cytosolic Sestrin proteins. SLC38A9 is necessary for leucine generated via lysosomal proteolysis to exit lysosomes and activate mTORC1. Pancreatic cancer cells, which use macropinocytosed protein as a nutrient source, require SLC38A9 to form tumors. Thus, through SLC38A9, arginine serves as a lysosomal messenger that couples mTORC1 activation to the release from lysosomes of the essential amino acids needed to drive cell growth.
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Affiliation(s)
- Gregory A Wyant
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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26
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Grouleff J, Koldsø H, Miao Y, Schiøtt B. Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT. ACS Chem Neurosci 2017; 8:619-628. [PMID: 27966884 DOI: 10.1021/acschemneuro.6b00359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human monoamine transporters (MATs) facilitate the reuptake of monoamine neurotransmitters from the synaptic cleft. MATs are linked to a number of neurological diseases and are the targets of both therapeutic and illicit drugs. Until recently, no high-resolution structures of the human MATs existed, and therefore, studies of this transporter family have relied on investigations of the homologues bacterial transporters such as the leucine transporter LeuT, which has been crystallized in several conformational states. A two-substrate transport mechanism has been suggested for this transporter family, which entails that high-affinity binding of a second substrate in an extracellular site is necessary for the substrate in the central binding site to be transported. Compelling evidence for this mechanism has been presented, however, a number of equally compelling accounts suggest that the transporters function through a mechanism involving only a single substrate and a single high-affinity site. To shed light on this apparent contradiction, we have performed extensive molecular dynamics simulations of LeuT in the outward-occluded conformation with either one or two substrates bound to the transporter. We have also calculated the substrate binding affinity in each of the two proposed binding sites through rigorous free energy simulations. Results show that substrate binding is unstable in the extracellular vestibule and the substrate binding affinity within the suggested extracellular site is very low (0.2 and 3.3 M for the two dominant binding modes) compared to the central substrate binding site (14 nM). This suggests that for LeuT in the outward-occluded conformation only a single high-affinity substrate binding site exists.
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Affiliation(s)
- Julie Grouleff
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Heidi Koldsø
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Yinglong Miao
- Howard
Hughes Medical Institute and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
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27
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Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer. Proc Natl Acad Sci U S A 2017; 114:E1786-E1795. [PMID: 28223522 DOI: 10.1073/pnas.1613293114] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) are integral membrane proteins responsible for the sodium-dependent reuptake of small-molecule neurotransmitters from the synaptic cleft. The symporters for the biogenic amines serotonin (SERT), dopamine (DAT), and norepinephrine (NET) are targets of multiple psychoactive agents, and their dysfunction has been implicated in numerous neuropsychiatric ailments. LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model protein for NSS members to canvass the conformational mechanism of transport with a combination of X-ray crystallography, cysteine accessibility, and solution spectroscopy. Despite yielding remarkable insights, these studies have primarily been conducted with protein in the detergent-solubilized state rather than embedded in a membrane mimic. In addition, solution spectroscopy has required site-specific labeling of nonnative cysteines, a labor-intensive process occasionally resulting in diminished transport and/or binding activity. Here, we overcome these limitations by reconstituting unlabeled LeuT in phospholipid bilayer nanodiscs, subjecting them to hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS), and facilitating interpretation of the data with molecular dynamics simulations. The data point to changes of accessibility and dynamics of structural elements previously implicated in the transport mechanism, in particular transmembrane helices (TMs) 1a and 7 as well as extracellular loops (ELs) 2 and 4. The results therefore illuminate the value of this strategy for interrogating the conformational mechanism of the more clinically significant mammalian membrane proteins including SERT and DAT, neither of which tolerates complete removal of endogenous cysteines, and whose activity is heavily influenced by neighboring lipids.
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28
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Erlendsson S, Gotfryd K, Larsen FH, Mortensen JS, Geiger MA, van Rossum BJ, Oschkinat H, Gether U, Teilum K, Loland CJ. Direct assessment of substrate binding to the Neurotransmitter:Sodium Symporter LeuT by solid state NMR. eLife 2017; 6. [PMID: 28117663 PMCID: PMC5262378 DOI: 10.7554/elife.19314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/02/2017] [Indexed: 12/21/2022] Open
Abstract
The Neurotransmitter:Sodium Symporters (NSSs) represent an important class of proteins mediating sodium-dependent uptake of neurotransmitters from the extracellular space. The substrate binding stoichiometry of the bacterial NSS protein, LeuT, and thus the principal transport mechanism, has been heavily debated. Here we used solid state NMR to specifically characterize the bound leucine ligand and probe the number of binding sites in LeuT. We were able to produce high-quality NMR spectra of substrate bound to microcrystalline LeuT samples and identify one set of sodium-dependent substrate-specific chemical shifts. Furthermore, our data show that the binding site mutants F253A and L400S, which probe the major S1 binding site and the proposed S2 binding site, respectively, retain sodium-dependent substrate binding in the S1 site similar to the wild-type protein. We conclude that under our experimental conditions there is only one detectable leucine molecule bound to LeuT. DOI:http://dx.doi.org/10.7554/eLife.19314.001 All living cells need amino acids – the building blocks of proteins – in order to survive, yet few cells can make all the amino acids that they need. Instead, transporter proteins in cell membranes must take these molecules from the outside of the cell and release them to the inside. Some cells, including those in the brain, also release amino acids and molecules derived from them into the spaces outside of the cell to send signals to other nearby cells. Again, transporter proteins must move these signaling molecules back inside cells, to stop the signaling and to allow the molecules to be recycled. Importantly, problems with these uptake mechanisms have been linked to disorders such as depression, epilepsy and Parkinson’s disease. One family of transporters involved in the uptake of amino acids are the “Neurotransmitter:Sodium Symporters”. Though these proteins are involved in processes that are fundamental to life, it remains unclear exactly how they work. Specifically, it has been heavily debated whether this family of transporters require one or two amino acid molecules to bind at the same time in order to help transport them across the membrane. Now Erlendsson, Gotfryd et al. have analyzed a bacterial protein in the Neurotransmitter:Sodium Symporter family. This transporter takes up an amino acid called leucine into cells, and is commonly used as a model to understand this family of transporter proteins more generally. Using a technique called solid state nuclear magnetic resonance, Erlendsson, Gotfryd et al. could detect a single molecule of leucine bound to each transporter, but not a second one. This technique could also pinpoint that the leucine was located at the transporter’s central binding site. Leucine was never found at the proposed secondary binding site. Together these findings suggest that only one molecule of leucine binds to the transporter at any one time, and that it binds to the transporter’s central binding site. Erlendsson, Gotfryd et al. have shown now how solid state nuclear magnetic resonance can be used to explore in detail how Neurotransmitter:Sodium Symporters move molecules across cell membranes. The next challenge is to use the same experimental setup to characterize other Neurotransmitter:Sodium Symporters. Doing so could potentially lay the groundwork for designing more specific and improved drugs to treat disorders like depression and Parkinson’s disease. DOI:http://dx.doi.org/10.7554/eLife.19314.002
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Affiliation(s)
- Simon Erlendsson
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kamil Gotfryd
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Hofmann Larsen
- Quality and Technology, Department of Food Science, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Sigurd Mortensen
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ulrik Gether
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claus J Loland
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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29
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The role of interfacial lipids in stabilizing membrane protein oligomers. Nature 2017; 541:421-424. [PMID: 28077870 DOI: 10.1038/nature20820] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability. For the bacterial homologue of the eukaryotic biogenic transporters (LeuT, one of the proteins with the lowest oligomeric stability), we found a precise cohort of lipids within the dimer interface. Delipidation, mutation of lipid-binding sites or expression in cardiolipin-deficient Escherichia coli abrogated dimer formation. Molecular dynamics simulation revealed that cardiolipin acts as a bidentate ligand, bridging across subunits. Subsequently, we show that for the Vibrio splendidus sugar transporter SemiSWEET, another protein with low oligomeric stability, cardiolipin shifts the equilibrium from monomer to functional dimer. We hypothesized that lipids are essential for dimerization of the Na+/H+ antiporter NhaA from E. coli, which has the lowest oligomeric strength, but not for the substantially more stable homologous Thermus thermophilus protein NapA. We found that lipid binding is obligatory for dimerization of NhaA, whereas NapA has adapted to form an interface that is stable without lipids. Overall, by correlating interfacial strength with the presence of interfacial lipids, we provide a rationale for understanding the role of lipids in both transient and stable interactions within a range of α-helical membrane proteins, including G-protein-coupled receptors.
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30
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Alternating access mechanisms of LeuT-fold transporters: trailblazing towards the promised energy landscapes. Curr Opin Struct Biol 2016; 45:100-108. [PMID: 28040635 DOI: 10.1016/j.sbi.2016.12.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/28/2016] [Accepted: 12/09/2016] [Indexed: 01/21/2023]
Abstract
Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles. Specifically, we compare findings for the Na+-coupled amino acid transporter LeuT and the Na+-coupled hydantoin transporter Mhp1. Although these studies have illuminated multiple aspects of transporter structures and dynamics, a number of questions remain unresolved that so far hinder understanding transport mechanisms in an energy landscape perspective.
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31
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Sohail A, Jayaraman K, Venkatesan S, Gotfryd K, Daerr M, Gether U, Loland CJ, Wanner KT, Freissmuth M, Sitte HH, Sandtner W, Stockner T. The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput Biol 2016; 12:e1005197. [PMID: 27835643 PMCID: PMC5105988 DOI: 10.1371/journal.pcbi.1005197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/12/2016] [Indexed: 12/27/2022] Open
Abstract
Human neurotransmitter transporters are found in the nervous system terminating synaptic signals by rapid removal of neurotransmitter molecules from the synaptic cleft. The homologous transporter LeuT, found in Aquifex aeolicus, was crystallized in different conformations. Here, we investigated the inward-open state of LeuT. We compared LeuT in membranes and micelles using molecular dynamics simulations and lanthanide-based resonance energy transfer (LRET). Simulations of micelle-solubilized LeuT revealed a stable and widely open inward-facing conformation. However, this conformation was unstable in a membrane environment. The helix dipole and the charged amino acid of the first transmembrane helix (TM1A) partitioned out of the hydrophobic membrane core. Free energy calculations showed that movement of TM1A by 0.30 nm was driven by a free energy difference of ~15 kJ/mol. Distance measurements by LRET showed TM1A movements, consistent with the simulations, confirming a substantially different inward-open conformation in lipid bilayer from that inferred from the crystal structure. Crystal structures of the bacterial small amino acid transporter LeuT provided structural evidence for the alternating access model. Thereby, these structures shaped our understanding of the mechanisms underlying substrate translocation by neurotransmitter transporters. However, it has been questioned, if the crystallized inward-open conformation of LeuT can exist in the membrane environment. Here we show that, while stable in detergent micelles, the inward-open conformation of LeuT is of high energy and undergoes structural readjustments. We use a multi-faceted approach including molecular dynamics simulations, scintillation proximity assays, free energy calculations and apply for the first time lanthanide resonance energy transfer measurements to verify the in silico predictions. In silico and in vitro approaches using the same conditions allowed us to combine the macroscopic experimental data with microscopic all atom results from simulations to identify the underlying driving forces: partitioning of charged and polar groups from the hydrophobic membrane interior to the hydrophilic environment. We propose that the inward-facing state shows a much smaller movement of TM1A, but large enough to create an access path to the S1 substrate binding site from the vestibule.
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Affiliation(s)
- Azmat Sohail
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kumaresan Jayaraman
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Santhoshkannan Venkatesan
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kamil Gotfryd
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
- University of Copenhagen, Faculty of Health Sciences Denmark, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Markus Daerr
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Ulrik Gether
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Claus J. Loland
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Klaus T. Wanner
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Michael Freissmuth
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Harald H. Sitte
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
- * E-mail:
| | - Walter Sandtner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
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32
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Yuan Y, Huang X, Zhu J, Zhan CG. Computational modeling of human dopamine transporter structures, mechanism and its interaction with HIV-1 transactivator of transcription. Future Med Chem 2016; 8:2077-2089. [PMID: 27739323 PMCID: PMC6113701 DOI: 10.4155/fmc-2016-0138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/20/2016] [Indexed: 11/17/2022] Open
Abstract
This is a brief review of computational modeling studies on the detailed structures and mechanism of human dopamine transporter (hDAT), as well as its interaction with HIV-1 transactivator of transcription (Tat). Extensive molecular modeling, docking and dynamics simulations have resulted in reasonable structural models of hDAT in three typical conformational states, its dopamine uptake mechanism and its interaction with Tat. The obtained hDAT models in different conformational states and their complexes with dopamine and Tat have provided novel structural and mechanistic insights concerning how hDAT uptakes dopamine and how Tat affects the dopamine uptake by hDAT. The computational insights, that are consistent with available experimental data, should be valuable for future rational design of novel therapeutic strategies for treatment of HIV-associated neurocognitive disorders.
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Affiliation(s)
- Yaxia Yuan
- Molecular Modeling & Biopharmaceutical Center, Center for Pharmaceutical Research & Innovation, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Xiaoqin Huang
- Molecular Modeling & Biopharmaceutical Center, Center for Pharmaceutical Research & Innovation, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Jun Zhu
- Department of Drug Discovery & Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Chang-Guo Zhan
- Molecular Modeling & Biopharmaceutical Center, Center for Pharmaceutical Research & Innovation, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
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33
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Talbot JN, Geffert LM, Jorvig JE, Goldstein RI, Nielsen CL, Wolters NE, Amos ME, Munro CA, Dallman E, Mereu M, Tanda G, Katz JL, Indarte M, Madura JD, Choi H, Leak RK, Surratt CK. Rapid and sustained antidepressant properties of an NMDA antagonist/monoamine reuptake inhibitor identified via transporter-based virtual screening. Pharmacol Biochem Behav 2016; 150-151:22-30. [DOI: 10.1016/j.pbb.2016.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/08/2023]
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34
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Andersen J, Ladefoged LK, Kristensen TNB, Munro L, Grouleff J, Stuhr-Hansen N, Kristensen AS, Schiøtt B, Strømgaard K. Interrogating the Molecular Basis for Substrate Recognition in Serotonin and Dopamine Transporters with High-Affinity Substrate-Based Bivalent Ligands. ACS Chem Neurosci 2016; 7:1406-1417. [PMID: 27425420 DOI: 10.1021/acschemneuro.6b00164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The transporters for the neurotransmitters serotonin and dopamine (SERT and DAT, respectively) are targets for drugs used in the treatment of mental disorders and widely used drugs of abuse. Studies of prokaryotic homologues have advanced our structural understanding of SERT and DAT, but it still remains enigmatic whether the human transporters contain one or two high-affinity substrate binding sites. We have designed and employed 24 bivalent ligands possessing a highly systematic combination of substrate moieties (serotonin and/or dopamine) and aliphatic or poly(ethylene glycol) spacers to reveal insight into substrate recognition in SERT and DAT. An optimized bivalent ligand comprising two serotonin moieties binds SERT with 3,800-fold increased affinity compared to that of serotonin, suggesting that the human transporters have two distinct substrate binding sites. We show that the bivalent ligands are inhibitors of SERT and an experimentally validated docking model suggests that the bivalent compounds bind with one substrate moiety in the central binding site (the S1 site), whereas the other substrate moiety binds in a distinct binding site (the S2 site). A systematic study of nonconserved SERT/DAT residues surrounding the proposed binding region showed that nonconserved binding site residues do not contribute to selective recognition of substrates in SERT or DAT. This study provides novel insight into the molecular basis for substrate recognition in human transporters and provides an improved foundation for the development of new drugs targeting SERT and DAT.
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Affiliation(s)
- Jacob Andersen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lucy Kate Ladefoged
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Trine N. Bjerre Kristensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lachlan Munro
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Julie Grouleff
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Nicolai Stuhr-Hansen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Anders S. Kristensen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Birgit Schiøtt
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kristian Strømgaard
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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35
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Transition metal ion FRET uncovers K + regulation of a neurotransmitter/sodium symporter. Nat Commun 2016; 7:12755. [PMID: 27678200 PMCID: PMC5052704 DOI: 10.1038/ncomms12755] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/29/2016] [Indexed: 01/14/2023] Open
Abstract
Neurotransmitter/sodium symporters (NSSs) are responsible for Na+-dependent reuptake of neurotransmitters and represent key targets for antidepressants and psychostimulants. LeuT, a prokaryotic NSS protein, constitutes a primary structural model for these transporters. Here we show that K+ inhibits Na+-dependent binding of substrate to LeuT, promotes an outward-closed/inward-facing conformation of the transporter and increases uptake. To assess K+-induced conformational dynamics we measured fluorescence resonance energy transfer (FRET) between fluorescein site-specifically attached to inserted cysteines and Ni2+ bound to engineered di-histidine motifs (transition metal ion FRET). The measurements supported K+-induced closure of the transporter to the outside, which was counteracted by Na+ and substrate. Promoting an outward-open conformation of LeuT by mutation abolished the K+-effect. The K+-effect depended on an intact Na1 site and mutating the Na2 site potentiated K+ binding by facilitating transition to the inward-facing state. The data reveal an unrecognized ability of K+ to regulate the LeuT transport cycle. The neurotransmitter transporter SERT counter transport K+ to transport serotonin. Here the authors show that the activity of the prokaryotic orthologue LeuT is also modulated by this cation, suggesting a general regulatory role for K+ on neutrotrasmitter:sodium symporters function.
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36
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Gur M, Zomot E, Cheng MH, Bahar I. Energy landscape of LeuT from molecular simulations. J Chem Phys 2016; 143:243134. [PMID: 26723619 DOI: 10.1063/1.4936133] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.
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Affiliation(s)
- Mert Gur
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Elia Zomot
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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37
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Sealover NR, Felts B, Kuntz CP, Jarrard RE, Hockerman GH, Lamb PW, Barker EL, Henry LK. The external gate of the human and Drosophila serotonin transporters requires a basic/acidic amino acid pair for 3,4-methylenedioxymethamphetamine (MDMA) translocation and the induction of substrate efflux. Biochem Pharmacol 2016; 120:46-55. [PMID: 27638414 DOI: 10.1016/j.bcp.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
The substituted amphetamine, 3,4-methylenedioxy-methamphetamine (MDMA, ecstasy), is a widely used drug of abuse that induces non-exocytotic release of serotonin, dopamine, and norepinephrine through their cognate transporters as well as blocking the reuptake of neurotransmitter by the same transporters. The resulting dramatic increase in volume transmission and signal duration of neurotransmitters leads to psychotropic, stimulant, and entactogenic effects. The mechanism by which amphetamines drive reverse transport of the monoamines remains largely enigmatic, however, promising outcomes for the therapeutic utility of MDMA for post-traumatic stress disorder and the long-time use of the dopaminergic and noradrenergic-directed amphetamines in treatment of attention-deficit hyperactivity disorder and narcolepsy increases the importance of understanding this phenomenon. Previously, we identified functional differences between the human and Drosophila melanogaster serotonin transporters (hSERT and dSERT, respectively) revealing that MDMA is an effective substrate for hSERT but not dSERT even though serotonin is a potent substrate for both transporters. Chimeric dSERT/hSERT transporters revealed that the molecular components necessary for recognition of MDMA as a substrate was linked to regions of the protein flanking transmembrane domains (TM) V through IX. Here, we performed species-scanning mutagenesis of hSERT, dSERT and C. elegans SERT (ceSERT) along with biochemical and electrophysiological analysis and identified a single amino acid in TM10 (Glu394, hSERT; Asn484, dSERT, Asp517, ceSERT) that is primarily responsible for the differences in MDMA recognition. Our findings reveal that an acidic residue is necessary at this position for MDMA recognition as a substrate and serotonin releaser.
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Affiliation(s)
- Natalie R Sealover
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Bruce Felts
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Charles P Kuntz
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Rachel E Jarrard
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Gregory H Hockerman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | | | - Eric L Barker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States.
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38
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Bianchi F, Klooster JSV', Ruiz SJ, Luck K, Pols T, Urbatsch IL, Poolman B. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae. Sci Rep 2016; 6:31443. [PMID: 27550794 PMCID: PMC4993999 DOI: 10.1038/srep31443] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023] Open
Abstract
The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels.
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Affiliation(s)
- Frans Bianchi
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Joury S van 't Klooster
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Stephanie J Ruiz
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Katja Luck
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Tjeerd Pols
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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39
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Khelashvili G, Schmidt SG, Shi L, Javitch JA, Gether U, Loland CJ, Weinstein H. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290. J Biol Chem 2016; 291:19786-99. [PMID: 27474737 DOI: 10.1074/jbc.m116.731455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K(+) ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na(+) Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K(+) binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na(+) ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na(+) in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu(290), either charged or neutral, point to the Glu(290) protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a "water gate" opens through coordinated motions of residues Leu(25), Tyr(108), and Phe(253) The resulting water channel enables the binding/dissociation of the Na(+) and K(+) ions that are prevalent, respectively, in the extracellular and intracellular environments.
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Affiliation(s)
- George Khelashvili
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065,
| | - Solveig Gaarde Schmidt
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224
| | - Jonathan A Javitch
- the Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, and
| | - Ulrik Gether
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Harel Weinstein
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065
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40
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Zhen J, Reith MEA. Impact of disruption of secondary binding site S2 on dopamine transporter function. J Neurochem 2016; 138:694-9. [PMID: 27315582 DOI: 10.1111/jnc.13704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/30/2022]
Abstract
The structures of the leucine transporter, drosophila dopamine transporter, and human serotonin transporter show a secondary binding site (designated S2 ) for drugs and substrate in the extracellular vestibule toward the membrane exterior in relation to the primary substrate recognition site (S1 ). The present experiments are aimed at disrupting S2 by mutating Asp476 and Ile159 to Ala. Both mutants displayed a profound decrease in [(3) H]DA uptake compared with wild-type associated with a reduced turnover rate kcat . This was not caused by a conformational bias as the mutants responded to Zn(2+) (10 μM) similarly as WT. The dopamine transporters with either the D476A or I159A mutation both displayed a higher Ki for dopamine for the inhibition of [3H](-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane binding than did the WT transporter, in accordance with an allosteric interaction between the S1 and S2 sites. The results provide evidence in favor of a general applicability of the two-site allosteric model of the Javitch/Weinstein group from LeuT to dopamine transporter and possibly other monoamine transporters. X-ray structures of transporters closely related to the dopamine (DA) transporter show a secondary binding site S2 in the extracellular vestibule proximal to the primary binding site S1 which is closely linked to one of the Na(+) binding sites. This work examines the relationship between S2 and S1 sites. We found that S2 site impairment severely reduced DA transport and allosterically reduced S1 site affinity for the cocaine analog [(3) H]CFT. Our results are the first to lend direct support for the application of the two-site allosteric model, advanced for bacterial LeuT, to the human DA transporter. The model states that, after binding of the first DA molecule (DA1 ) to the primary S1 site (along with Na(+) ), binding of a second DA (DA2 ) to the S2 site triggers, through an allosteric interaction, the release of DA1 and Na(+) into the cytoplasm.
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Affiliation(s)
- Juan Zhen
- Department of Psychiatry, New York University School of Medicine, New York City, New York, USA
| | - Maarten E A Reith
- Department of Psychiatry, New York University School of Medicine, New York City, New York, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York City, New York, USA
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41
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Heteromeric amino acid transporters. In search of the molecular bases of transport cycle mechanisms1. Biochem Soc Trans 2016; 44:745-52. [DOI: 10.1042/bst20150294] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 01/18/2023]
Abstract
Heteromeric amino acid transporters (HATs) are relevant targets for structural studies. On the one hand, HATs are involved in inherited and acquired human pathologies. On the other hand, these molecules are the only known examples of solute transporters composed of two subunits (heavy and light) linked by a disulfide bridge. Unfortunately, structural knowledge of HATs is scarce and limited to the atomic structure of the ectodomain of a heavy subunit (human 4F2hc-ED) and distant prokaryotic homologues of the light subunits that share a LeuT-fold. Recent data on human 4F2hc/LAT2 at nanometer resolution revealed 4F2hc-ED positioned on top of the external loops of the light subunit LAT2. Improved resolution of the structure of HATs, combined with conformational studies, is essential to establish the structural bases for light subunit recognition and to evaluate the functional relevance of heavy and light subunit interactions for the amino acid transport cycle.
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42
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Role of Histidine 547 of Human Dopamine Transporter in Molecular Interaction with HIV-1 Tat and Dopamine Uptake. Sci Rep 2016; 6:27314. [PMID: 27250920 PMCID: PMC4890318 DOI: 10.1038/srep27314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/13/2016] [Indexed: 12/16/2022] Open
Abstract
HIV-1 Tat plays an important role in HIV-associated neurocognitive disorders (HAND) by disrupting neurotransmission including dopamine uptake by human dopamine transporter (hDAT). Previous studies have demonstrated that HIV-1 Tat directly binds to hDAT and some amino-acid mutations that attenuate the hDAT-Tat binding also significantly decreased dopamine uptake activity of hDAT. This combined computational-experimental study demonstrates that histidine-547 (H547) of hDAT plays a crucial role in the hDAT-Tat binding and dopamine uptake by hDAT, and that the H547A mutation can not only considerably attenuate Tat-induced inhibition of dopamine uptake, but also significantly increase the Vmax of hDAT for dopamine uptake. The finding of such an unusual hDAT mutant capable of both increasing the Vmax of hDAT for dopamine uptake and disrupting the hDAT-Tat binding may provide an exciting knowledge basis for development of novel concepts for therapeutic treatment of the HAND.
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43
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Grouleff J, Søndergaard S, Koldsø H, Schiøtt B. Properties of an inward-facing state of LeuT: conformational stability and substrate release. Biophys J 2016; 108:1390-1399. [PMID: 25809252 DOI: 10.1016/j.bpj.2015.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 01/12/2023] Open
Abstract
The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wild-type transporter, with and without the cocrystallized Fab antibody fragment, to investigate the properties of this inward-facing conformation in relation to transport by LeuT within the membrane environment. In all of the simulations, local conformational changes with respect to the crystal structure are consistently observed, especially in TM1a. Umbrella sampling revealed a soft potential for TM1a tilting. Furthermore, simulations of inward-facing LeuT with Na(+) ions and substrate bound suggest that one of the Na(+) ion binding sites is fully disrupted. Release of alanine and the second Na(+) ion is also observed, giving insight into the final stage of the translocation process in atomistic detail.
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Affiliation(s)
- Julie Grouleff
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Siri Søndergaard
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Heidi Koldsø
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark.
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44
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LeVine MV, Cuendet MA, Khelashvili G, Weinstein H. Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters. Chem Rev 2016; 116:6552-87. [PMID: 26892914 DOI: 10.1021/acs.chemrev.5b00627] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Solute transport across cell membranes is ubiquitous in biology as an essential physiological process. Secondary active transporters couple the unfavorable process of solute transport against its concentration gradient to the energetically favorable transport of one or several ions. The study of such transporters over several decades indicates that their function involves complex allosteric mechanisms that are progressively being revealed in atomistic detail. We focus on two well-characterized sodium-coupled symporters: the bacterial amino acid transporter LeuT, which is the prototype for the "gated pore" mechanism in the mammalian synaptic monoamine transporters, and the archaeal GltPh, which is the prototype for the "elevator" mechanism in the mammalian excitatory amino acid transporters. We present the evidence for the role of allostery in the context of a quantitative formalism that can reconcile biochemical and biophysical data and thereby connects directly to recent insights into the molecular structure and dynamics of these proteins. We demonstrate that, while the structures and mechanisms of these transporters are very different, the available data suggest a common role of specific models of allostery in their functions. We argue that such allosteric mechanisms appear essential not only for sodium-coupled symport in general but also for the function of other types of molecular machines in the membrane.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Michel A Cuendet
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, ‡HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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45
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LeVine MV, Khelashvili G, Shi L, Quick M, Javitch JA, Weinstein H. Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles. Biochemistry 2016; 55:850-9. [PMID: 26811944 PMCID: PMC4757857 DOI: 10.1021/acs.biochem.5b01268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Recent
work has shown that the choice of the type and concentration
of detergent used for the solubilization of membrane proteins can
strongly influence the results of functional experiments. In particular,
the amino acid transporter LeuT can bind two substrate molecules in
low concentrations of n-dodecyl β-d-maltopyranoside (DDM), whereas high concentrations reduce the molar
binding stoichiometry to 1:1. Subsequent molecular dynamics (MD) simulations
of LeuT in DDM proteomicelles revealed that DDM can penetrate to the
extracellular vestibule and make stable contacts in the functionally
important secondary substrate binding site (S2), suggesting a potential
competitive mechanism for the reduction in binding stoichiometry.
Because annular lipids can be retained during solubilization, we performed
MD simulations of LeuT proteomicelles at various stages of the solubilization
process. We find that at low DDM concentrations, lipids are retained
around the protein and penetration of detergent into the S2 site does
not occur, whereas at high concentrations, lipids are displaced and
the probability of DDM binding in the S2 site is increased. This behavior
is dependent on the type of detergent, however, as we find in the
simulations that the detergent lauryl maltose-neopentyl glycol, which
is approximately twice the size of DDM and structurally more closely
resembles lipids, does not penetrate the protein even at very high
concentrations. We present functional studies that confirm the computational
findings, emphasizing the need for careful consideration of experimental
conditions, and for cautious interpretation of data in gathering mechanistic
information about membrane proteins.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health , Baltimore, Maryland 21224, United States
| | | | - Jonathan A Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute , New York, New York 10032, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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46
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Wein T, Petrera M, Allmendinger L, Höfner G, Pabel J, Wanner KT. Different Binding Modes of Small and Large Binders of GAT1. ChemMedChem 2016; 11:509-18. [DOI: 10.1002/cmdc.201500534] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Wein
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | | | - Lars Allmendinger
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Georg Höfner
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Jörg Pabel
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Klaus T. Wanner
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
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47
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Chloride requirement for monoamine transporters. Pflugers Arch 2016; 468:503-11. [PMID: 26794730 DOI: 10.1007/s00424-015-1783-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/20/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022]
Abstract
This review focuses on the Cl(-) requirement for dopamine, serotonin, and norepinephrine (DA, 5-HT, and NE) transport and induced current via the transporters for these transmitters, DAT, SERT, and NET. Indirect evidence exists for the passage of Cl(-) ions through monoamine transporters; however, direct evidence is sparse. An unanswered question is why in some preparations, notably native neurons, it appears that Cl(-) ions carry the current through DAT, whereas in heterologous expression systems Na(+) ions carry the current often referred to as the uncoupled current. It is suggested that different functional states in monoamine transporters represent conformational states that carry dominantly Cl(-) or Na(+). Structures of monoamine transporters contribute enormously to structure-function relationships; however, thus far no structural features support the functionally relevant ionic currents that are known to exist in monoamine transporters.
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48
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman A, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rong Zhu
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Doris Sinwel
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Peter S. Hasenhuetl
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Vivek Kumar
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Peng Zhang
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH; Mooslackengasse 17 1190 Vienna Austria
| | - Marion Holy
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Andreas Karner
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Hermann J. Gruber
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Harald H. Sitte
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Peter Hinterdorfer
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
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49
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman AH, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015; 55:1719-22. [PMID: 26695726 DOI: 10.1002/anie.201508755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/11/2015] [Indexed: 11/11/2022]
Abstract
Controversy regarding the number and function of ligand binding sites in neurotransmitter/sodium symporters arose from conflicting data in crystal structures and molecular pharmacology. Here, we have designed novel tools for atomic force microscopy that directly measure the interaction forces between the serotonin transporter (SERT) and the S- and R-enantiomers of citalopram on the single molecule level. This approach is based on force spectroscopy, which allows for the extraction of dynamic information under physiological conditions thus inaccessible via X-ray crystallography. Two distinct populations of characteristic binding strengths of citalopram to SERT were revealed in Na(+)-containing buffer. In contrast, in Li(+) -containing buffer, SERT showed only low force interactions. Conversely, the vestibular mutant SERT-G402H merely displayed the high force population. These observations provide physical evidence for the existence of two binding sites in SERT when accessed in a physiological context. Competition experiments revealed that these two sites are allosterically coupled and exert reciprocal modulation.
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Affiliation(s)
- Rong Zhu
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Doris Sinwel
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Peter S Hasenhuetl
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Vivek Kumar
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Peng Zhang
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Marion Holy
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Andreas Karner
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Hermann J Gruber
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Harald H Sitte
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria.
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Andersen J, Ladefoged LK, Wang D, Kristensen TNB, Bang-Andersen B, Kristensen AS, Schiøtt B, Strømgaard K. Binding of the multimodal antidepressant drug vortioxetine to the human serotonin transporter. ACS Chem Neurosci 2015; 6:1892-900. [PMID: 26389667 DOI: 10.1021/acschemneuro.5b00225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Selective inhibitors of the human serotonin transporter (hSERT) have been first-line treatment against depression for several decades. Recently, vortioxetine was approved as a new therapeutic option for the treatment of depression. Vortioxetine represents a new class of antidepressant drugs with a multimodal pharmacological profile that in addition to potent inhibition of hSERT include agonistic or antagonistic effects at different serotonin receptors. We used a combination of computational, chemical, and biological methods to decipher the molecular basis for high affinity binding of vortioxetine in hSERT. X-ray crystal structures of the bacterial amino acid transporter LeuT and the Drosophila melanogaster dopamine transporter were used to build homology models of hSERT. Comparative modeling and ligand docking suggest that vortioxetine can adopt several distinct binding modes within the central binding site of hSERT. To distinguish between the identified binding modes, we determined the effect of 57 functional hSERT point mutants on vortioxetine potency and characterized seven structurally related analogs of vortioxetine in a subset of the point mutants. This allowed us to determine the orientation of vortioxetine within the central binding site and showed that only one of the proposed binding modes is functionally relevant. The findings provide important new insight about the molecular basis for high affinity recognition of vortioxetine in hSERT, which is essential for future structure-based drug discovery of novel multimodal drugs with fine-tuned selectivity across different transporter and receptor proteins in the human brain.
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Affiliation(s)
- Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lucy Kate Ladefoged
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Danyang Wang
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Trine N. Bjerre Kristensen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Benny Bang-Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Lundbeck Research Denmark, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark
| | - Anders S. Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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