51
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Erol I, Aksoydan B, Kantarcioglu I, Salmas RE, Durdagi S. Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study. J Mol Graph Model 2017; 74:193-202. [DOI: 10.1016/j.jmgm.2017.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/26/2017] [Accepted: 02/02/2017] [Indexed: 10/19/2022]
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52
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Sahai MA, Davidson C, Khelashvili G, Barrese V, Dutta N, Weinstein H, Opacka-Juffry J. Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB. Prog Neuropsychopharmacol Biol Psychiatry 2017; 75:1-9. [PMID: 27890676 DOI: 10.1016/j.pnpbp.2016.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/19/2016] [Accepted: 11/21/2016] [Indexed: 01/07/2023]
Abstract
Novel psychoactive substances (NPS) are increasingly prevalent world-wide although their pharmacological characteristics are largely unknown; those with stimulant properties, due to interactions with the dopamine transporter (DAT), have addictive potential which their users may not realise. We evaluated the binding of 1-(1-benzofuran-5-yl)-N-methylpropan-2-amine (5-MAPB) to rat striatal DAT by means of quantitative autoradiography with [125I]RTI-121, and the effects of 5-MAPB on electrically-evoked dopamine efflux by fast-cyclic voltammetry in rat brain slices. 5-MAPB displaced [125I]RTI-121 in a concentration-dependent manner, with significant effects at 10 and 30μM. The voltammetry data suggest that 5-MAPB reduces the rate of dopamine reuptake; while the peak dopamine efflux was not increased, the area under the curve was augmented. 5-MAPB can also cause reverse dopamine transport consistent with stimulant properties, more similar to amphetamine than cocaine. Molecular modelling and docking studies compared the binding site of DAT in complex with 5-MAPB to dopamine, amphetamine, 5-APB, MDMA, cocaine and RTI-121. This structural comparison reveals a binding mode for 5-MAPB found in the primary binding (S1) site, central to transmembrane domains 1, 3, 6 and 8, which overlaps with the binding modes of dopamine, cocaine and its analogues. Atomistic molecular dynamics simulations further show that, when in complex with 5-MAPB, DAT can exhibit conformational transitions that spontaneously isomerize the transporter into inward-facing state, similarly to that observed in dopamine-bound DAT. These novel insights, offered by the combination of computational methods of biophysics with neurobiological procedures, provide structural context for NPS at DAT and relate them with their functional properties at DAT as the molecular target of stimulants.
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Affiliation(s)
| | - Colin Davidson
- St George's University of London, Cranmer Terrace, London SW17 0RE, UK; Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA
| | - Vincenzo Barrese
- St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Neelakshi Dutta
- St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY, 10065, USA; HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
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53
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Stolzenberg S, Li Z, Quick M, Malinauskaite L, Nissen P, Weinstein H, Javitch JA, Shi L. The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state. J Biol Chem 2017; 292:7372-7384. [PMID: 28320858 DOI: 10.1074/jbc.m116.757153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 03/07/2017] [Indexed: 11/06/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) terminate neurotransmission by the reuptake of released neurotransmitters. This active accumulation of substrate against its concentration gradient is driven by the transmembrane Na+ gradient and requires that the transporter traverses several conformational states. LeuT, a prokaryotic NSS homolog, has been crystallized in outward-open, outward-occluded, and inward-open states. Two crystal structures of another prokaryotic NSS homolog, the multihydrophobic amino acid transporter (MhsT) from Bacillus halodurans, have been resolved in novel inward-occluded states, with the extracellular vestibule closed and the intracellular portion of transmembrane segment 5 (TM5i) in either an unwound or a helical conformation. We have investigated the potential involvement of TM5i in binding and unbinding of Na2, i.e. the Na+ bound in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived from the two MhsT structures. We find that the helical TM5i conformation is associated with a higher propensity for Na2 release, which leads to the repositioning of the N terminus and transition to an inward-open state. By using comparative interaction network analysis, we also identify allosteric pathways connecting TM5i and the Na2 binding site to the extracellular and intracellular regions. Based on our combined computational and mutagenesis studies of MhsT and LeuT, we propose that TM5i plays a key role in Na2 binding and release associated with the conformational transition toward the inward-open state, a role that is likely to be shared across the NSS family.
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Affiliation(s)
- Sebastian Stolzenberg
- From the Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, 14195 Berlin, Germany.,the Department of Physiology and Biophysics and.,the Department of Physics, Cornell University, Ithaca, New York, 14850
| | - Zheng Li
- the Department of Physiology and Biophysics and
| | - Matthias Quick
- the Departments of Psychiatry and.,the Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, 10032
| | - Lina Malinauskaite
- the Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C DK-8000, Denmark, and
| | - Poul Nissen
- the Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C DK-8000, Denmark, and
| | - Harel Weinstein
- the Department of Physiology and Biophysics and.,the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, 10065
| | - Jonathan A Javitch
- the Departments of Psychiatry and.,the Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, 10032.,Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York, 10032
| | - Lei Shi
- the Department of Physiology and Biophysics and .,the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, 10065.,the Computational Chemistry and Molecular Biophysics Unit, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
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54
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Wellendorph P, Jacobsen J, Skovgaard-Petersen J, Jurik A, Vogensen SB, Ecker G, Schousboe A, Krogsgaard-Larsen P, Clausen RP. γ-Aminobutyric Acid and Glycine Neurotransmitter Transporters. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527679430.ch4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Petrine Wellendorph
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Julie Jacobsen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Jonas Skovgaard-Petersen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Andreas Jurik
- University of Vienna; Department of Pharmaceutical Chemistry; Althanstrasse 14, A-1090 Vienna Austria
| | - Stine B. Vogensen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Gerhard Ecker
- University of Vienna; Department of Pharmaceutical Chemistry; Althanstrasse 14, A-1090 Vienna Austria
| | - Arne Schousboe
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Povl Krogsgaard-Larsen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Rasmus P. Clausen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
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55
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Rastedt DE, Vaughan RA, Foster JD. Palmitoylation mechanisms in dopamine transporter regulation. J Chem Neuroanat 2017; 83-84:3-9. [PMID: 28115272 DOI: 10.1016/j.jchemneu.2017.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/21/2016] [Accepted: 01/17/2017] [Indexed: 02/01/2023]
Abstract
The neurotransmitter dopamine (DA) plays a key role in several biological processes including reward, mood, motor activity and attention. Synaptic DA homeostasis is controlled by the dopamine transporter (DAT) which transports extracellular DA into the presynaptic neuron after release and regulates its availability to receptors. Many neurological disorders such as schizophrenia, bipolar disorder, Parkinson disease and attention-deficit hyperactivity disorder are associated with imbalances in DA homeostasis that may be related to DAT dysfunction. DAT is also a target of psychostimulant and therapeutic drugs that inhibit DA reuptake and lead to elevated dopaminergic neurotransmission. We have recently demonstrated the acute and chronic modulation of DA reuptake activity and DAT stability through S-palmitoylation, the linkage of a 16-carbon palmitate group to cysteine via a thioester bond. This review summarizes the properties and regulation of DAT palmitoylation and describes how it serves to affect various transporter functions. Better understanding of the role of palmitoylation in regulation of DAT function may lead to identification of therapeutic targets for modulation of DA homeostasis in the treatment of dopaminergic disorders.
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Affiliation(s)
- Danielle E Rastedt
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58202, United States.
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56
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Damgaard M, Haugaard AS, Kickinger S, Al-Khawaja A, Lie MEK, Ecker GF, Clausen RP, Frølund B. Development of Non-GAT1-Selective Inhibitors: Challenges and Achievements. ADVANCES IN NEUROBIOLOGY 2017; 16:315-332. [DOI: 10.1007/978-3-319-55769-4_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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57
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Eskandari S, Willford SL, Anderson CM. Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters. ADVANCES IN NEUROBIOLOGY 2017; 16:85-116. [PMID: 28828607 DOI: 10.1007/978-3-319-55769-4_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The purpose of this review is to highlight recent evidence in support of a 3 Na+: 1 Cl-: 1 GABA coupling stoichiometry for plasma membrane GABA transporters (SLC6A1 , SLC6A11 , SLC6A12 , SLC6A13 ) and how the revised stoichiometry impacts our understanding of the contribution of GABA transporters to GABA homeostasis in synaptic and extrasynaptic regions in the brain under physiological and pathophysiological states. Recently, our laboratory probed the GABA transporter stoichiometry by analyzing the results of six independent measurements, which included the shifts in the thermodynamic transporter reversal potential caused by changes in the extracellular Na+, Cl-, and GABA concentrations, as well as the ratio of charge flux to substrate flux for Na+, Cl-, and GABA under voltage-clamp conditions. The shifts in the transporter reversal potential for a tenfold change in the external concentration of Na+, Cl-, and GABA were 84 ± 4, 30 ± 1, and 29 ± 1 mV, respectively. Charge flux to substrate flux ratios were 0.7 ± 0.1 charges/Na+, 2.0 ± 0.2 charges/Cl-, and 2.1 ± 0.1 charges/GABA. We then compared these experimental results with the predictions of 150 different transporter stoichiometry models, which included 1-5 Na+, 0-5 Cl-, and 1-5 GABA per transport cycle. Only the 3 Na+: 1 Cl-: 1 GABA stoichiometry model correctly predicts the results of all six experimental measurements. Using the revised 3 Na+: 1 Cl-: 1 GABA stoichiometry, we propose that the GABA transporters mediate GABA uptake under most physiological conditions. Transporter-mediated GABA release likely takes place under pathophysiological or extreme physiological conditions.
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Affiliation(s)
- Sepehr Eskandari
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, 91768, USA.
| | - Samantha L Willford
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, 91768, USA
| | - Cynthia M Anderson
- Biological Sciences Department, California State Polytechnic University, Pomona, CA, 91768, USA
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58
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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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59
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Subramanian N, Scopelitti AJ, Carland JE, Ryan RM, O’Mara ML, Vandenberg RJ. Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2. PLoS One 2016; 11:e0157583. [PMID: 27337045 PMCID: PMC4919009 DOI: 10.1371/journal.pone.0157583] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/01/2016] [Indexed: 12/25/2022] Open
Abstract
The Na+/Cl- dependent glycine transporters GlyT1 and GlyT2 regulate synaptic glycine concentrations. Glycine transport by GlyT2 is coupled to the co-transport of three Na+ ions, whereas transport by GlyT1 is coupled to the co-transport of only two Na+ ions. These differences in ion-flux coupling determine their respective concentrating capacities and have a direct bearing on their functional roles in synaptic transmission. The crystal structures of the closely related bacterial Na+-dependent leucine transporter, LeuTAa, and the Drosophila dopamine transporter, dDAT, have allowed prediction of two Na+ binding sites in GlyT2, but the physical location of the third Na+ site in GlyT2 is unknown. A bacterial betaine transporter, BetP, has also been crystallized and shows structural similarity to LeuTAa. Although betaine transport by BetP is coupled to the co-transport of two Na+ ions, the first Na+ site is not conserved between BetP and LeuTAa, the so called Na1' site. We hypothesized that the third Na+ binding site (Na3 site) of GlyT2 corresponds to the BetP Na1' binding site. To identify the Na3 binding site of GlyT2, we performed molecular dynamics (MD) simulations. Surprisingly, a Na+ placed at the location consistent with the Na1' site of BetP spontaneously dissociated from its initial location and bound instead to a novel Na3 site. Using a combination of MD simulations of a comparative model of GlyT2 together with an analysis of the functional properties of wild type and mutant GlyTs we have identified an electrostatically favorable novel third Na+ binding site in GlyT2 formed by Trp263 and Met276 in TM3, Ala481 in TM6 and Glu648 in TM10.
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Affiliation(s)
- Nandhitha Subramanian
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Amanda J. Scopelitti
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, United States of America
| | - Jane E. Carland
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Renae M. Ryan
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Robert J. Vandenberg
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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60
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Synthesis and inhibitory evaluation of 3-linked imipramines for the exploration of the S2 site of the human serotonin transporter. Bioorg Med Chem 2016; 24:2725-38. [PMID: 27160055 DOI: 10.1016/j.bmc.2016.04.039] [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] [Received: 11/19/2015] [Revised: 04/16/2016] [Accepted: 04/20/2016] [Indexed: 01/10/2023]
Abstract
The human serotonin transporter is the primary target of several antidepressant drugs, and the importance of a primary, high affinity binding site (S1) for antidepressant binding is well documented. The existence of a lower affinity, secondary binding site (S2) has, however, been debated. Herein we report the synthesis of 3-position coupled imipramine ligands from clomipramine using a copper free Sonogashira reaction. Ligand design was inspired by results from docking and steered molecular dynamics simulations, and the ligands were utilized in a structure-activity relationship study of the positional relationship between the S1 and S2 sites. The computer simulations suggested that the S2 site does indeed exist although with lower affinity for imipramine than observed within the S1 site. Additionally, it was possible to dock the 3-linked imipramine analogs into positions which occupy the S1 and the S2 site simultaneously. The structure activity relationship study showed that the shortest ligands were the most potent, and mutations enlarging the proposed S2 site were found to affect the larger ligands positively, while the smaller ligands were mostly unaffected.
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61
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Davis BA, Nagarajan A, Forrest LR, Singh SK. Mechanism of Paroxetine (Paxil) Inhibition of the Serotonin Transporter. Sci Rep 2016; 6:23789. [PMID: 27032980 PMCID: PMC4817154 DOI: 10.1038/srep23789] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/15/2016] [Indexed: 11/11/2022] Open
Abstract
The serotonin transporter (SERT) is an integral membrane protein that exploits preexisting sodium-, chloride-, and potassium ion gradients to catalyze the thermodynamically unfavorable movement of synaptic serotonin into the presynaptic neuron. SERT has garnered significant clinical attention partly because it is the target of multiple psychoactive agents, including the antidepressant paroxetine (Paxil), the most potent selective serotonin reuptake inhibitor known. However, the binding site and orientation of paroxetine in SERT remain controversial. To provide molecular insight, we constructed SERT homology models based on the Drosophila melanogaster dopamine transporter and docked paroxetine to these models. We tested the predicted binding configurations with a combination of radioligand binding and flux assays on wild-type and mutant SERTs. Our data suggest that the orientation of paroxetine, specifically its fluorophenyl ring, in SERT’s substrate binding site directly depends on this pocket’s charge distribution, and thereby provide an avenue toward understanding and enhancing high-affinity antidepressant activity.
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Affiliation(s)
- Bruce A Davis
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
| | - Anu Nagarajan
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, 35 Convent Drive, Bethesda, MD 20892 USA
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, 35 Convent Drive, Bethesda, MD 20892 USA
| | - Satinder K Singh
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
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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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63
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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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Khelashvili G, Stanley N, Sahai MA, Medina J, LeVine MV, Shi L, De Fabritiis G, Weinstein H. Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus. ACS Chem Neurosci 2015; 6:1825-37. [PMID: 26255829 PMCID: PMC4653762 DOI: 10.1021/acschemneuro.5b00179] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
![]()
We
present the dynamic mechanism of concerted motions in a full-length
molecular model of the human dopamine transporter (hDAT), a member
of the neurotransmitter/sodium symporter (NSS) family, involved in
state-to-state transitions underlying function. The findings result
from an analysis of unbiased atomistic molecular dynamics simulation
trajectories (totaling >14 μs) of the hDAT molecule immersed
in lipid membrane environments with or without phosphatidylinositol
4,5-biphosphate (PIP2) lipids. The N-terminal region of
hDAT (N-term) is shown to have an essential mechanistic role in correlated
rearrangements of specific structural motifs relevant to state-to-state
transitions in the hDAT. The mechanism involves PIP2-mediated
electrostatic interactions between the N-term and the intracellular
loops of the transporter molecule. Quantitative analyses of collective
motions in the trajectories reveal that these interactions correlate
with the inward-opening dynamics of hDAT and are allosterically coupled
to the known functional sites of the transporter. The observed large-scale
motions are enabled by specific reconfiguration of the network of
ionic interactions at the intracellular end of the protein. The isomerization
to the inward-facing state in hDAT is accompanied by concomitant movements
in the extracellular vestibule and results in the release of an Na+ ion from the Na2 site and destabilization of the substrate
dopamine in the primary substrate binding S1 site. The dynamic mechanism
emerging from the findings highlights the involvement of the PIP2-regulated interactions between the N-term and the intracellular
loop 4 in the functionally relevant conformational transitions that
are also similar to those found to underlie state-to-state transitions
in the leucine transporter (LeuT), a prototypical bacterial homologue
of the NSS.
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Affiliation(s)
- George Khelashvili
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Nathaniel Stanley
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Michelle A. Sahai
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Jaime Medina
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Michael V. LeVine
- 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
- HRH
Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Gianni De Fabritiis
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - 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 of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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65
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Grouleff J, Ladefoged LK, Koldsø H, Schiøtt B. Monoamine transporters: insights from molecular dynamics simulations. Front Pharmacol 2015; 6:235. [PMID: 26528185 PMCID: PMC4607855 DOI: 10.3389/fphar.2015.00235] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/01/2015] [Indexed: 01/31/2023] Open
Abstract
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson's disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na(+) symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
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Affiliation(s)
- Julie Grouleff
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Lucy Kate Ladefoged
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford Oxford, UK
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
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66
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Cheng MH, Bahar I. Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter. Structure 2015; 23:2171-81. [PMID: 26481814 DOI: 10.1016/j.str.2015.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/31/2015] [Accepted: 09/06/2015] [Indexed: 01/16/2023]
Abstract
Dopamine transporters (DATs) control neurotransmitter dopamine (DA) homeostasis by reuptake of excess DA, assisted by sodium and chloride ions. The recent resolution of DAT structure (dDAT) from Drosophila permits us for the first time to directly view the sequence of events involved in DA reuptake in human DAT (hDAT) using homology modeling and full-atomic microseconds accelerated simulations. Major observations are spontaneous closure of extracellular gates prompted by DA binding; stabilization of a holo-occluded intermediate; disruption of N82-N353 hydrogen bond and exposure to intracellular (IC) water triggered by Na2 dislocation; redistribution of a network of salt bridges at the IC surface in the inward-facing state; concerted tilting of IC-exposed helices to enable the release of Na(+) and Cl(-) ions; and DA release after protonation of D79. The observed time-resolved interactions confirm the conserved dynamics of LeuT-fold family, while providing insights into the mechanistic role of specific residues in hDAT.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3064 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3064 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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67
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Jursky F, Baliova M, Juhasova A. Structural insights into the benzophenanthridines binding to human glycine transporter GlyT1. Eur J Pharmacol 2015; 765:1-6. [PMID: 26272436 DOI: 10.1016/j.ejphar.2015.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/20/2015] [Accepted: 08/07/2015] [Indexed: 11/29/2022]
Abstract
We previously identified cysteine 475 as a key residue for the inhibitory action of sanguinarine on the human glycine transporter GlyT1c. To define potential benzophenanthridine binding pocket more closely, we created a structural homology model of GlyT1 and also mutated several amino acids in the vicinity of cysteine 475. Even though this area contains the molecular determinants of the glycine and sodium permeation pathways, and several mutations resulted in an inactive transporter, we found that the mutation of a polar aromatic tyrosine 370 to purely aromatic phenylalanine, but not to an aliphatic leucine, significantly increased the sensitivity of GlyT1 to both sanguinarine and chelerythrine. The reduction of sanguinarine to dihydrosanguinarine completely eliminated the alkaloid's inhibitory potency. Both these results suggest that aromaticity is important in the interaction of benzophenanthridines with GlyT1. Even though tyrosine 370 is part of the conformationaly highly flexible glycine binding site, and is accesible during the transport process from both intra and extracellular sites, the cytoplasmic location of the second alkaloid sensitive residue, cysteine 475, suggests that the benzophenanthridines might attack the area of the GlyT1 intracellular gates.
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Affiliation(s)
- Frantisek Jursky
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
| | - Martina Baliova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
| | - Anna Juhasova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia
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68
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Fairweather SJ, Bröer A, Subramanian N, Tumer E, Cheng Q, Schmoll D, O'Mara ML, Bröer S. Molecular basis for the interaction of the mammalian amino acid transporters B0AT1 and B0AT3 with their ancillary protein collectrin. J Biol Chem 2015; 290:24308-25. [PMID: 26240152 PMCID: PMC4591816 DOI: 10.1074/jbc.m115.648519] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/19/2015] [Indexed: 12/19/2022] Open
Abstract
Many solute carrier 6 (SLC6) family transporters require ancillary subunits to modify their expression and activity. The main apical membrane neutral amino acid transporters in mouse intestine and kidney, B(0)AT1 and B(0)AT3, require the ancillary protein collectrin or ACE2 for plasma membrane expression. Expression and activity of SLC6 neurotransmitter transporters are modulated by interaction with syntaxin 1A. Utilizing monocarboxylate-B(0)AT1/3 fusion constructs, we discovered that collectrin is also necessary for B(0)AT1 and B(0)AT3 catalytic function. Syntaxin 1A and syntaxin 3 inhibit the membrane expression of B(0)AT1 by competing with collectrin for access. A mutagenesis screening approach identified residues on trans-membrane domains 1α, 5, and 7 on one face of B(0)AT3 as a key region involved in interaction with collectrin. Mutant analysis established residues that were involved in collectrin-dependent functions as follows: plasma membrane expression of B(0)AT3, catalytic activation, or both. These results identify a potential binding site for collectrin and other SLC6 ancillary proteins.
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Affiliation(s)
| | | | - Nandhitha Subramanian
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia and
| | | | - Qi Cheng
- From the Research School of Biology and
| | - Dieter Schmoll
- the Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, Frankfurt am Main 65926, Germany
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia and
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69
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Moritz AE, Rastedt DE, Stanislowski DJ, Shetty M, Smith MA, Vaughan RA, Foster JD. Reciprocal Phosphorylation and Palmitoylation Control Dopamine Transporter Kinetics. J Biol Chem 2015; 290:29095-105. [PMID: 26424792 DOI: 10.1074/jbc.m115.667055] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 11/06/2022] Open
Abstract
The dopamine transporter is a neuronal protein that drives the presynaptic reuptake of dopamine (DA) and is the major determinant of transmitter availability in the brain. Dopamine transporter function is regulated by protein kinase C (PKC) and other signaling pathways through mechanisms that are complex and poorly understood. Here we investigate the role of Ser-7 phosphorylation and Cys-580 palmitoylation in mediating steady-state transport kinetics and PKC-stimulated transport down-regulation. Using both mutational and pharmacological approaches, we demonstrate that these post-translational modifications are reciprocally regulated, leading to transporter populations that display high phosphorylation-low palmitoylation or low phosphorylation-high palmitoylation. The balance between the modifications dictates transport capacity, as conditions that promote high phosphorylation or low palmitoylation reduce transport Vmax and enhance PKC-stimulated down-regulation, whereas conditions that promote low phosphorylation or high palmitoylation increase transport Vmax and suppress PKC-stimulated down-regulation. Transitions between these functional states occur when endocytosis is blocked or undetectable, indicating that the modifications kinetically regulate the velocity of surface transporters. These findings reveal a novel mechanism for control of DA reuptake that may represent a point of dysregulation in DA imbalance disorders.
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Affiliation(s)
- Amy E Moritz
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - Danielle E Rastedt
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - Daniel J Stanislowski
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - Madhur Shetty
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - Margaret A Smith
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - Roxanne A Vaughan
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
| | - James D Foster
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9061
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70
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Koldsø H, Grouleff J, Schiøtt B. Insights to ligand binding to the monoamine transporters-from homology modeling to LeuBAT and dDAT. Front Pharmacol 2015; 6:208. [PMID: 26441663 PMCID: PMC4585151 DOI: 10.3389/fphar.2015.00208] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2015] [Indexed: 11/20/2022] Open
Abstract
Understanding of drug binding to the human biogenic amine transporters (BATs) is essential to explain the mechanism of action of these pharmaceuticals but more importantly to be able to develop new and improved compounds to be used in the treatment of depression or drug addiction. Until recently no high resolution structure was available of the BATs and homology modeling was a necessity. Various studies have revealed experimentally validated binding modes of numerous ligands to the BATs using homology modeling. Here we examine and discuss the similarities between the binding models of substrates, antidepressants, psychostimulants, and mazindol in homology models of the human BATs and the recently published crystal structures of the Drosophila dopamine transporter and the engineered protein, LeuBAT. The comparison reveals that careful computational modeling combined with experimental data can be utilized to predict binding of molecules to proteins that agree very well with crystal structures.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford , Oxford, UK ; inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
| | - Julie Grouleff
- inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
| | - Birgit Schiøtt
- inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
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71
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Damgaard M, Al-Khawaja A, Vogensen SB, Jurik A, Sijm M, Lie MEK, Bæk MI, Rosenthal E, Jensen AA, Ecker GF, Frølund B, Wellendorph P, Clausen RP. Identification of the First Highly Subtype-Selective Inhibitor of Human GABA Transporter GAT3. ACS Chem Neurosci 2015; 6:1591-9. [PMID: 26154082 DOI: 10.1021/acschemneuro.5b00150] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Screening a library of small-molecule compounds using a cell line expressing human GABA transporter 3 (hGAT3) in a [(3)H]GABA uptake assay identified isatin derivatives as a new class of hGAT3 inhibitors. A subsequent structure-activity relationship (SAR) study led to the identification of hGAT3-selective inhibitors (i.e., compounds 20 and 34) that were superior to the reference hGAT3 inhibitor, (S)-SNAP-5114, in terms of potency (low micromolar IC50 values) and selectivity (>30-fold selective for hGAT3 over hGAT1/hGAT2/hBGT1). Further pharmacological characterization of compound 20 (5-(thiophen-2-yl)indoline-2,3-dione) revealed a noncompetitive mode of inhibition at hGAT3. This suggests that this compound class, which has no structural resemblance to GABA, has a binding site different from the substrate, GABA. This was supported by a molecular modeling study that suggested a unique binding site that matched the observed selectivity, inhibition kinetics, and SAR of the compound series. These compounds are the most potent GAT3 inhibitors reported to date that provide selectivity for GAT3 over other GABA transporter subtypes.
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Affiliation(s)
| | | | | | - Andreas Jurik
- Department
of Pharmaceutical Chemistry, University of Vienna, Althanstrasse
14, A-1090 Vienna, Austria
| | | | | | | | | | | | - Gerhard F. Ecker
- Department
of Pharmaceutical Chemistry, University of Vienna, Althanstrasse
14, A-1090 Vienna, Austria
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72
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Billesbølle CB, Krüger MB, Shi L, Quick M, Li Z, Stolzenberg S, Kniazeff J, Gotfryd K, Mortensen JS, Javitch JA, Weinstein H, Loland CJ, Gether U. Substrate-induced unlocking of the inner gate determines the catalytic efficiency of a neurotransmitter:sodium symporter. J Biol Chem 2015; 290:26725-38. [PMID: 26363074 DOI: 10.1074/jbc.m115.677658] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/06/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) mediate reuptake of neurotransmitters from the synaptic cleft and are targets for several therapeutics and psychostimulants. The prokaryotic NSS homologue, LeuT, represents a principal structural model for Na(+)-coupled transport catalyzed by these proteins. Here, we used site-directed fluorescence quenching spectroscopy to identify in LeuT a substrate-induced conformational rearrangement at the inner gate conceivably leading to formation of a structural intermediate preceding transition to the inward-open conformation. The substrate-induced, Na(+)-dependent change required an intact primary substrate-binding site and involved increased water exposure of the cytoplasmic end of transmembrane segment 5. The findings were supported by simulations predicting disruption of an intracellular interaction network leading to a discrete rotation of transmembrane segment 5 and the adjacent intracellular loop 2. The magnitude of the spectroscopic response correlated inversely with the transport rate for different substrates, suggesting that stability of the intermediate represents an unrecognized rate-limiting barrier in the NSS transport mechanism.
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Affiliation(s)
- Christian B Billesbølle
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Mie B Krüger
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- Department of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10065
| | - Matthias Quick
- Center for Molecular Recognition and Departments of Psychiatry and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032
| | - Zheng Li
- Department of Physiology and Biophysics and
| | | | - Julie Kniazeff
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kamil Gotfryd
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jonas S Mortensen
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jonathan A Javitch
- Center for Molecular Recognition and Departments of Psychiatry and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032 Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, and
| | - Harel Weinstein
- Department of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10065
| | - Claus J Loland
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ulrik Gether
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark,
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73
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Simon Á, Bencsura Á, Héja L, Magyar C, Kardos J. Sodium-assisted formation of binding and traverse conformations of the substrate in a neurotransmitter sodium symporter model. Curr Drug Discov Technol 2015; 11:227-33. [PMID: 25138914 PMCID: PMC4443782 DOI: 10.2174/1570163811666140812110735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 11/22/2022]
Abstract
Therapeutics designed to increase synaptic neurotransmitter levels by inhibiting neurotransmitter sodium symporters (NSSs) classify a strategic approach to treat brain disorders such as depression or epilepsy, however, the critical elementary steps that couple downhill flux of sodium to uphill transport of neurotransmitter are not distinguished as yet. Here we present modelling of NSS member neuronal GAT1 with the substrate γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter. GABA binding is simulated with the occluded conformation of GAT1 homodimer in an explicit lipid/water environment. Simulations performed in the 1-10 ns range of time elucidated persistent formation of halfextended minor and H-bridged major GABA conformations, referred to as binding and traverse conformations, respectively. The traverse GABA conformation was further stabilized by GAT1-bound Na(+)(1). We also observed Na(+)(1) translocation to GAT1-bound Cl(-) as well as the appearance of water molecules at GABA and GAT1-bound Na(+)(2), conjecturing causality. Scaling dynamics suggest that the traverse GABA conformation may be valid for developing substrate inhibitors with high efficacy. The potential for this finding is significant with impact not only in pharmacology but wherever understanding of the mechanism of neurotransmitter uptake is valuable.
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Affiliation(s)
| | | | | | | | - Julianna Kardos
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, PO Box 17, H-1525 Budapest, Hungary.
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74
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Söderhielm PC, Andersen J, Munro L, Nielsen AT, Kristensen AS. Substrate and Inhibitor-Specific Conformational Changes in the Human Serotonin Transporter Revealed by Voltage-Clamp Fluorometry. Mol Pharmacol 2015; 88:676-88. [PMID: 26174773 DOI: 10.1124/mol.115.099911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/13/2015] [Indexed: 01/05/2023] Open
Abstract
The serotonin transporter (SERT) regulates neurotransmission by the biogenic monoamine neurotransmitter serotonin (5-HT, 5-hydroxytryptamine) in the central nervous system, and drugs inhibiting SERT are widely used for the treatment of a variety of central nervous system diseases. The conformational dynamics of SERT transport function and inhibition is currently poorly understood. We used voltage-clamp fluorometry to study conformational changes in human SERT (hSERT) during 5-HT transport and inhibitor binding. Cys residues were introduced at 12 positions in hSERT to enable covalent attachment of a rhodamine-based fluorophore. Transport-associated changes in fluorescence from fluorophore-labeled hSERT expressed in Xenopus oocytes could be robustly detected at four positions in hSERT: endogenous Cys109 in the top of transmembrane domain (TM) 1b, Cys substituted for Thr323 in the top of TM6, Ala419 in the interface between TM8 and extracellular loop (EL) 4, and Leu481 in EL5. The reporter positions were used for time-resolved measurement of conformational changes during 5-HT transport and binding of cocaine and the selective serotonin reuptake inhibitors fluoxetine and escitalopram. At all reporter positions, fluorescence changes observed upon substrate application were distinctly different from those observed upon inhibitor application, with respect to relative amplitude or direction. Furthermore, escitalopram, fluoxetine, and cocaine induced a very similar pattern of fluorescent changes overall, which included movements within or around TM1b, EL4, and EL5. Taken together, our data lead us to suggest that competitive inhibitors stabilize hSERT in a state that is different from the apo outward-open conformation as well as inward-facing conformations.
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Affiliation(s)
- Pella C Söderhielm
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Lachlan Munro
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Anne T Nielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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75
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Michino M, Beuming T, Donthamsetti P, Newman AH, Javitch JA, Shi L. What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands? Pharmacol Rev 2015; 67:198-213. [PMID: 25527701 DOI: 10.1124/pr.114.009944] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are integral membrane proteins that represent an important class of drug targets. In particular, aminergic GPCRs interact with a significant portion of drugs currently on the market. However, most drugs that target these receptors are associated with undesirable side effects, which are due in part to promiscuous interactions with close homologs of the intended target receptors. Here, based on a systematic analysis of all 37 of the currently available high-resolution crystal structures of aminergic GPCRs, we review structural elements that contribute to and can be exploited for designing subtype-selective compounds. We describe the roles of secondary binding pockets (SBPs), as well as differences in ligand entry pathways to the orthosteric binding site, in determining selectivity. In addition, using the available crystal structures, we have identified conformational changes in the SBPs that are associated with receptor activation and explore the implications of these changes for the rational development of selective ligands with tailored efficacy.
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Affiliation(s)
- Mayako Michino
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Thijs Beuming
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Prashant Donthamsetti
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Amy Hauck Newman
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Jonathan A Javitch
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Lei Shi
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
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Wang KH, Penmatsa A, Gouaux E. Neurotransmitter and psychostimulant recognition by the dopamine transporter. Nature 2015; 521:322-7. [PMID: 25970245 DOI: 10.1038/nature14431] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/23/2015] [Indexed: 12/17/2022]
Abstract
Na(+)/Cl(-)-coupled biogenic amine transporters are the primary targets of therapeutic and abused drugs, ranging from antidepressants to the psychostimulants cocaine and amphetamines, and to their cognate substrates. Here we determine X-ray crystal structures of the Drosophila melanogaster dopamine transporter (dDAT) bound to its substrate dopamine, a substrate analogue 3,4-dichlorophenethylamine, the psychostimulants d-amphetamine and methamphetamine, or to cocaine and cocaine analogues. All ligands bind to the central binding site, located approximately halfway across the membrane bilayer, in close proximity to bound sodium and chloride ions. The central binding site recognizes three chemically distinct classes of ligands via conformational changes that accommodate varying sizes and shapes, thus illustrating molecular principles that distinguish substrates from inhibitors in biogenic amine transporters.
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Affiliation(s)
- Kevin H Wang
- Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
| | - Aravind Penmatsa
- Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
| | - Eric Gouaux
- 1] Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2] Howard Hughes Medical Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA
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77
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Hinz KM, Meyer K, Kinne A, Schülein R, Köhrle J, Krause G. Structural insights into thyroid hormone transport mechanisms of the L-type amino acid transporter 2. Mol Endocrinol 2015; 29:933-42. [PMID: 25945809 DOI: 10.1210/me.2015-1044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Thyroid hormones (THs) are transported across cell membranes by different transmembrane transporter proteins. In previous studies, we showed marked 3,3'-diiodothyronine (3,3'-T2) but moderate T3 uptake by the L-type amino acid transporter 2 (Lat2). We have now studied the structure-function relationships of this transporter and TH-like molecules. Our Lat2 homology model is based on 2 crystal structures of the homologous 12-transmembrane helix transporters arginine/agmatine antiporter and amino acid/polyamine/organocation transporter. Model-driven mutagenesis of residues lining an extracellular recognition site and a TH-traversing channel identified 9 sensitive residues. Using Xenopus laevis oocytes as expression system, we found that side chain shortening (N51S, N133S, N248S, and Y130A) expanded the channel and increased 3,3'-T2 transport. Side chain enlargements (T140F, Y130R, and I137M) decreased 3,3'-T2 uptake, indicating channel obstructions. The opposite results with mutations maintaining (F242W) or impairing (F242V) uptake suggest that F242 may have a gating function. Competitive inhibition studies of 14 TH-like compounds revealed that recognition by Lat2 requires amino and carboxylic acid groups. The size of the adjacent hydrophobic group is restricted. Bulky substituents in positions 3 and 5 of the tyrosine ring are allowed. The phenolic ring may be enlarged, provided that the whole molecule is flexible enough to fit into the distinctly shaped TH-traversing channel of Lat2. Taken together, the next Lat2 features were identified 1) TH recognition site; 2) TH-traversing channel in the center of Lat2; and 3) switch site that potentially facilitates intracellular substrate release. Together with identified substrate features, these data help to elucidate the molecular mechanisms and role of Lat2 in T2 transport.
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Affiliation(s)
- Katrin M Hinz
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Katja Meyer
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Anita Kinne
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Ralf Schülein
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Josef Köhrle
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP) (K.M.H., K.M., A.K., R.S., G.K.), 13125 Berlin, Germany; and Institut für Experimentelle Endokrinologie (J.K.), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
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78
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Rannversson H, Wilson P, Kristensen KB, Sinning S, Kristensen AS, Strømgaard K, Andersen J. Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation. J Biol Chem 2015; 290:14582-94. [PMID: 25903124 DOI: 10.1074/jbc.m114.629071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 12/20/2022] Open
Abstract
The serotonin transporter (SERT) terminates serotonergic neurotransmission by performing reuptake of released serotonin, and SERT is the primary target for antidepressants. SERT mediates the reuptake of serotonin through an alternating access mechanism, implying that a central substrate site is connected to both sides of the membrane by permeation pathways, of which only one is accessible at a time. The coordinated conformational changes in SERT associated with substrate translocation are not fully understood. Here, we have identified a Leu to Glu mutation at position 406 (L406E) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced by L406E are not simply charge-related effects. Leu(406) is located >10 Å from the central inhibitor binding site indicating that the mutation affects inhibitor binding in an indirect manner. We found that L406E decreased accessibility to a residue in the cytoplasmic pathway. The shift in equilibrium to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4 has an important role in controlling the conformational equilibrium of human SERT.
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Affiliation(s)
- Hafsteinn Rannversson
- From the Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen and
| | - Pamela Wilson
- From the Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen and
| | - Kristina Birch Kristensen
- the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, DK-8240 Risskov, Denmark
| | - Steffen Sinning
- the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, DK-8240 Risskov, Denmark
| | - Anders Skov Kristensen
- From the Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen and
| | - Kristian Strømgaard
- From the Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen and
| | - Jacob Andersen
- From the Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen and
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79
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Yuan Y, Huang X, Midde NM, Quizon PM, Sun WL, Zhu J, Zhan CG. Molecular mechanism of HIV-1 Tat interacting with human dopamine transporter. ACS Chem Neurosci 2015; 6:658-665. [PMID: 25695767 DOI: 10.1021/acschemneuro.5b00001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Nearly 70% of HIV-1-infected individuals suffer from HIV-associated neurocognitive disorders (HAND). HIV-1 transactivator of transcription (Tat) protein is known to synergize with abused drugs and exacerbate the progression of central nervous system (CNS) pathology. Cumulative evidence suggest that the HIV-1 Tat protein exerts the neurotoxicity through interaction with human dopamine transporter (hDAT) in the CNS. Through computational modeling and molecular dynamics (MD) simulations, we develop a three-dimensional (3D) structural model for HIV-1 Tat binding with hDAT. The model provides novel mechanistic insights concerning how HIV-1 Tat interacts with hDAT and inhibits dopamine uptake by hDAT. In particular, according to the computational modeling, Tat binds most favorably with the outward-open state of hDAT. Residues Y88, K92, and Y470 of hDAT are predicted to be key residues involved in the interaction between hDAT and Tat. The roles of these hDAT residues in the interaction with Tat are validated by experimental tests through site-directed mutagensis and dopamine uptake assays. The agreement between the computational and experimental data suggests that the computationally predicted hDAT-Tat binding mode and mechanistic insights are reasonable and provide a new starting point to design further pharmacological studies on the molecular mechanism of HIV-1-associated neurocognitive disorders.
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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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Xiaoqin Huang
- 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Narasimha M. Midde
- 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Pamela M. Quizon
- 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Wei-Lun Sun
- 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jun Zhu
- 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, 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
- Department of Drug Discovery and Biomedical Sciences, South Carolina
College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
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80
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Functional mechanisms of neurotransmitter transporters regulated by lipid-protein interactions of their terminal loops. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1765-74. [PMID: 25847498 DOI: 10.1016/j.bbamem.2015.03.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 01/28/2023]
Abstract
The physiological functions of neurotransmitter:sodium symporters (NSS) in reuptake of neurotransmitters from the synapse into the presynaptic nerve have been shown to be complemented by their involvement, together with non-plasma membrane neurotransmitter transporters, in the reverse transport of substrate (efflux) in response to psychostimulants. Recent experimental evidence implicates highly anionic phosphatidylinositol 4,5-biphosphate (PIP(2)) lipids in such functions of the serotonin (SERT) and dopamine (DAT) transporters. Thus, for both SERT and DAT, neurotransmitter efflux has been shown to be strongly regulated by the presence of PIP(2) lipids in the plasma membrane, and the electrostatic interaction of the N-terminal region of DAT with the negatively charged PIP(2) lipids. We examine the experimentally established phenotypes in a structural context obtained from computational modeling based on recent crystallographic data. The results are shown to set the stage for a mechanistic understanding of physiological actions of neurotransmitter transporters in the NSS family of membrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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81
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Khelashvili G, Doktorova M, Sahai MA, Johner N, Shi L, Weinstein H. Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes. Proteins 2015; 83:952-69. [PMID: 25739722 DOI: 10.1002/prot.24792] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/05/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Abstract
The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N-terminal segment. Here we report a computational model of the N-term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N-term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 μs). Combining MD simulations with continuum mean-field modeling we found that the N-term engages with lipid membranes through electrostatic interactions with the charged lipids PIP2 (phosphatidylinositol 4,5-Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N-term implicated in such interactions and show that differential modes of N-term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure-based studies that will elucidate the mechanistic role of the N-term in DAT function.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
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82
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Jurik A, Zdrazil B, Holy M, Stockner T, Sitte HH, Ecker GF. A binding mode hypothesis of tiagabine confirms liothyronine effect on γ-aminobutyric acid transporter 1 (GAT1). J Med Chem 2015; 58:2149-58. [PMID: 25679268 PMCID: PMC4360375 DOI: 10.1021/jm5015428] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Elevating
GABA levels in the synaptic cleft by inhibiting its reuptake
carrier GAT1 is an established approach for the treatment of CNS disorders
like epilepsy. With the increasing availability of crystal structures
of transmembrane transporters, structure-based approaches to elucidate
the molecular basis of ligand–transporter interaction also
become feasible. Experimental data guided docking of derivatives of
the GAT1 inhibitor tiagabine into a protein homology model of GAT1
allowed derivation of a common binding mode for this class of inhibitors
that is able to account for the distinct structure–activity
relationship pattern of the data set. Translating essential binding
features into a pharmacophore model followed by in silico screening
of the DrugBank identified liothyronine as a drug potentially exerting
a similar effect on GAT1. Experimental testing further confirmed the
GAT1 inhibiting properties of this thyroid hormone.
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Affiliation(s)
- Andreas Jurik
- University of Vienna , Department of Pharmaceutical Chemistry, Division of Drug Design and Medicinal Chemistry, Althanstraße 14, 1090 Vienna, Austria
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83
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Bjerregaard H, Severinsen K, Said S, Wiborg O, Sinning S. A dualistic conformational response to substrate binding in the human serotonin transporter reveals a high affinity state for serotonin. J Biol Chem 2015; 290:7747-55. [PMID: 25614630 DOI: 10.1074/jbc.m114.573477] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Serotonergic neurotransmission is modulated by the membrane-embedded serotonin transporter (SERT). SERT mediates the reuptake of serotonin into the presynaptic neurons. Conformational changes in SERT occur upon binding of ions and substrate and are crucial for translocation of serotonin across the membrane. Our understanding of these conformational changes is mainly based on crystal structures of a bacterial homolog in various conformations, derived homology models of eukaryotic neurotransmitter transporters, and substituted cysteine accessibility method of SERT. However, the dynamic changes that occur in the human SERT upon binding of ions, the translocation of substrate, and the role of cholesterol in this interplay are not fully elucidated. Here we show that serotonin induces a dualistic conformational response in SERT. We exploited the substituted cysteine scanning method under conditions that were sensitized to detect a more outward-facing conformation of SERT. We found a novel high affinity outward-facing conformational state of the human SERT induced by serotonin. The ionic requirements for this new conformational response to serotonin mirror the ionic requirements for translocation. Furthermore, we found that membrane cholesterol plays a role in the dualistic conformational response in SERT induced by serotonin. Our results indicate the existence of a subpopulation of SERT responding differently to serotonin binding than hitherto believed and that membrane cholesterol plays a role in this subpopulation of SERT.
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Affiliation(s)
- Henriette Bjerregaard
- From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark
| | - Kasper Severinsen
- From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark
| | - Saida Said
- From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark
| | - Ove Wiborg
- From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark
| | - Steffen Sinning
- From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark
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84
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85
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Bhutia YD, Babu E, Prasad PD, Ganapathy V. The amino acid transporter SLC6A14 in cancer and its potential use in chemotherapy. Asian J Pharm Sci 2014. [DOI: 10.1016/j.ajps.2014.04.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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86
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Li Z, Lee ASE, Bracher S, Jung H, Paz A, Kumar JP, Abramson J, Quick M, Shi L. Identification of a second substrate-binding site in solute-sodium symporters. J Biol Chem 2014; 290:127-41. [PMID: 25398883 DOI: 10.1074/jbc.m114.584383] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The structure of the sodium/galactose transporter (vSGLT), a solute-sodium symporter (SSS) from Vibrio parahaemolyticus, shares a common structural fold with LeuT of the neurotransmitter-sodium symporter family. Structural alignments between LeuT and vSGLT reveal that the crystallographically identified galactose-binding site in vSGLT is located in a more extracellular location relative to the central substrate-binding site (S1) in LeuT. Our computational analyses suggest the existence of an additional galactose-binding site in vSGLT that aligns to the S1 site of LeuT. Radiolabeled galactose saturation binding experiments indicate that, like LeuT, vSGLT can simultaneously bind two substrate molecules under equilibrium conditions. Mutating key residues in the individual substrate-binding sites reduced the molar substrate-to-protein binding stoichiometry to ~1. In addition, the related and more experimentally tractable SSS member PutP (the Na(+)/proline transporter) also exhibits a binding stoichiometry of 2. Targeting residues in the proposed sites with mutations results in the reduction of the binding stoichiometry and is accompanied by severely impaired translocation of proline. Our data suggest that substrate transport by SSS members requires both substrate-binding sites, thereby implying that SSSs and neurotransmitter-sodium symporters share common mechanistic elements in substrate transport.
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Affiliation(s)
- Zheng Li
- From the Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065
| | - Ashley S E Lee
- the Center for Molecular Recognition and Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, New York 10032
| | - Susanne Bracher
- the Ludwig Maximilian University of Munich, Biocentre, Microbiology, Grosshaderner Strasse 2-4, Martinsried, D-82152, Germany
| | - Heinrich Jung
- the Ludwig Maximilian University of Munich, Biocentre, Microbiology, Grosshaderner Strasse 2-4, Martinsried, D-82152, Germany
| | - Aviv Paz
- the Department of Physiology, UCLA, Los Angeles, California 90095
| | - Jay P Kumar
- the Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bellary Road, Bangalore-560065, Karnataka, India
| | - Jeff Abramson
- the Department of Physiology, UCLA, Los Angeles, California 90095, the Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bellary Road, Bangalore-560065, Karnataka, India
| | - Matthias Quick
- the Center for Molecular Recognition and Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, New York 10032, the Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, and
| | - Lei Shi
- From the Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, the Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10021
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87
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Dahal RA, Pramod AB, Sharma B, Krout D, Foster JD, Cha JH, Cao J, Newman AH, Lever JR, Vaughan RA, Henry LK. Computational and biochemical docking of the irreversible cocaine analog RTI 82 directly demonstrates ligand positioning in the dopamine transporter central substrate-binding site. J Biol Chem 2014; 289:29712-27. [PMID: 25179220 PMCID: PMC4207985 DOI: 10.1074/jbc.m114.571521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/09/2014] [Indexed: 12/20/2022] Open
Abstract
The dopamine transporter (DAT) functions as a key regulator of dopaminergic neurotransmission via re-uptake of synaptic dopamine (DA). Cocaine binding to DAT blocks this activity and elevates extracellular DA, leading to psychomotor stimulation and addiction, but the mechanisms by which cocaine interacts with DAT and inhibits transport remain incompletely understood. Here, we addressed these questions using computational and biochemical methodologies to localize the binding and adduction sites of the photoactivatable irreversible cocaine analog 3β-(p-chlorophenyl)tropane-2β-carboxylic acid, 4'-azido-3'-iodophenylethyl ester ([(125)I]RTI 82). Comparative modeling and small molecule docking indicated that the tropane pharmacophore of RTI 82 was positioned in the central DA active site with an orientation that juxtaposed the aryliodoazide group for cross-linking to rat DAT Phe-319. This prediction was verified by focused methionine substitution of residues flanking this site followed by cyanogen bromide mapping of the [(125)I]RTI 82-labeled mutants and by the substituted cysteine accessibility method protection analyses. These findings provide positive functional evidence linking tropane pharmacophore interaction with the core substrate-binding site and support a competitive mechanism for transport inhibition. This synergistic application of computational and biochemical methodologies overcomes many uncertainties inherent in other approaches and furnishes a schematic framework for elucidating the ligand-protein interactions of other classes of DA transport inhibitors.
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Affiliation(s)
- Rejwi Acharya Dahal
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Akula Bala Pramod
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Babita Sharma
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Danielle Krout
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - James D Foster
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Joo Hwan Cha
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Jianjing Cao
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Amy Hauck Newman
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - John R Lever
- the Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, Missouri 65201, and the Department of Radiology, Radiopharmaceutical Sciences Institute, and Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri 65211
| | - Roxanne A Vaughan
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
| | - L Keith Henry
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
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88
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Pedersen AV, Andreassen TF, Loland CJ. A conserved salt bridge between transmembrane segments 1 and 10 constitutes an extracellular gate in the dopamine transporter. J Biol Chem 2014; 289:35003-14. [PMID: 25339174 DOI: 10.1074/jbc.m114.586982] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neurotransmitter transporters play an important role in termination of synaptic transmission by mediating reuptake of neurotransmitter, but the molecular processes behind translocation are still unclear. The crystal structures of the bacterial homologue, LeuT, provided valuable insight into the structural and dynamic requirements for substrate transport. These structures support the existence of gating domains controlling access to a central binding site. On the extracellular side, access is controlled by the "thin gate" formed by an interaction between Arg-30 and Asp-404. In the human dopamine transporter (DAT), the corresponding residues are Arg-85 and Asp-476. Here, we present results supporting the existence of a similar interaction in DAT. The DAT R85D mutant has a complete loss of function, but the additional insertion of an arginine in opposite position (R85D/D476R), causing a charge reversal, results in a rescue of binding sites for the cocaine analogue [(3)H]CFT. Also, the coordination of Zn(2+) between introduced histidines (R85H/D476H) caused a ∼ 2.5-fold increase in [(3)H]CFT binding (Bmax). Importantly, Zn(2+) also inhibited [(3)H]dopamine transport in R85H/D476H, suggesting that a dynamic interaction is required for the transport process. Furthermore, cysteine-reactive chemistry shows that mutation of the gating residues causes a higher proportion of transporters to reside in the outward facing conformation. Finally, we show that charge reversal of the corresponding residues (R104E/E493R) in the serotonin transporter also rescues [(3)H](S)-citalopram binding, suggesting a conserved feature. Taken together, these data suggest that the extracellular thin gate is present in monoamine transporters and that a dynamic interaction is required for substrate transport.
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Affiliation(s)
- Anders V Pedersen
- From the Department of Neuroscience and Pharmacology, Molecular Neuropharmacology Laboratory, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Thorvald F Andreassen
- From the Department of Neuroscience and Pharmacology, Molecular Neuropharmacology Laboratory, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Claus J Loland
- From the Department of Neuroscience and Pharmacology, Molecular Neuropharmacology Laboratory, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
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89
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A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters. Nat Struct Mol Biol 2014; 21:1006-12. [PMID: 25282149 DOI: 10.1038/nsmb.2894] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Neurotransmitter/sodium symporters (NSSs) terminate synaptic signal transmission by Na+-dependent reuptake of released neurotransmitters. Key conformational states have been reported for the bacterial homolog LeuT and an inhibitor-bound Drosophila dopamine transporter. However, a coherent mechanism of Na+-driven transport has not been described. Here, we present two crystal structures of MhsT, an NSS member from Bacillus halodurans, in occluded inward-facing states with bound Na+ ions and L-tryptophan, providing insight into the cytoplasmic release of Na+. The switch from outward- to inward-oriented states is centered on the partial unwinding of transmembrane helix 5, facilitated by a conserved GlyX9Pro motif that opens an intracellular pathway for water to access the Na2 site. We propose a mechanism, based on our structural and functional findings, in which solvation through the TM5 pathway facilitates Na+ release from Na2 and the transition to an inward-open state.
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90
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Hansen FH, Skjørringe T, Yasmeen S, Arends NV, Sahai MA, Erreger K, Andreassen TF, Holy M, Hamilton PJ, Neergheen V, Karlsborg M, Newman AH, Pope S, Heales SJR, Friberg L, Law I, Pinborg LH, Sitte HH, Loland C, Shi L, Weinstein H, Galli A, Hjermind LE, Møller LB, Gether U. Missense dopamine transporter mutations associate with adult parkinsonism and ADHD. J Clin Invest 2014; 124:3107-20. [PMID: 24911152 DOI: 10.1172/jci73778] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/24/2014] [Indexed: 11/17/2022] Open
Abstract
Parkinsonism and attention deficit hyperactivity disorder (ADHD) are widespread brain disorders that involve disturbances of dopaminergic signaling. The sodium-coupled dopamine transporter (DAT) controls dopamine homeostasis, but its contribution to disease remains poorly understood. Here, we analyzed a cohort of patients with atypical movement disorder and identified 2 DAT coding variants, DAT-Ile312Phe and a presumed de novo mutant DAT-Asp421Asn, in an adult male with early-onset parkinsonism and ADHD. According to DAT single-photon emission computed tomography (DAT-SPECT) scans and a fluoro-deoxy-glucose-PET/MRI (FDG-PET/MRI) scan, the patient suffered from progressive dopaminergic neurodegeneration. In heterologous cells, both DAT variants exhibited markedly reduced dopamine uptake capacity but preserved membrane targeting, consistent with impaired catalytic activity. Computational simulations and uptake experiments suggested that the disrupted function of the DAT-Asp421Asn mutant is the result of compromised sodium binding, in agreement with Asp421 coordinating sodium at the second sodium site. For DAT-Asp421Asn, substrate efflux experiments revealed a constitutive, anomalous efflux of dopamine, and electrophysiological analyses identified a large cation leak that might further perturb dopaminergic neurotransmission. Our results link specific DAT missense mutations to neurodegenerative early-onset parkinsonism. Moreover, the neuropsychiatric comorbidity provides additional support for the idea that DAT missense mutations are an ADHD risk factor and suggests that complex DAT genotype and phenotype correlations contribute to different dopaminergic pathologies.
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91
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Mondal S, Khelashvili G, Weinstein H. Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins. Biophys J 2014; 106:2305-16. [PMID: 24896109 PMCID: PMC4052241 DOI: 10.1016/j.bpj.2014.04.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/31/2014] [Accepted: 04/23/2014] [Indexed: 01/12/2023] Open
Abstract
The membrane environment, its composition, dynamics, and remodeling, have been shown to participate in the function and organization of a wide variety of transmembrane (TM) proteins, making it necessary to study the molecular mechanisms of such proteins in the context of their membrane settings. We review some recent conceptual advances enabling such studies, and corresponding computational models and tools designed to facilitate the concerted experimental and computational investigation of protein-membrane interactions. To connect productively with the high resolution achieved by cognate experimental approaches, the computational methods must offer quantitative data at an atomistically detailed level. We show how such a quantitative method illuminated the mechanistic importance of a structural characteristic of multihelical TM proteins, that is, the likely presence of adjacent polar and hydrophobic residues at the protein-membrane interface. Such adjacency can preclude the complete alleviation of the well-known hydrophobic mismatch between TM proteins and the surrounding membrane, giving rise to an energy cost of residual hydrophobic mismatch. The energy cost and biophysical formulation of hydrophobic mismatch and residual hydrophobic mismatch are reviewed in the context of their mechanistic role in the function of prototypical members of multihelical TM protein families: 1), LeuT, a bacterial homolog of mammalian neurotransmitter sodium symporters; and 2), rhodopsin and the β1- and β2-adrenergic receptors from the G-protein coupled receptor family. The type of computational analysis provided by these examples is poised to translate the rapidly growing structural data for the many TM protein families that are of great importance to cell function into ever more incisive insights into mechanisms driven by protein-ligand and protein-protein interactions in the membrane environment.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York.
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92
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Thomas JR, Gedeon PC, Madura JD. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins 2014; 82:2289-302. [PMID: 24753369 DOI: 10.1002/prot.24588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/29/2014] [Accepted: 04/10/2014] [Indexed: 01/28/2023]
Abstract
The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.
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Affiliation(s)
- James R Thomas
- Department of Chemistry and Biochemistry and the Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania; Mylan School of Pharmacy, Duquesne University, Pittsburgh, Pennsylvania
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93
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Kazmier K, Sharma S, Quick M, Islam SM, Roux B, Weinstein H, Javitch JA, McHaourab HS. Conformational dynamics of ligand-dependent alternating access in LeuT. Nat Struct Mol Biol 2014; 21:472-9. [PMID: 24747939 PMCID: PMC4050370 DOI: 10.1038/nsmb.2816] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 03/27/2014] [Indexed: 12/12/2022]
Abstract
The leucine transporter (LeuT) from Aquifex aeolicus is a bacterial homolog of neurotransmitter/sodium symporters (NSSs) that catalyze reuptake of neurotransmitters at the synapse. Crystal structures of wild-type and mutants of LeuT have been interpreted as conformational states in the coupled transport cycle. However, the mechanistic identities inferred from these structures have not been validated, and the ligand-dependent conformational equilibrium of LeuT has not been defined. Here, we used distance measurements between spin-label pairs to elucidate Na(+)- and leucine-dependent conformational changes on the intracellular and extracellular sides of the transporter. The results identify structural motifs that underlie the isomerization of LeuT between outward-facing, inward-facing and occluded states. The conformational changes reported here present a dynamic picture of the alternating-access mechanism of LeuT and NSSs that is different from the inferences reached from currently available structural models.
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Affiliation(s)
- Kelli Kazmier
- 1] Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA. [2]
| | - Shruti Sharma
- 1] Department of Molecular Physiology and Biophysics, Nashville, Tennessee, USA. [2]
| | - Matthias Quick
- 1] Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, New York, New York, USA. [2] Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, New York, USA. [3] New York State Psychiatric Institute, Division of Molecular Therapeutics, New York, New York, USA
| | - Shahidul M Islam
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Harel Weinstein
- 1] Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA. [2] HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Jonathan A Javitch
- 1] Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, New York, New York, USA. [2] Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, New York, USA. [3] New York State Psychiatric Institute, Division of Molecular Therapeutics, New York, New York, USA. [4] Department of Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Hassane S McHaourab
- 1] Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA. [2] Department of Molecular Physiology and Biophysics, Nashville, Tennessee, USA
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94
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LeVine MV, Weinstein H. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol 2014; 10:e1003603. [PMID: 24785005 PMCID: PMC4006702 DOI: 10.1371/journal.pcbi.1003603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/24/2014] [Indexed: 11/23/2022] Open
Abstract
Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems. We developed the new information theory-based analysis framework presented here, NbIT analysis, for the study of allosteric mechanisms in biomolecular systems from Molecular Dynamics trajectories. The illustrative application of NbIT to the analysis of the occluded state in the bacterial transporter LeuT, produced a quantitative representation of the allosteric behavior, and identified intramolecular channels that enable the long-distance information transmission. Our findings, identifying the roles of specific residues in the communication of the allosteric information, were validated by the recognition of residues that have been previously shown to play functional roles in this very well studied system. In addition, we show that application of NbIT analysis leads to the discrimination of functional roles by differentiating between residues that are essential to the dynamics within functional sites (e.g., the substrate binding sites), and residues whose role is to communicate between such functional sites. These results demonstrate that the information theoretical analysis presented here is a powerful tool for quantifying complex allosteric behavior in biomolecular systems and for identifying the crucial components underlying those behaviors.
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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, United States of America
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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95
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Schlessinger A, Khuri N, Giacomini KM, Sali A. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Curr Top Med Chem 2014; 13:843-56. [PMID: 23578028 DOI: 10.2174/1568026611313070007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 12/21/2022]
Abstract
Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy coupling mechanisms. In human, there are 386 SLC transporters, many of which contribute to the absorption, distribution, metabolism, and excretion of drugs and/or can be targeted directly by therapeutics. Recent atomic structures of SLC transporters determined by X-ray crystallography and NMR spectroscopy have significantly expanded the applicability of structure-based prediction of SLC transporter ligands, by enabling both comparative modeling of additional SLC transporters and virtual screening of small molecules libraries against experimental structures as well as comparative models. In this review, we begin by describing computational tools, including sequence analysis, comparative modeling, and virtual screening, that are used to predict the structures and functions of membrane proteins such as SLC transporters. We then illustrate the applications of these tools to predicting ligand specificities of select SLC transporters, followed by experimental validation using uptake kinetic measurements and other assays. We conclude by discussing future directions in the discovery of the SLC transporter ligands.
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Affiliation(s)
- Avner Schlessinger
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
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96
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Loland CJ. The use of LeuT as a model in elucidating binding sites for substrates and inhibitors in neurotransmitter transporters. Biochim Biophys Acta Gen Subj 2014; 1850:500-10. [PMID: 24769398 DOI: 10.1016/j.bbagen.2014.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 01/24/2023]
Abstract
BACKGROUND The mammalian neurotransmitter transporters are complex proteins playing a central role in synaptic transmission between neurons by rapid reuptake of neurotransmitters. The proteins which transport dopamine, noradrenaline and serotonin belong to the Neurotransmitter:Sodium Symporters (NSS). Due to their important role, dysfunctions are associated with several psychiatric and neurological diseases and they also serve as targets for a wide range of therapeutic and illicit drugs. Despite the central physiological and pharmacological importance, direct evidence on structure-function relationships on mammalian NSS proteins has so far been unsuccessful. The crystal structure of the bacterial NSS protein, LeuT, has been a turning point in structural investigations. SCOPE OF REVIEW To provide an update on what is known about the binding sites for substrates and inhibitors in the LeuT. The different binding modes and binding sites will be discussed with special emphasis on the possible existence of a second substrate binding site. It is the goal to give an insight into how investigations on ligand binding in LeuT have provided basic knowledge about transporter conformations and translocation mechanism which can pave the road for a deeper understanding of drug binding and function of the mammalian transporters. MAJOR CONCLUSIONS The LeuT is a suitable model for the structural investigation of NSS proteins including the possible location of drug binding sites. It is still debated whether the LeuT is a suitable model for the molecular mechanisms behind substrate translocation. GENERAL SIGNIFICANCE Structure and functional aspects of NSS proteins are central for understanding synaptic transmission. With the purification and crystallization of LeuT as well as the dopamine transporter from Drosophila melanogaster, the application of biophysical methods such as fluorescence spectroscopy, neutron- or x-ray scattering and NMR for understanding its function becomes increasingly available. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Claus J Loland
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, The Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
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97
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Sørensen L, Strømgaard K, Kristensen AS. Characterization of intracellular regions in the human serotonin transporter for phosphorylation sites. ACS Chem Biol 2014; 9:935-44. [PMID: 24450286 DOI: 10.1021/cb4007198] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the central nervous system, synaptic levels of the monoamine neurotransmitter serotonin are mainly controlled by the serotonin transporter (SERT), and drugs used in the treatment of various psychiatric diseases have SERT as primary target. SERT is a phosphoprotein that undergoes phosphorylation/dephosphorylation during transporter regulation by multiple pathways. In particular, activation and/or inhibition of kinases including PKC, PKG, p38MAPK, and CaMKII modulate SERT function and trafficking. The molecular mechanisms by which kinase activity is linked to SERT regulation are poorly understood, including the identity of specific phosphorylated residues. To elucidate SERT phosphorylation sites, we have generated peptides corresponding to the entire intracellular region of human SERT and performed in vitro phosphorylation assays with a panel of kinases suggested to be involved in SERT regulation or for which canonical phosphorylation sites are predicted. Peptide analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify and quantify site-specific phosphorylation. Five residues located in the N- and C-termini and in intracellular loop 1 and 2 were identified as phosphorylation sites; Ser149, Ser277, and Thr603 for PKC, Ser13 for CaMKII, and Thr616 for p38MAPK. Possible regulatory roles of these potential phosphoacceptors for SERT function and surface expression were investigated using phospho-mimicking and phosphodeficient mutations, coexpression of constitutively active kinases and pharmacological kinase induction in a heterologous expression system. Our results suggest that Ser277 is involved in an initial phase of PKC-mediated down-regulation of SERT. The five identified sites can guide future studies of direct links between SERT phosphorylation and regulatory processes.
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Affiliation(s)
- Lena Sørensen
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders S. Kristensen
- Department of Drug Design
and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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98
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Wilson JN, Ladefoged LK, Babinchak WM, Schiøtt B. Binding-induced fluorescence of serotonin transporter ligands: A spectroscopic and structural study of 4-(4-(dimethylamino)phenyl)-1-methylpyridinium (APP(+)) and APP(+) analogues. ACS Chem Neurosci 2014; 5:296-304. [PMID: 24460204 DOI: 10.1021/cn400230x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The binding-induced fluorescence of 4-(4-(dimethylamino)-phenyl)-1-methylpyridinium (APP(+)) and two new serotonin transporter (SERT)-binding fluorescent analogues, 1-butyl-4-[4-(1-dimethylamino)phenyl]-pyridinium bromide (BPP(+)) and 1-methyl-4-[4-(1-piperidinyl)phenyl]-pyridinium (PPP(+)), has been investigated. Optical spectroscopy reveals that these probes are highly sensitive to their chemical microenvironment, responding to variations in polarity with changes in transition energies and responding to changes in viscosity or rotational freedom with emission enhancements. Molecular docking calculations reveal that the probes are able to access the nonpolar and conformationally restrictive binding pocket of SERT. As a result, the probes exhibit previously not identified binding-induced turn-on emission that is spectroscopically distinct from dyes that have accumulated intracellularly. Thus, binding and transport dynamics of SERT ligands can be resolved both spatially and spectroscopically.
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Affiliation(s)
- James N. Wilson
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | - Lucy Kate Ladefoged
- inSPIN
and iNANO Centers, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - W. Michael Babinchak
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, United States
| | - Birgit Schiøtt
- inSPIN
and iNANO Centers, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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99
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Ng J, Zhen J, Meyer E, Erreger K, Li Y, Kakar N, Ahmad J, Thiele H, Kubisch C, Rider NL, Morton DH, Strauss KA, Puffenberger EG, D'Agnano D, Anikster Y, Carducci C, Hyland K, Rotstein M, Leuzzi V, Borck G, Reith MEA, Kurian MA. Dopamine transporter deficiency syndrome: phenotypic spectrum from infancy to adulthood. ACTA ACUST UNITED AC 2014; 137:1107-19. [PMID: 24613933 PMCID: PMC3959557 DOI: 10.1093/brain/awu022] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dopamine transporter deficiency syndrome is an SLC6A3-related progressive infantile-onset parkinsonism-dystonia that mimics cerebral palsy. Ng et al. describe clinical features and molecular findings in a new cohort of patients. They report infants with classical disease, as well as young adults manifesting as atypical juvenile-onset parkinsonism-dystonia, thereby expanding the disease spectrum. Dopamine transporter deficiency syndrome due to SLC6A3 mutations is the first inherited dopamine ‘transportopathy’ to be described, with a classical presentation of early infantile-onset progressive parkinsonism dystonia. In this study we have identified a new cohort of patients with dopamine transporter deficiency syndrome, including, most significantly, atypical presentation later in childhood with a milder disease course. We report the detailed clinical features, molecular genetic findings and in vitro functional investigations undertaken for adult and paediatric cases. Patients presenting with parkinsonism dystonia or a neurotransmitter profile characteristic of dopamine transporter deficiency syndrome were recruited for study. SLC6A3 mutational analysis was undertaken in all patients. The functional consequences of missense variants on the dopamine transporter were evaluated by determining the effect of mutant dopamine transporter on dopamine uptake, protein expression and amphetamine-mediated dopamine efflux using an in vitro cellular heterologous expression system. We identified eight new patients from five unrelated families with dopamine transporter deficiency syndrome. The median age at diagnosis was 13 years (range 1.5–34 years). Most significantly, the case series included three adolescent males with atypical dopamine transporter deficiency syndrome of juvenile onset (outside infancy) and progressive parkinsonism dystonia. The other five patients in the cohort presented with classical infantile-onset parkinsonism dystonia, with one surviving into adulthood (currently aged 34 years) and labelled as having ‘juvenile parkinsonism’. All eight patients harboured homozygous or compound heterozygous mutations in SLC6A3, of which the majority are previously unreported variants. In vitro studies of mutant dopamine transporter demonstrated multifaceted loss of dopamine transporter function. Impaired dopamine uptake was universally present, and more severely impacted in dopamine transporter mutants causing infantile-onset rather than juvenile-onset disease. Dopamine transporter mutants also showed diminished dopamine binding affinity, reduced cell surface transporter, loss of post-translational dopamine transporter glycosylation and failure of amphetamine-mediated dopamine efflux. Our data series expands the clinical phenotypic continuum of dopamine transporter deficiency syndrome and indicates that there is a phenotypic spectrum from infancy (early onset, rapidly progressive disease) to childhood/adolescence and adulthood (later onset, slower disease progression). Genotype–phenotype analysis in this cohort suggests that higher residual dopamine transporter activity is likely to contribute to postponing disease presentation in these later-onset adult cases. Dopamine transporter deficiency syndrome remains under-recognized and our data highlights that dopamine transporter deficiency syndrome should be considered as a differential diagnosis for both infantile- and juvenile-onset movement disorders, including cerebral palsy and juvenile parkinsonism.
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Affiliation(s)
- Joanne Ng
- 1 Neurosciences Unit, UCL Institute of Child Health, London, UK
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100
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Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model 2014; 54:933-43. [PMID: 24521202 PMCID: PMC3982395 DOI: 10.1021/ci400742s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The serotonin (5-hydroxytryptamine, 5-HT) transporter (SERT) plays an essential role in the termination of serotonergic neurotransmission by removing 5-HT from the synaptic cleft into the presynaptic neuron. It is also of pharmacological importance being targeted by antidepressants and psychostimulant drugs. Here, five commercial databases containing approximately 3.24 million drug-like compounds have been screened using a combination of two-dimensional (2D) fingerprint-based and three-dimensional (3D) pharmacophore-based screening and flexible docking into multiple conformations of the binding pocket detected in an outward-open SERT homology model. Following virtual screening (VS), selected compounds were evaluated using in vitro screening and full binding assays and an in silico hit-to-lead (H2L) screening was performed to obtain analogues of the identified compounds. Using this multistep VS/H2L approach, 74 active compounds, 46 of which had K(i) values of ≤1000 nM, belonging to 16 structural classes, have been identified, and multiple compounds share no structural resemblance with known SERT binders.
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Affiliation(s)
- Mari Gabrielsen
- Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway , 9037 Tromsø, Norway
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