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Frangos ZJ, Cantwell Chater RP, Vandenberg RJ. Glycine Transporter 2: Mechanism and Allosteric Modulation. Front Mol Biosci 2021; 8:734427. [PMID: 34805268 PMCID: PMC8602798 DOI: 10.3389/fmolb.2021.734427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023] Open
Abstract
Neurotransmitter sodium symporters (NSS) are a subfamily of SLC6 transporters responsible for regulating neurotransmitter signalling. They are a major target for psychoactive substances including antidepressants and drugs of abuse, prompting substantial research into their modulation and structure-function dynamics. Recently, a series of allosteric transport inhibitors have been identified, which may reduce side effect profiles, compared to orthosteric inhibitors. Allosteric inhibitors are also likely to provide different clearance kinetics compared to competitive inhibitors and potentially better clinical outcomes. Crystal structures and homology models have identified several allosteric modulatory sites on NSS including the vestibule allosteric site (VAS), lipid allosteric site (LAS) and cholesterol binding site (CHOL1). Whilst the architecture of eukaryotic NSS is generally well conserved there are differences in regions that form the VAS, LAS, and CHOL1. Here, we describe ligand-protein interactions that stabilize binding in each allosteric site and explore how differences between transporters could be exploited to generate NSS specific compounds with an emphasis on GlyT2 modulation.
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Affiliation(s)
- Zachary J Frangos
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ryan P Cantwell Chater
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Robert J Vandenberg
- Transporter Biology Group, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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2
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Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
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3
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Stoichiometric analysis of protein complexes by cell fusion and single molecule imaging. Sci Rep 2020; 10:14866. [PMID: 32913201 PMCID: PMC7483473 DOI: 10.1038/s41598-020-71630-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/28/2020] [Indexed: 11/22/2022] Open
Abstract
The composition, stoichiometry and interactions of supramolecular protein complexes are a critical determinant of biological function. Several techniques have been developed to study molecular interactions and quantify subunit stoichiometry at the single molecule level. However, these typically require artificially low expression levels or detergent isolation to achieve the low fluorophore concentrations required for single molecule imaging, both of which may bias native subunit interactions. Here we present an alternative approach where protein complexes are assembled at physiological concentrations and subsequently diluted in situ for single-molecule level observations while preserving them in a near-native cellular environment. We show that coupling this dilution strategy with fluorescence correlation spectroscopy permits quantitative assessment of cytoplasmic oligomerization, while stepwise photobleaching and single molecule colocalization may be used to study the subunit stoichiometry of membrane receptors. Single protein recovery after dilution (SPReAD) is a simple and versatile means of extending the concentration range of single molecule measurements into the cellular regime while minimizing potential artifacts and perturbations of protein complex stoichiometry.
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4
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Xu L, Chen LY. Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. J Chem Inf Model 2020; 60:3958-3968. [PMID: 32649824 PMCID: PMC7484383 DOI: 10.1021/acs.jcim.0c00346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dopamine (DA) transporter (DAT) is a major target for psychostimulant drugs of abuse such as cocaine that competitively binds to DAT, inhibits DA reuptake, and consequently increases synaptic DA levels. In addition to the central binding site inside DAT, the available experimental evidence suggests the existence of alternative binding sites on DAT, but detection and characterization of these sites are challenging by experiments alone. Here, we integrate multiple computational approaches to probe the potential binding sites on the wild-type Drosophila melanogaster DAT and identify a new allosteric site that displays high affinity for cocaine. This site is located on the surface of DAT, and binding of cocaine is primarily dominated by interactions with hydrophobic residues surrounding the site. We show that cocaine binding to this new site allosterically reduces the binding of DA/cocaine to the central binding pocket, and simultaneous binding of two cocaine molecules to a single DAT seems infeasible. Furthermore, we find that binding of cocaine to this site stabilizes the conformation of DAT but alters the conformational population and thereby reduces the accessibility by DA, providing molecular insights into the inhibitory mechanism of cocaine. In addition, our results indicate that the conformations induced by cocaine binding to this site may be relevant to the oligomerization of DAT, highlighting a potential role of this new site in modulating the function of DAT.
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Affiliation(s)
- Liang Xu
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Liao Y Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
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5
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Schmidpeter PAM, Sukomon N, Nimigean CM. Reconstitution of Membrane Proteins into Platforms Suitable for Biophysical and Structural Analyses. Methods Mol Biol 2020; 2127:191-205. [PMID: 32112324 PMCID: PMC9288841 DOI: 10.1007/978-1-0716-0373-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Integral membrane proteins have historically been challenging targets for biophysical research due to their low solubility in aqueous solution. Their importance for chemical and electrical signaling between cells, however, makes them fascinating targets for investigators interested in the regulation of cellular and physiological processes. Since membrane proteins shunt the barrier imposed by the cell membrane, they also serve as entry points for drugs, adding pharmaceutical research and development to the interests. In recent years, detailed understanding of membrane protein function has significantly increased due to high-resolution structural information obtained from single-particle cryo-EM, X-ray crystallography, and NMR. In order to further advance our mechanistic understanding on membrane proteins as well as foster drug development, it is crucial to generate more biophysical and functional data on these proteins under defined conditions. To that end, different techniques have been developed to stabilize integral membrane proteins in native-like environments that allow both structural and biophysical investigations-amphipols, lipid bicelles, and lipid nanodiscs. In this chapter, we provide detailed protocols for the reconstitution of membrane proteins according to these three techniques. We also outline some of the possible applications of each technique and discuss their advantages and possible caveats.
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Affiliation(s)
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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6
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Abstract
Escherichia coli is the workhorse of the structural biology lab. In addition to routine cloning and molecular biology, E. coli can be used as a factory for the production of recombinant membrane proteins. Purification of homogeneous samples of membrane protein expressed in E. coli is a significant bottleneck for researchers, and the protocol we present here for the overexpression and purification of membrane proteins in E. coli will provide a solid basis to develop lab- and protein-specific protocols for your membrane protein of interest. We additionally provide extensive notes on the purification process, as well as the theory surrounding principles of purification.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Ali A Kermani
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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7
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Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Nature 2019; 576:315-320. [PMID: 31776516 PMCID: PMC6911266 DOI: 10.1038/s41586-019-1795-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/06/2019] [Indexed: 01/21/2023]
Abstract
The emergence and spread of drug-resistant Plasmodium falciparum impedes global efforts to control and eliminate malaria. For decades, treatment of malaria has relied on chloroquine (CQ), a safe and affordable 4-aminoquinoline that was highly effective against intra-erythrocytic asexual blood-stage parasites, until resistance arose in Southeast Asia and South America and spread worldwide1. Clinical resistance to the chemically related current first-line combination drug piperaquine (PPQ) has now emerged regionally, reducing its efficacy2. Resistance to CQ and PPQ has been associated with distinct sets of point mutations in the P. falciparum CQ-resistance transporter PfCRT, a 49-kDa member of the drug/metabolite transporter superfamily that traverses the membrane of the acidic digestive vacuole of the parasite3-9. Here we present the structure, at 3.2 Å resolution, of the PfCRT isoform of CQ-resistant, PPQ-sensitive South American 7G8 parasites, using single-particle cryo-electron microscopy and antigen-binding fragment technology. Mutations that contribute to CQ and PPQ resistance localize primarily to moderately conserved sites on distinct helices that line a central negatively charged cavity, indicating that this cavity is the principal site of interaction with the positively charged CQ and PPQ. Binding and transport studies reveal that the 7G8 isoform binds both drugs with comparable affinities, and that these drugs are mutually competitive. The 7G8 isoform transports CQ in a membrane potential- and pH-dependent manner, consistent with an active efflux mechanism that drives CQ resistance5, but does not transport PPQ. Functional studies on the newly emerging PfCRT F145I and C350R mutations, associated with decreased PPQ susceptibility in Asia and South America, respectively6,9, reveal their ability to mediate PPQ transport in 7G8 variant proteins and to confer resistance in gene-edited parasites. Structural, functional and in silico analyses suggest that distinct mechanistic features mediate the resistance to CQ and PPQ in PfCRT variants. These data provide atomic-level insights into the molecular mechanism of this key mediator of antimalarial treatment failures.
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8
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Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nat Struct Mol Biol 2019; 26:545-556. [PMID: 31270469 DOI: 10.1038/s41594-019-0253-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022]
Abstract
Monoamine transporters (MATs) regulate neurotransmission via the reuptake of dopamine, serotonin and norepinephrine from extra-neuronal regions and thus maintain neurotransmitter homeostasis. As targets of a wide range of compounds, including antidepressants, substances of abuse and drugs for neuropsychiatric and neurodegenerative disorders, their mechanism of action and their modulation by small molecules have long been of broad interest. Recent advances in the structural characterization of dopamine and serotonin transporters have opened the way for structure-based modeling and simulations, which, together with experimental data, now provide mechanistic understanding of their transport function and interactions. Here we review recent progress in the elucidation of the structural dynamics of MATs and their conformational landscape and transitions, as well as allosteric regulation mechanisms.
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9
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Schumann-Gillett A, Blyth MT, O’Mara ML. Is protein structure enough? A review of the role of lipids in SLC6 transporter function. Neurosci Lett 2019; 700:64-69. [DOI: 10.1016/j.neulet.2018.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/17/2022]
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10
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Yarravarapu N, Geffert L, Surratt CK, Cascio M, Lapinsky DJ. Clickable photoaffinity ligands for the human serotonin transporter based on the selective serotonin reuptake inhibitor (S)-citalopram. Bioorg Med Chem Lett 2018; 28:3431-3435. [PMID: 30266542 DOI: 10.1016/j.bmcl.2018.09.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 12/16/2022]
Abstract
To date, the development of photoaffinity ligands targeting the human serotonin transporter (hSERT), a key protein involved in disease states such as depression and anxiety, have been radioisotope-based (i.e., 3H or 125I). This letter instead highlights three derivatives of the selective serotonin reuptake inhibitor (SSRI) (S)-citalopram that were rationally designed and synthesized to contain a photoreactive benzophenone or an aryl azide for protein target capture via photoaffinity labeling and a terminal alkyne or an aliphatic azide for click chemistry-based proteomics. Specifically, clickable benzophenone-based (S)-citalopram photoprobe 6 (hSERT Ki = 0.16 nM) displayed 11-fold higher binding affinity at hSERT when compared to (S)-citalopram (hSERT Ki = 1.77 nM), and was subsequently shown to successfully undergo tandem photoaffinity labeling-biorthogonal conjugation using purified hSERT. Given clickable photoprobes can be used for various applications depending on which reporter is attached by click chemistry subsequent to photoaffinity labeling, photoprobe 6 is expected to find value in structure-function studies and other research applications involving hSERT (e.g., imaging).
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Affiliation(s)
- Nageswari Yarravarapu
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Laura Geffert
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Christopher K Surratt
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Michael Cascio
- Bayer School of Natural and Environmental Sciences, Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - David J Lapinsky
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States.
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11
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Structural elements required for coupling ion and substrate transport in the neurotransmitter transporter homolog LeuT. Proc Natl Acad Sci U S A 2018; 115:E8854-E8862. [PMID: 30181291 DOI: 10.1073/pnas.1716870115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The coupled transport of ions and substrates allows transporters to accumulate substrates using the energy of transmembrane ion gradients and electrical potentials. During transport, conformational changes that switch accessibility of substrate and ion binding sites from one side of the membrane to the other must be controlled so as to prevent uncoupled movement of ions or substrates. In the neurotransmitter:sodium symporter (NSS) family, Na+ stabilizes the transporter in an outward-open state, thus decreasing the likelihood of uncoupled Na+ transport. Substrate binding, in a step essential for coupled transport, must overcome the effect of Na+, allowing intracellular substrate and Na+ release from an inward-open state. However, the specific elements of the protein that mediate this conformational response to substrate binding are unknown. Previously, we showed that in the prokaryotic NSS transporter LeuT, the effect of Na+ on conformation requires the Na2 site, where it influences conformation by fostering interaction between two domains of the protein. Here, we used cysteine accessibility to measure conformational changes of LeuT in Escherichia coli membranes. We identified a conserved tyrosine residue in the substrate binding site required for substrate to convert LeuT to inward-open states by establishing an interaction between the two transporter domains. We further identify additional required interactions between the two transporter domains in the extracellular pathway. Together with our previous work on the conformational effect of Na+, these results identify mechanistic components underlying ion-substrate coupling in NSS transporters.
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12
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The LeuT-fold neurotransmitter:sodium symporter MhsT has two substrate sites. Proc Natl Acad Sci U S A 2018; 115:E7924-E7931. [PMID: 30082383 DOI: 10.1073/pnas.1717444115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Crystal structures of the neurotransmitter:sodium symporter MhsT revealed occluded inward-facing states with one substrate (Trp) bound in the primary substrate (S1) site and a collapsed extracellular vestibule, which in LeuT contains the second substrate (S2) site. In n-dodecyl-β-d-maltoside, the detergent used to prepare MhsT for crystallization, the substrate-to-protein binding stoichiometry was determined by using scintillation proximity to be 1 Trp:MhsT. Here, using the same experimental approach, as well as equilibrium dialysis, we report that in n-decyl-β-d-maltoside, or after reconstitution in lipid, MhsT, like LeuT, can simultaneously bind two Trp substrate molecules. Trp binding to the S2 site sterically blocks access to a substituted Cys at position 33 in the S2 site, as well as access to the deeper S1 site. Mutation of either the S1 or S2 site disrupts transport, consistent with previous studies in LeuT showing that substrate binding to the S2 site is an essential component of the transport mechanism.
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13
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Bai X, Moraes TF, Reithmeier RAF. Structural biology of solute carrier (SLC) membrane transport proteins. Mol Membr Biol 2018; 34:1-32. [PMID: 29651895 DOI: 10.1080/09687688.2018.1448123] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.
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Affiliation(s)
- Xiaoyun Bai
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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14
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Carland JE, Thomas M, Mostyn SN, Subramanian N, O’Mara ML, Ryan RM, Vandenberg RJ. Molecular Determinants for Substrate Interactions with the Glycine Transporter GlyT2. ACS Chem Neurosci 2018; 9:603-614. [PMID: 29120604 DOI: 10.1021/acschemneuro.7b00407] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Transporters in the SLC6 family play key roles in regulating neurotransmission and are the targets for a wide range of therapeutics. Important insights into the transport mechanisms and the specificity of drug interactions of SLC6 transporters have been obtained from the crystal structures of a bacterial homologue of the family, LeuTAa, and more recently the Drosophila dopamine transporter and the human serotonin transporter. However, there is disputed evidence that the bacterial leucine transporter, LeuTAa, contains two substrate binding sites that work cooperatively in the mechanism of transport, with the binding of a second substrate being required for the release of the substrate from the primary site. An alternate proposal is that there may be low affinity binding sites that serve to direct the flow of substrates to the primary site. We have used a combination of molecular dynamics simulations of substrate interactions with a homology model of GlyT2, together with radiolabeled amino acid uptake assays and electrophysiological analysis of wild-type and mutant transporters, to provide evidence that substrate selectivity of GlyT2 is determined entirely by the primary substrate binding site and, furthermore, if a secondary site exists then it is a low affinity nonselective amino acid binding site.
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Affiliation(s)
- Jane E. Carland
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Thomas
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Shannon N. Mostyn
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Nandhitha Subramanian
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Renae M. Ryan
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
| | - Robert J. Vandenberg
- Discipline of Pharmacology, School of Medical Sciences, Molecular Biosciences Building, University of Sydney, Sydney, NSW 2006, Australia
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15
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Lipid bilayer composition modulates the unfolding free energy of a knotted α-helical membrane protein. Proc Natl Acad Sci U S A 2018; 115:E1799-E1808. [PMID: 29432185 DOI: 10.1073/pnas.1714668115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
α-Helical membrane proteins have eluded investigation of their thermodynamic stability in lipid bilayers. Reversible denaturation curves have enabled some headway in determining unfolding free energies. However, these parameters have been limited to detergent micelles or lipid bicelles, which do not possess the same mechanical properties as lipid bilayers that comprise the basis of natural membranes. We establish reversible unfolding of the membrane transporter LeuT in lipid bilayers, enabling the comparison of apparent unfolding free energies in different lipid compositions. LeuT is a bacterial ortholog of neurotransmitter transporters and contains a knot within its 12-transmembrane helical structure. Urea is used as a denaturant for LeuT in proteoliposomes, resulting in the loss of up to 30% helical structure depending upon the lipid bilayer composition. Urea unfolding of LeuT in liposomes is reversible, with refolding in the bilayer recovering the original helical structure and transport activity. A linear dependence of the unfolding free energy on urea concentration enables the free energy to be extrapolated to zero denaturant. Increasing lipid headgroup charge or chain lateral pressure increases the thermodynamic stability of LeuT. The mechanical and charge properties of the bilayer also affect the ability of urea to denature the protein. Thus, we not only gain insight to the long-sought-after thermodynamic stability of an α-helical protein in a lipid bilayer but also provide a basis for studies of the folding of knotted proteins in a membrane environment.
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16
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Terry DS, Kolster RA, Quick M, LeVine MV, Khelashvili G, Zhou Z, Weinstein H, Javitch JA, Blanchard SC. A partially-open inward-facing intermediate conformation of LeuT is associated with Na + release and substrate transport. Nat Commun 2018; 9:230. [PMID: 29335402 PMCID: PMC5768729 DOI: 10.1038/s41467-017-02202-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/12/2017] [Indexed: 12/20/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSS), targets of antidepressants and psychostimulants, clear neurotransmitters from the synaptic cleft through sodium (Na+)-coupled transport. Substrate and Na+ are thought to be transported from the extracellular to intracellular space through an alternating access mechanism by coordinated conformational rearrangements in the symporter that alternately expose the binding sites to each side of the membrane. However, the mechanism by which the binding of ligands coordinates conformational changes occurring on opposite sides of the membrane is not well understood. Here, we report the use of single-molecule fluorescence resonance energy transfer (smFRET) techniques to image transitions between distinct conformational states on both the extracellular and intracellular sides of the prokaryotic NSS LeuT, including partially open intermediates associated with transport activity. The nature and functional context of these hitherto unidentified intermediate states shed new light on the allosteric mechanism that couples substrate and Na+ symport by the NSS family through conformational dynamics.
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Affiliation(s)
- Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Rachel A Kolster
- Department of Psychiatry, Division of Molecular Therapeutics, Columbia University College of Physicians and Surgeons and New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Matthias Quick
- Department of Psychiatry, Division of Molecular Therapeutics, Columbia University College of Physicians and Surgeons and New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY, 10032, USA
| | - Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Avenue, New York, NY, 10021, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Avenue, New York, NY, 10021, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, 1305 York Avenue, New York, NY, 10021, USA
| | - Jonathan A Javitch
- Department of Psychiatry, Division of Molecular Therapeutics, Columbia University College of Physicians and Surgeons and New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY, 10032, USA.
- Department of Pharmacology, Columbia University College of Physicians and Surgeons, 1051 Riverside Drive, New York, NY, 10032, USA.
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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17
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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18
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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19
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Zhu R, Gruber HJ, Hinterdorfer P. Two Ligand Binding Sites in Serotonin Transporter Revealed by Nanopharmacological Force Sensing. Methods Mol Biol 2018; 1814:19-33. [PMID: 29956224 DOI: 10.1007/978-1-4939-8591-3_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The number of ligand binding sites in neurotransmitter-sodium symporters has been determined by crystal structure analysis and molecular pharmacology with controversial results. Here, we designed molecular tools to measure the interaction forces between the serotonin transporter (SERT) and S-citalopram on the single-molecule level by means of atomic force microscopy. Force spectroscopy allows for the extraction of dynamic information under physiological conditions which is inaccessible via X-ray crystallography. Two populations of distinctly different binding strength between S-citalopram and SERT were demonstrated in Na+-containing buffer. In Li+-containing buffer, SERT showed merely low-force interactions, whereas the vestibular mutant SERT-G402H only displayed the high force population. These observations provide physical evidence for the existence of two different binding sites in SERT when tested under near-physiological conditions.
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Affiliation(s)
- Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Hermann J Gruber
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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20
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Wyant GA, Abu-Remaileh M, Wolfson RL, Chen WW, Freinkman E, Danai LV, Vander Heiden MG, Sabatini DM. mTORC1 Activator SLC38A9 Is Required to Efflux Essential Amino Acids from Lysosomes and Use Protein as a Nutrient. Cell 2017; 171:642-654.e12. [PMID: 29053970 DOI: 10.1016/j.cell.2017.09.046] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/18/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022]
Abstract
The mTORC1 kinase is a master growth regulator that senses many environmental cues, including amino acids. Activation of mTORC1 by arginine requires SLC38A9, a poorly understood lysosomal membrane protein with homology to amino acid transporters. Here, we validate that SLC38A9 is an arginine sensor for the mTORC1 pathway, and we uncover an unexpectedly central role for SLC38A9 in amino acid homeostasis. SLC38A9 mediates the transport, in an arginine-regulated fashion, of many essential amino acids out of lysosomes, including leucine, which mTORC1 senses through the cytosolic Sestrin proteins. SLC38A9 is necessary for leucine generated via lysosomal proteolysis to exit lysosomes and activate mTORC1. Pancreatic cancer cells, which use macropinocytosed protein as a nutrient source, require SLC38A9 to form tumors. Thus, through SLC38A9, arginine serves as a lysosomal messenger that couples mTORC1 activation to the release from lysosomes of the essential amino acids needed to drive cell growth.
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Affiliation(s)
- Gregory A Wyant
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Rachel L Wolfson
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School M.D.-Ph.D. Program, Daniel C. Tosteson Medical Education Center, 260 Longwood Avenue, Boston, MA 02115, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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21
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Wang Y, Wang J, Wu S, Zhu H. The unexpected structures of hepatitis C virus envelope proteins. Exp Ther Med 2017; 14:1859-1865. [PMID: 28962094 PMCID: PMC5609170 DOI: 10.3892/etm.2017.4745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 11/18/2016] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) envelope proteins are essential not only for maintaining the viral life cycle, but also for evading the host's immune response and in clinical intervention. A thorough understanding of HCV envelope proteins depends on the availability of detailed structural information. Two crystal structures of the E2 core portion and of the E2 ectodomain, and one structure of the N-terminus of E1 ectodomain have shed new light on the complexity of HCV envelope proteins. In addition, the full-length E1-E2 complex has recently been modeled. The present review focuses on these advancements, introduces the recently solved structures and their biological implications and proposes novel ideas for studying the full-length E1-E2 complex.
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Affiliation(s)
- Yunyun Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Shanshan Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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22
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Rives ML, Javitch JA, Wickenden AD. Potentiating SLC transporter activity: Emerging drug discovery opportunities. Biochem Pharmacol 2017; 135:1-11. [DOI: 10.1016/j.bcp.2017.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/13/2017] [Indexed: 12/12/2022]
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23
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Grouleff J, Koldsø H, Miao Y, Schiøtt B. Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT. ACS Chem Neurosci 2017; 8:619-628. [PMID: 27966884 DOI: 10.1021/acschemneuro.6b00359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human monoamine transporters (MATs) facilitate the reuptake of monoamine neurotransmitters from the synaptic cleft. MATs are linked to a number of neurological diseases and are the targets of both therapeutic and illicit drugs. Until recently, no high-resolution structures of the human MATs existed, and therefore, studies of this transporter family have relied on investigations of the homologues bacterial transporters such as the leucine transporter LeuT, which has been crystallized in several conformational states. A two-substrate transport mechanism has been suggested for this transporter family, which entails that high-affinity binding of a second substrate in an extracellular site is necessary for the substrate in the central binding site to be transported. Compelling evidence for this mechanism has been presented, however, a number of equally compelling accounts suggest that the transporters function through a mechanism involving only a single substrate and a single high-affinity site. To shed light on this apparent contradiction, we have performed extensive molecular dynamics simulations of LeuT in the outward-occluded conformation with either one or two substrates bound to the transporter. We have also calculated the substrate binding affinity in each of the two proposed binding sites through rigorous free energy simulations. Results show that substrate binding is unstable in the extracellular vestibule and the substrate binding affinity within the suggested extracellular site is very low (0.2 and 3.3 M for the two dominant binding modes) compared to the central substrate binding site (14 nM). This suggests that for LeuT in the outward-occluded conformation only a single high-affinity substrate binding site exists.
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Affiliation(s)
- Julie Grouleff
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Heidi Koldsø
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Yinglong Miao
- Howard
Hughes Medical Institute and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
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24
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Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer. Proc Natl Acad Sci U S A 2017; 114:E1786-E1795. [PMID: 28223522 DOI: 10.1073/pnas.1613293114] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) are integral membrane proteins responsible for the sodium-dependent reuptake of small-molecule neurotransmitters from the synaptic cleft. The symporters for the biogenic amines serotonin (SERT), dopamine (DAT), and norepinephrine (NET) are targets of multiple psychoactive agents, and their dysfunction has been implicated in numerous neuropsychiatric ailments. LeuT, a thermostable eubacterial NSS homolog, has been exploited as a model protein for NSS members to canvass the conformational mechanism of transport with a combination of X-ray crystallography, cysteine accessibility, and solution spectroscopy. Despite yielding remarkable insights, these studies have primarily been conducted with protein in the detergent-solubilized state rather than embedded in a membrane mimic. In addition, solution spectroscopy has required site-specific labeling of nonnative cysteines, a labor-intensive process occasionally resulting in diminished transport and/or binding activity. Here, we overcome these limitations by reconstituting unlabeled LeuT in phospholipid bilayer nanodiscs, subjecting them to hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS), and facilitating interpretation of the data with molecular dynamics simulations. The data point to changes of accessibility and dynamics of structural elements previously implicated in the transport mechanism, in particular transmembrane helices (TMs) 1a and 7 as well as extracellular loops (ELs) 2 and 4. The results therefore illuminate the value of this strategy for interrogating the conformational mechanism of the more clinically significant mammalian membrane proteins including SERT and DAT, neither of which tolerates complete removal of endogenous cysteines, and whose activity is heavily influenced by neighboring lipids.
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25
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Erlendsson S, Gotfryd K, Larsen FH, Mortensen JS, Geiger MA, van Rossum BJ, Oschkinat H, Gether U, Teilum K, Loland CJ. Direct assessment of substrate binding to the Neurotransmitter:Sodium Symporter LeuT by solid state NMR. eLife 2017; 6. [PMID: 28117663 PMCID: PMC5262378 DOI: 10.7554/elife.19314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/02/2017] [Indexed: 12/21/2022] Open
Abstract
The Neurotransmitter:Sodium Symporters (NSSs) represent an important class of proteins mediating sodium-dependent uptake of neurotransmitters from the extracellular space. The substrate binding stoichiometry of the bacterial NSS protein, LeuT, and thus the principal transport mechanism, has been heavily debated. Here we used solid state NMR to specifically characterize the bound leucine ligand and probe the number of binding sites in LeuT. We were able to produce high-quality NMR spectra of substrate bound to microcrystalline LeuT samples and identify one set of sodium-dependent substrate-specific chemical shifts. Furthermore, our data show that the binding site mutants F253A and L400S, which probe the major S1 binding site and the proposed S2 binding site, respectively, retain sodium-dependent substrate binding in the S1 site similar to the wild-type protein. We conclude that under our experimental conditions there is only one detectable leucine molecule bound to LeuT. DOI:http://dx.doi.org/10.7554/eLife.19314.001 All living cells need amino acids – the building blocks of proteins – in order to survive, yet few cells can make all the amino acids that they need. Instead, transporter proteins in cell membranes must take these molecules from the outside of the cell and release them to the inside. Some cells, including those in the brain, also release amino acids and molecules derived from them into the spaces outside of the cell to send signals to other nearby cells. Again, transporter proteins must move these signaling molecules back inside cells, to stop the signaling and to allow the molecules to be recycled. Importantly, problems with these uptake mechanisms have been linked to disorders such as depression, epilepsy and Parkinson’s disease. One family of transporters involved in the uptake of amino acids are the “Neurotransmitter:Sodium Symporters”. Though these proteins are involved in processes that are fundamental to life, it remains unclear exactly how they work. Specifically, it has been heavily debated whether this family of transporters require one or two amino acid molecules to bind at the same time in order to help transport them across the membrane. Now Erlendsson, Gotfryd et al. have analyzed a bacterial protein in the Neurotransmitter:Sodium Symporter family. This transporter takes up an amino acid called leucine into cells, and is commonly used as a model to understand this family of transporter proteins more generally. Using a technique called solid state nuclear magnetic resonance, Erlendsson, Gotfryd et al. could detect a single molecule of leucine bound to each transporter, but not a second one. This technique could also pinpoint that the leucine was located at the transporter’s central binding site. Leucine was never found at the proposed secondary binding site. Together these findings suggest that only one molecule of leucine binds to the transporter at any one time, and that it binds to the transporter’s central binding site. Erlendsson, Gotfryd et al. have shown now how solid state nuclear magnetic resonance can be used to explore in detail how Neurotransmitter:Sodium Symporters move molecules across cell membranes. The next challenge is to use the same experimental setup to characterize other Neurotransmitter:Sodium Symporters. Doing so could potentially lay the groundwork for designing more specific and improved drugs to treat disorders like depression and Parkinson’s disease. DOI:http://dx.doi.org/10.7554/eLife.19314.002
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Affiliation(s)
- Simon Erlendsson
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kamil Gotfryd
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Hofmann Larsen
- Quality and Technology, Department of Food Science, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Sigurd Mortensen
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ulrik Gether
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claus J Loland
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Lundbeck Foundation Center for Biomembranes in Nanomedicine, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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26
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Razavi AM, Khelashvili G, Weinstein H. A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter. Sci Rep 2017; 7:40076. [PMID: 28059145 PMCID: PMC5216462 DOI: 10.1038/srep40076] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/30/2016] [Indexed: 12/24/2022] Open
Abstract
The dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation. We have constructed Markov State Models (MSMs) from extensive molecular dynamics simulations of human DAT (hDAT) to explore the mechanism of this sodium release. Our results quantify the release process triggered by hydration of the Na2 site that occurs concomitantly with a conformational transition from an outward-facing to an inward-facing state of the transporter. The kinetics of the release process are computed from the MSM, and transition path theory is used to identify the most probable sodium release pathways. An intermediate state is discovered on the sodium release pathway, and the results reveal the importance of various modes of interaction of the N-terminus of hDAT in controlling the pathways of release.
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Affiliation(s)
- Asghar M Razavi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA.,Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY 10065, USA
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27
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Sealover NR, Felts B, Kuntz CP, Jarrard RE, Hockerman GH, Lamb PW, Barker EL, Henry LK. The external gate of the human and Drosophila serotonin transporters requires a basic/acidic amino acid pair for 3,4-methylenedioxymethamphetamine (MDMA) translocation and the induction of substrate efflux. Biochem Pharmacol 2016; 120:46-55. [PMID: 27638414 DOI: 10.1016/j.bcp.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022]
Abstract
The substituted amphetamine, 3,4-methylenedioxy-methamphetamine (MDMA, ecstasy), is a widely used drug of abuse that induces non-exocytotic release of serotonin, dopamine, and norepinephrine through their cognate transporters as well as blocking the reuptake of neurotransmitter by the same transporters. The resulting dramatic increase in volume transmission and signal duration of neurotransmitters leads to psychotropic, stimulant, and entactogenic effects. The mechanism by which amphetamines drive reverse transport of the monoamines remains largely enigmatic, however, promising outcomes for the therapeutic utility of MDMA for post-traumatic stress disorder and the long-time use of the dopaminergic and noradrenergic-directed amphetamines in treatment of attention-deficit hyperactivity disorder and narcolepsy increases the importance of understanding this phenomenon. Previously, we identified functional differences between the human and Drosophila melanogaster serotonin transporters (hSERT and dSERT, respectively) revealing that MDMA is an effective substrate for hSERT but not dSERT even though serotonin is a potent substrate for both transporters. Chimeric dSERT/hSERT transporters revealed that the molecular components necessary for recognition of MDMA as a substrate was linked to regions of the protein flanking transmembrane domains (TM) V through IX. Here, we performed species-scanning mutagenesis of hSERT, dSERT and C. elegans SERT (ceSERT) along with biochemical and electrophysiological analysis and identified a single amino acid in TM10 (Glu394, hSERT; Asn484, dSERT, Asp517, ceSERT) that is primarily responsible for the differences in MDMA recognition. Our findings reveal that an acidic residue is necessary at this position for MDMA recognition as a substrate and serotonin releaser.
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Affiliation(s)
- Natalie R Sealover
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Bruce Felts
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Charles P Kuntz
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Rachel E Jarrard
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | - Gregory H Hockerman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States
| | | | - Eric L Barker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, West Lafayette, IN 47907, United States.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States.
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28
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Khelashvili G, Schmidt SG, Shi L, Javitch JA, Gether U, Loland CJ, Weinstein H. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290. J Biol Chem 2016; 291:19786-99. [PMID: 27474737 DOI: 10.1074/jbc.m116.731455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K(+) ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na(+) Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K(+) binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na(+) ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na(+) in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu(290), either charged or neutral, point to the Glu(290) protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a "water gate" opens through coordinated motions of residues Leu(25), Tyr(108), and Phe(253) The resulting water channel enables the binding/dissociation of the Na(+) and K(+) ions that are prevalent, respectively, in the extracellular and intracellular environments.
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Affiliation(s)
- George Khelashvili
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065,
| | - Solveig Gaarde Schmidt
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224
| | - Jonathan A Javitch
- the Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, and
| | - Ulrik Gether
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Harel Weinstein
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065
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29
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Zhen J, Reith MEA. Impact of disruption of secondary binding site S2 on dopamine transporter function. J Neurochem 2016; 138:694-9. [PMID: 27315582 DOI: 10.1111/jnc.13704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/30/2022]
Abstract
The structures of the leucine transporter, drosophila dopamine transporter, and human serotonin transporter show a secondary binding site (designated S2 ) for drugs and substrate in the extracellular vestibule toward the membrane exterior in relation to the primary substrate recognition site (S1 ). The present experiments are aimed at disrupting S2 by mutating Asp476 and Ile159 to Ala. Both mutants displayed a profound decrease in [(3) H]DA uptake compared with wild-type associated with a reduced turnover rate kcat . This was not caused by a conformational bias as the mutants responded to Zn(2+) (10 μM) similarly as WT. The dopamine transporters with either the D476A or I159A mutation both displayed a higher Ki for dopamine for the inhibition of [3H](-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane binding than did the WT transporter, in accordance with an allosteric interaction between the S1 and S2 sites. The results provide evidence in favor of a general applicability of the two-site allosteric model of the Javitch/Weinstein group from LeuT to dopamine transporter and possibly other monoamine transporters. X-ray structures of transporters closely related to the dopamine (DA) transporter show a secondary binding site S2 in the extracellular vestibule proximal to the primary binding site S1 which is closely linked to one of the Na(+) binding sites. This work examines the relationship between S2 and S1 sites. We found that S2 site impairment severely reduced DA transport and allosterically reduced S1 site affinity for the cocaine analog [(3) H]CFT. Our results are the first to lend direct support for the application of the two-site allosteric model, advanced for bacterial LeuT, to the human DA transporter. The model states that, after binding of the first DA molecule (DA1 ) to the primary S1 site (along with Na(+) ), binding of a second DA (DA2 ) to the S2 site triggers, through an allosteric interaction, the release of DA1 and Na(+) into the cytoplasm.
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Affiliation(s)
- Juan Zhen
- Department of Psychiatry, New York University School of Medicine, New York City, New York, USA
| | - Maarten E A Reith
- Department of Psychiatry, New York University School of Medicine, New York City, New York, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York City, New York, USA
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30
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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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31
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LeVine MV, Khelashvili G, Shi L, Quick M, Javitch JA, Weinstein H. Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles. Biochemistry 2016; 55:850-9. [PMID: 26811944 PMCID: PMC4757857 DOI: 10.1021/acs.biochem.5b01268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Recent
work has shown that the choice of the type and concentration
of detergent used for the solubilization of membrane proteins can
strongly influence the results of functional experiments. In particular,
the amino acid transporter LeuT can bind two substrate molecules in
low concentrations of n-dodecyl β-d-maltopyranoside (DDM), whereas high concentrations reduce the molar
binding stoichiometry to 1:1. Subsequent molecular dynamics (MD) simulations
of LeuT in DDM proteomicelles revealed that DDM can penetrate to the
extracellular vestibule and make stable contacts in the functionally
important secondary substrate binding site (S2), suggesting a potential
competitive mechanism for the reduction in binding stoichiometry.
Because annular lipids can be retained during solubilization, we performed
MD simulations of LeuT proteomicelles at various stages of the solubilization
process. We find that at low DDM concentrations, lipids are retained
around the protein and penetration of detergent into the S2 site does
not occur, whereas at high concentrations, lipids are displaced and
the probability of DDM binding in the S2 site is increased. This behavior
is dependent on the type of detergent, however, as we find in the
simulations that the detergent lauryl maltose-neopentyl glycol, which
is approximately twice the size of DDM and structurally more closely
resembles lipids, does not penetrate the protein even at very high
concentrations. We present functional studies that confirm the computational
findings, emphasizing the need for careful consideration of experimental
conditions, and for cautious interpretation of data in gathering mechanistic
information about membrane proteins.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health , Baltimore, Maryland 21224, United States
| | | | - Jonathan A Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute , New York, New York 10032, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University , New York, New York 10065, United States
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32
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Wein T, Petrera M, Allmendinger L, Höfner G, Pabel J, Wanner KT. Different Binding Modes of Small and Large Binders of GAT1. ChemMedChem 2016; 11:509-18. [DOI: 10.1002/cmdc.201500534] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Wein
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | | | - Lars Allmendinger
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Georg Höfner
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Jörg Pabel
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
| | - Klaus T. Wanner
- Department for Pharmacy-Center for Drug Research; Ludwig-Maximilians-Universität München; Butenandtstr. 7-13 81377 Munich Germany
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33
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Dörr JM, Scheidelaar S, Koorengevel MC, Dominguez JJ, Schäfer M, van Walree CA, Killian JA. The styrene-maleic acid copolymer: a versatile tool in membrane research. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2016; 45:3-21. [PMID: 26639665 PMCID: PMC4698303 DOI: 10.1007/s00249-015-1093-y] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 10/28/2022]
Abstract
A new and promising tool in membrane research is the detergent-free solubilization of membrane proteins by styrene-maleic acid copolymers (SMAs). These amphipathic molecules are able to solubilize lipid bilayers in the form of nanodiscs that are bounded by the polymer. Thus, membrane proteins can be directly extracted from cells in a water-soluble form while conserving a patch of native membrane around them. In this review article, we briefly discuss current methods of membrane protein solubilization and stabilization. We then zoom in on SMAs, describe their physico-chemical properties, and discuss their membrane-solubilizing effect. This is followed by an overview of studies in which SMA has been used to isolate and investigate membrane proteins. Finally, potential future applications of the methodology are discussed for structural and functional studies on membrane proteins in a near-native environment and for characterizing protein-lipid and protein-protein interactions.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Juan J Dominguez
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, 5001, Australia
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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34
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman A, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rong Zhu
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Doris Sinwel
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Peter S. Hasenhuetl
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Vivek Kumar
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Peng Zhang
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH; Mooslackengasse 17 1190 Vienna Austria
| | - Marion Holy
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Andreas Karner
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Hermann J. Gruber
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Harald H. Sitte
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Peter Hinterdorfer
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
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35
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman AH, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015; 55:1719-22. [PMID: 26695726 DOI: 10.1002/anie.201508755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/11/2015] [Indexed: 11/11/2022]
Abstract
Controversy regarding the number and function of ligand binding sites in neurotransmitter/sodium symporters arose from conflicting data in crystal structures and molecular pharmacology. Here, we have designed novel tools for atomic force microscopy that directly measure the interaction forces between the serotonin transporter (SERT) and the S- and R-enantiomers of citalopram on the single molecule level. This approach is based on force spectroscopy, which allows for the extraction of dynamic information under physiological conditions thus inaccessible via X-ray crystallography. Two distinct populations of characteristic binding strengths of citalopram to SERT were revealed in Na(+)-containing buffer. In contrast, in Li(+) -containing buffer, SERT showed only low force interactions. Conversely, the vestibular mutant SERT-G402H merely displayed the high force population. These observations provide physical evidence for the existence of two binding sites in SERT when accessed in a physiological context. Competition experiments revealed that these two sites are allosterically coupled and exert reciprocal modulation.
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Affiliation(s)
- Rong Zhu
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Doris Sinwel
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Peter S Hasenhuetl
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Vivek Kumar
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Peng Zhang
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Marion Holy
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Andreas Karner
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Hermann J Gruber
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Harald H Sitte
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria.
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36
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Tavoulari S, Margheritis E, Nagarajan A, DeWitt DC, Zhang YW, Rosado E, Ravera S, Rhoades E, Forrest LR, Rudnick G. Two Na+ Sites Control Conformational Change in a Neurotransmitter Transporter Homolog. J Biol Chem 2015; 291:1456-71. [PMID: 26582198 DOI: 10.1074/jbc.m115.692012] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 12/13/2022] Open
Abstract
In LeuT, a prokaryotic homolog of neurotransmitter transporters, Na(+) stabilizes outward-open conformational states. We examined how each of the two LeuT Na(+) binding sites contributes to Na(+)-dependent closure of the cytoplasmic pathway using biochemical and biophysical assays of conformation. Mutating either of two residues that contribute to the Na2 site completely prevented cytoplasmic closure in response to Na(+), suggesting that Na2 is essential for this conformational change, whereas Na1 mutants retained Na(+) responsiveness. However, mutation of Na1 residues also influenced the Na(+)-dependent conformational change in ways that varied depending on the position mutated. Computational analyses suggest those mutants influence the ability of Na1 binding to hydrate the substrate pathway and perturb an interaction network leading to the extracellular gate. Overall, the results demonstrate that occupation of Na2 stabilizes outward-facing conformations presumably through a direct interaction between Na(+) and transmembrane helices 1 and 8, whereas Na(+) binding at Na1 influences conformational change through a network of intermediary interactions. The results also provide evidence that N-terminal release and helix motions represent distinct steps in cytoplasmic pathway opening.
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Affiliation(s)
| | | | - Anu Nagarajan
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Rockville, Maryland 20852
| | - David C DeWitt
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | | | | | | | - Elizabeth Rhoades
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Lucy R Forrest
- the Computational Structural Biology Section, NINDS, National Institutes of Health, Rockville, Maryland 20852
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37
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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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38
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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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39
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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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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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41
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Claxton DP, Kazmier K, Mishra S, Mchaourab HS. Navigating Membrane Protein Structure, Dynamics, and Energy Landscapes Using Spin Labeling and EPR Spectroscopy. Methods Enzymol 2015; 564:349-87. [PMID: 26477257 DOI: 10.1016/bs.mie.2015.07.026] [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] [Indexed: 12/22/2022]
Abstract
A detailed understanding of the functional mechanism of a protein entails the characterization of its energy landscape. Achieving this ambitious goal requires the integration of multiple approaches including determination of high-resolution crystal structures, uncovering conformational sampling under distinct biochemical conditions, characterizing the kinetics and thermodynamics of transitions between functional intermediates using spectroscopic techniques, and interpreting and harmonizing the data into novel computational models. With increasing sophistication in solution-based and ensemble-oriented biophysical approaches such as electron paramagnetic resonance (EPR) spectroscopy, atomic resolution structural information can be directly linked to conformational sampling in solution. Here, we detail how recent methodological and technological advances in EPR spectroscopy have contributed to the elucidation of membrane protein mechanisms. Furthermore, we aim to assist investigators interested in pursuing EPR studies by providing an introduction to the technique, a primer on experimental design, and a description of the practical considerations of the method toward generating high quality data.
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Affiliation(s)
- Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| | - Kelli Kazmier
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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42
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Stolzenberg S, Quick M, Zhao C, Gotfryd K, Khelashvili G, Gether U, Loland CJ, Javitch JA, Noskov S, Weinstein H, Shi L. Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. J Biol Chem 2015; 290:13992-4003. [PMID: 25869126 PMCID: PMC4447972 DOI: 10.1074/jbc.m114.625343] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/16/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) terminate neurotransmission by Na+-dependent reuptake of released neurotransmitters. Previous studies suggested that Na+-binding reconfigures dynamically coupled structural elements in an allosteric interaction network (AIN) responsible for function-related conformational changes, but the intramolecular pathway of this mechanism has remained uncharted. We describe a new approach for the modeling and analysis of intramolecular dynamics in the bacterial NSS homolog LeuT. From microsecond-scale molecular dynamics simulations and cognate experimental verifications in both LeuT and human dopamine transporter (hDAT), we apply the novel method to identify the composition and the dynamic properties of their conserved AIN. In LeuT, two different perturbations disrupting Na+ binding and transport (i.e. replacing Na+ with Li+ or the Y268A mutation at the intracellular gate) affect the AIN in strikingly similar ways. In contrast, other mutations that affect the intracellular gate (i.e. R5A and D369A) do not significantly impair Na+ cooperativity and transport. Our analysis shows these perturbations to have much lesser effects on the AIN, underscoring the sensitivity of this novel method to the mechanistic nature of the perturbation. Notably, this set of observations holds as well for hDAT, where the aligned Y335A, R60A, and D436A mutations also produce different impacts on Na+ dependence. Thus, the detailed AIN generated from our method is shown to connect Na+ binding with global conformational changes that are critical for the transport mechanism. That the AIN between the Na+ binding sites and the intracellular gate in bacterial LeuT resembles that in eukaryotic hDAT highlights the conservation of allosteric pathways underlying NSS function.
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Affiliation(s)
- Sebastian Stolzenberg
- From the Department of Physiology and Biophysics and the Department of Physics, Cornell University, Ithaca, New York, 14850
| | - Matthias Quick
- the Departments of Psychiatry and the Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032
| | - Chunfeng Zhao
- the Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Kamil Gotfryd
- the Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark, and
| | | | - Ulrik Gether
- the Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark, and
| | - Claus J Loland
- the Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark, and
| | - 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
| | - Sergei Noskov
- the Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Harel Weinstein
- From the Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, 10065,
| | - Lei Shi
- From the Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, 10065, the Computational Chemistry and Molecular Biophysics Unit, NIDA, Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224
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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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44
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Singh SK, Pal A. Biophysical Approaches to the Study of LeuT, a Prokaryotic Homolog of Neurotransmitter Sodium Symporters. Methods Enzymol 2015; 557:167-98. [PMID: 25950965 DOI: 10.1016/bs.mie.2015.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ion-coupled secondary transport is utilized by multiple integral membrane proteins as a means of achieving the thermodynamically unfavorable translocation of solute molecules across the lipid bilayer. The chemical nature of these molecules is diverse and includes sugars, amino acids, neurotransmitters, and other ions. LeuT is a sodium-coupled, nonpolar amino acid symporter and eubacterial member of the solute carrier 6 (SLC6) family of Na(+)/Cl(-)-dependent neurotransmitter transporters. Eukaryotic counterparts encompass the clinically and pharmacologically significant transporters for γ-aminobutyric acid (GABA), glycine, serotonin (5-hydroxytryptamine, 5-HT), dopamine (DA), and norepinephrine (NE). Since the crystal structure of LeuT was first solved in 2005, subsequent crystallographic, binding, flux, and spectroscopic studies, complemented with homology modeling and molecular dynamic simulations, have allowed this protein to emerge as a remarkable mechanistic paradigm for both the SLC6 class as well as several other sequence-unrelated SLCs whose members possess astonishingly similar architectures. Despite yielding groundbreaking conceptual advances, this vast treasure trove of data has also been the source of contentious hypotheses. This chapter will present a historical scientific overview of SLC6s; recount how the initial and subsequent LeuT structures were solved, describing the insights they each provided; detail the accompanying functional techniques, emphasizing how they either supported or refuted the static crystallographic data; and assemble these individual findings into a mechanism of transport and inhibition.
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Affiliation(s)
- Satinder K Singh
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Aritra Pal
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut, USA
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45
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Reith ME, Blough BE, Hong WC, Jones KT, Schmitt KC, Baumann MH, Partilla JS, Rothman RB, Katz JL. Behavioral, biological, and chemical perspectives on atypical agents targeting the dopamine transporter. Drug Alcohol Depend 2015; 147:1-19. [PMID: 25548026 PMCID: PMC4297708 DOI: 10.1016/j.drugalcdep.2014.12.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/04/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Treatment of stimulant-use disorders remains a formidable challenge, and the dopamine transporter (DAT) remains a potential target for antagonist or agonist-like substitution therapies. METHODS This review focuses on DAT ligands, such as benztropine, GBR 12909, modafinil, and DAT substrates derived from phenethylamine or cathinone that have atypical DAT-inhibitor effects, either in vitro or in vivo. The compounds are described from a molecular mechanistic, behavioral, and medicinal-chemical perspective. RESULTS Possible mechanisms for atypicality at the molecular level can be deduced from the conformational cycle for substrate translocation. For each conformation, a crystal structure of a bacterial homolog is available, with a possible role of cholesterol, which is also present in the crystal of Drosophila DAT. Although there is a direct relationship between behavioral potencies of most DAT inhibitors and their DAT affinities, a number of compounds bind to the DAT and inhibit dopamine uptake but do not share cocaine-like effects. Such atypical behavior, depending on the compound, may be related to slow DAT association, combined sigma-receptor actions, or bias for cytosol-facing DAT. Some structures are sterically small enough to serve as DAT substrates but large enough to also inhibit transport. Such compounds may display partial DA releasing effects, and may be combined with release or uptake inhibition at other monoamine transporters. CONCLUSIONS Mechanisms of atypical DAT inhibitors may serve as targets for the development of treatments for stimulant abuse. These mechanisms are novel and their further exploration may produce compounds with unique therapeutic potential as treatments for stimulant abuse.
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Affiliation(s)
- Maarten E.A. Reith
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA,Corresponding author: Maarten E.A. Reith, Department of Psychiatry, Alexandria Center of Life Sciences, New York University School of Medicine, 450 E 29th Street, Room 803, New York, NY 10016. Tel.: 212 - 263 8267; Fax: 212 – 263 8183;
| | - Bruce E. Blough
- Center for Drug Discovery, Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - Weimin C. Hong
- Psychobiology Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kymry T. Jones
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Kyle C. Schmitt
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Michael H. Baumann
- Medicinal Chemistry Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - John S. Partilla
- Medicinal Chemistry Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Richard B. Rothman
- Medicinal Chemistry Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jonathan L. Katz
- Psychobiology Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
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46
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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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47
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Zomot E, Gur M, Bahar I. Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. J Biol Chem 2014; 290:544-55. [PMID: 25381247 PMCID: PMC4281755 DOI: 10.1074/jbc.m114.617555] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial sodium-coupled leucine/alanine transporter LeuT is broadly used as a model system for studying the transport mechanism of neurotransmitters because of its structural and functional homology to mammalian transporters such as serotonin, dopamine, or norepinephrine transporters, and because of the resolution of its structure in different states. Although the binding sites (S1 for substrate, and Na1 and Na2 for two co-transported sodium ions) have been resolved, we still lack a mechanistic understanding of coupled Na(+)- and substrate-binding events. We present here results from extensive (>20 μs) unbiased molecular dynamics simulations generated using the latest computing technology. Simulations show that sodium binds initially the Na1 site, but not Na2, and, consistently, sodium unbinding/escape to the extracellular (EC) region first takes place at Na2, succeeded by Na1. Na2 diffusion back to the EC medium requires prior dissociation of substrate from S1. Significantly, Na(+) binding (and unbinding) consistently involves a transient binding to a newly discovered site, Na1″, near S1, as an intermediate state. A robust sequence of substrate uptake events coupled to sodium bindings and translocations between those sites assisted by hydration emerges from the simulations: (i) bindings of a first Na(+) to Na1″, translocation to Na1, a second Na(+) to vacated Na1″ and then to Na2, and substrate to S1; (ii) rotation of Phe(253) aromatic group to seclude the substrate from the EC region; and (iii) concerted tilting of TM1b and TM6a toward TM3 and TM8 to close the EC vestibule.
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Affiliation(s)
- Elia Zomot
- From the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Mert Gur
- From the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Ivet Bahar
- From the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
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48
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Cheng MH, Bahar I. Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle. PLoS Comput Biol 2014; 10:e1003879. [PMID: 25299050 PMCID: PMC4191883 DOI: 10.1371/journal.pcbi.1003879] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 08/26/2014] [Indexed: 11/19/2022] Open
Abstract
Neurotransmitter: sodium symporters (NSSs) regulate neuronal signal transmission by clearing excess neurotransmitters from the synapse, assisted by the co-transport of sodium ions. Extensive structural data have been collected in recent years for several members of the NSS family, which opened the way to structure-based studies for a mechanistic understanding of substrate transport. Leucine transporter (LeuT), a bacterial orthologue, has been broadly adopted as a prototype in these studies. This goal has been elusive, however, due to the complex interplay of global and local events as well as missing structural data on LeuT N-terminal segment. We provide here for the first time a comprehensive description of the molecular events leading to substrate/Na+ release to the postsynaptic cell, including the structure and dynamics of the N-terminal segment using a combination of molecular simulations. Substrate and Na+-release follows an influx of water molecules into the substrate/Na+-binding pocket accompanied by concerted rearrangements of transmembrane helices. A redistribution of salt bridges and cation-π interactions at the N-terminal segment prompts substrate release. Significantly, substrate release is followed by the closure of the intracellular gate and a global reconfiguration back to outward-facing state to resume the transport cycle. Two minimally hydrated intermediates, not structurally resolved to date, are identified: one, substrate-bound, stabilized during the passage from outward- to inward-facing state (holo-occluded), and another, substrate-free, along the reverse transition (apo-occluded).
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States of America
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States of America
- * E-mail:
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49
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Nolan TL, Geffert LM, Kolber BJ, Madura JD, Surratt CK. Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter. ACS Chem Neurosci 2014; 5:784-92. [PMID: 25003748 PMCID: PMC4176318 DOI: 10.1021/cn500133b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
![]()
Discovery of new inhibitors of the
plasmalemmal monoamine transporters
(MATs) continues to provide pharmacotherapeutic options for depression,
addiction, attention deficit disorders, psychosis, narcolepsy, and
Parkinson’s disease. The windfall of high-resolution MAT structural
information afforded by X-ray crystallography has enabled the construction
of credible computational models. Elucidation of lead compounds, creation
of compound structure–activity series, and pharmacologic testing
are staggering expenses that could be reduced by using a MAT computational
model for virtual screening (VS) of structural libraries containing
millions of compounds. Here, VS of the PubChem small molecule structural
database using the S1 (primary substrate) ligand pocket of a serotonin
transporter homology model yielded 19 prominent “hit”
compounds. In vitro pharmacology of these VS hits revealed four structurally
unique MAT substrate uptake inhibitors with high nanomolar affinity
at one or more of the three MATs. In vivo characterization of three
of these hits revealed significant activity in a mouse model of acute
depression at doses that did not elicit untoward locomotor effects.
This constitutes the first report of MAT inhibitor discovery using
exclusively the primary substrate pocket as a VS tool. Novel-scaffold
MAT inhibitors offer hope of new medications that lack the many classic
adverse effects of existing antidepressant drugs.
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Affiliation(s)
- Tammy L. Nolan
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Laura M. Geffert
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Benedict J. Kolber
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffry D. Madura
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Christopher K. Surratt
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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HCV E2 core structures and mAbs: something is still missing. Drug Discov Today 2014; 19:1964-70. [PMID: 25172800 DOI: 10.1016/j.drudis.2014.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/17/2014] [Accepted: 08/21/2014] [Indexed: 02/07/2023]
Abstract
The lack of structural information on hepatitis C virus (HCV) surface proteins has so far hampered the development of effective vaccines. Recently, two crystallographic structures have described the core portion (E2c) of E2 surface glycoprotein, the primary mediator of HCV entry. Despite the importance of these studies, the E2 overall structure is still unknown and, most importantly, several biochemical and functional studies are in disagreement with E2c structures. Here, the main literature will be discussed and an alternative disulfide bridge pattern will be proposed, based on unpublished human monoclonal antibody reactivity. A modeling strategy aiming at recapitulating the available structural and functional studies of E2 will also be proposed.
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