1
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van Veggel L, Mocking TA, Sijben HJ, Liu R, Gorostiola González M, Dilweg MA, Royakkers J, Li A, Kumar V, Dong YY, Bullock A, Sauer DB, Diliën H, van Westen GJ, Schreiber R, Heitman LH, Vanmierlo T. Still in Search for an EAAT Activator: GT949 Does Not Activate EAAT2, nor EAAT3 in Impedance and Radioligand Uptake Assays. ACS Chem Neurosci 2024; 15:1424-1431. [PMID: 38478848 PMCID: PMC10995951 DOI: 10.1021/acschemneuro.3c00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Excitatory amino acid transporters (EAATs) are important regulators of amino acid transport and in particular glutamate. Recently, more interest has arisen in these transporters in the context of neurodegenerative diseases. This calls for ways to modulate these targets to drive glutamate transport, EAAT2 and EAAT3 in particular. Several inhibitors (competitive and noncompetitive) exist to block glutamate transport; however, activators remain scarce. Recently, GT949 was proposed as a selective activator of EAAT2, as tested in a radioligand uptake assay. In the presented research, we aimed to validate the use of GT949 to activate EAAT2-driven glutamate transport by applying an innovative, impedance-based, whole-cell assay (xCELLigence). A broad range of GT949 concentrations in a variety of cellular environments were tested in this assay. As expected, no activation of EAAT3 could be detected. Yet, surprisingly, no biological activation of GT949 on EAAT2 could be observed in this assay either. To validate whether the impedance-based assay was not suited to pick up increased glutamate uptake or if the compound might not induce activation in this setup, we performed radioligand uptake assays. Two setups were utilized; a novel method compared to previously published research, and in a reproducible fashion copying the methods used in the existing literature. Nonetheless, activation of neither EAAT2 nor EAAT3 could be observed in these assays. Furthermore, no evidence of GT949 binding or stabilization of purified EAAT2 could be observed in a thermal shift assay. To conclude, based on experimental evidence in the present study GT949 requires specific assay conditions, which are difficult to reproduce, and the compound cannot simply be classified as an activator of EAAT2 based on the presented evidence. Hence, further research is required to develop the tools needed to identify new EAAT modulators and use their potential as a therapeutic target.
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Affiliation(s)
- Lieve van Veggel
- Department
of Neuroscience, BIOMED Biomedical Research Institute, Faculty of
Medicine and Life Sciences, Hasselt University, 3590 Hasselt, Belgium
- Department
of Psychiatry and Neuropsychology, Division of Translational Neuroscience,
European Graduate School of Neuroscience, School for Mental Health
and Neuroscience, Maastricht University, 6200 Maastricht, The Netherlands
- University
MS Center (UMSC), 3900 Hasselt-Pelt, Belgium
| | - Tamara A.M. Mocking
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Hubert J. Sijben
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Rongfang Liu
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Marina Gorostiola González
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Majlen A. Dilweg
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Jeroen Royakkers
- Sensor
Engineering
Department, Faculty of Science and Engineering, Maastricht University, 6200 Maastricht, The Netherlands
| | - Anna Li
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, U.K.
| | - Vijay Kumar
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, U.K.
| | - Yin Yao Dong
- Nuffield
Department of Clinical Neurosciences, Weatherall Institute of Molecular
Medicine, University of Oxford, OX3 7BN Oxford, U.K.
| | - Alex Bullock
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, U.K.
| | - David B. Sauer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, U.K.
| | - Hanne Diliën
- Sensor
Engineering
Department, Faculty of Science and Engineering, Maastricht University, 6200 Maastricht, The Netherlands
| | - Gerard J.P. van Westen
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
| | - Rudy Schreiber
- Section
of Psychopharmacology, Neuropsychology and Psychopharmacology, Faculty
of Psychology and Neuroscience, Maastricht
University, 6200 Maastricht, The Netherlands
| | - Laura H. Heitman
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 Leiden, The Netherlands
- Oncode
Institute, Einsteinweg
55, 2333 Leiden, The Netherlands
| | - Tim Vanmierlo
- Department
of Neuroscience, BIOMED Biomedical Research Institute, Faculty of
Medicine and Life Sciences, Hasselt University, 3590 Hasselt, Belgium
- Department
of Psychiatry and Neuropsychology, Division of Translational Neuroscience,
European Graduate School of Neuroscience, School for Mental Health
and Neuroscience, Maastricht University, 6200 Maastricht, The Netherlands
- University
MS Center (UMSC), 3900 Hasselt-Pelt, Belgium
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2
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Liang Q, Chi G, Cirqueira L, Zhi L, Marasco A, Pilati N, Gunthorpe MJ, Alvaro G, Large CH, Sauer DB, Treptow W, Covarrubias M. The binding and mechanism of a positive allosteric modulator of Kv3 channels. Nat Commun 2024; 15:2533. [PMID: 38514618 PMCID: PMC10957983 DOI: 10.1038/s41467-024-46813-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Small-molecule modulators of diverse voltage-gated K+ (Kv) channels may help treat a wide range of neurological disorders. However, developing effective modulators requires understanding of their mechanism of action. We apply an orthogonal approach to elucidate the mechanism of action of an imidazolidinedione derivative (AUT5), a highly selective positive allosteric modulator of Kv3.1 and Kv3.2 channels. AUT5 modulation involves positive cooperativity and preferential stabilization of the open state. The cryo-EM structure of the Kv3.1/AUT5 complex at a resolution of 2.5 Å reveals four equivalent AUT5 binding sites at the extracellular inter-subunit interface between the voltage-sensing and pore domains of the channel's tetrameric assembly. Furthermore, we show that the unique extracellular turret regions of Kv3.1 and Kv3.2 essentially govern the selective positive modulation by AUT5. High-resolution apo and bound structures of Kv3.1 demonstrate how AUT5 binding promotes turret rearrangements and interactions with the voltage-sensing domain to favor the open conformation.
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Affiliation(s)
- Qiansheng Liang
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Leonardo Cirqueira
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Lianteng Zhi
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Agostino Marasco
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Nadia Pilati
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Martin J Gunthorpe
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - Giuseppe Alvaro
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Charles H Large
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Werner Treptow
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Manuel Covarrubias
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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3
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Raturi S, Li H, Chang YN, Scacioc A, Bohstedt T, Fernandez-Cid A, Evans A, Abrusci P, Balakrishnan A, Pascoa TC, He D, Chi G, Kaur Singh N, Ye M, Li A, Shrestha L, Wang D, Williams EP, Burgess-Brown NA, Dürr KL, Puetter V, Ingles-Prieto A, Sauer DB. High-Throughput Expression and Purification of Human Solute Carriers for Structural and Biochemical Studies. J Vis Exp 2023. [PMID: 37843272 DOI: 10.3791/65878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Solute carriers (SLCs) are membrane transporters that import and export a range of endogenous and exogenous substrates, including ions, nutrients, metabolites, neurotransmitters, and pharmaceuticals. Despite having emerged as attractive therapeutic targets and markers of disease, this group of proteins is still relatively underdrugged by current pharmaceuticals. Drug discovery projects for these transporters are impeded by limited structural, functional, and physiological knowledge, ultimately due to the difficulties in the expression and purification of this class of membrane-embedded proteins. Here, we demonstrate methods to obtain high-purity, milligram quantities of human SLC transporter proteins using codon-optimized gene sequences. In conjunction with a systematic exploration of construct design and high-throughput expression, these protocols ensure the preservation of the structural integrity and biochemical activity of the target proteins. We also highlight critical steps in the eukaryotic cell expression, affinity purification, and size-exclusion chromatography of these proteins. Ultimately, this workflow yields pure, functionally active, and stable protein preparations suitable for high-resolution structure determination, transport studies, small-molecule engagement assays, and high-throughput in vitro screening.
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Affiliation(s)
- Sagar Raturi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | | | - Adam Evans
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Patrizia Abrusci
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Abilasha Balakrishnan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Tomas C Pascoa
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Didi He
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Nanki Kaur Singh
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Mingda Ye
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Anna Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Leela Shrestha
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Dong Wang
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | - Eleanor P Williams
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford
| | | | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford;
| | | | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences;
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford;
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4
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Tang H, Li H, Prakaash D, Pedebos C, Qiu X, Sauer DB, Khalid S, Duerr K, Robinson CV. The solute carrier SPNS2 recruits PI(4,5)P 2 to synergistically regulate transport of sphingosine-1-phosphate. Mol Cell 2023; 83:2739-2752.e5. [PMID: 37499662 PMCID: PMC10790328 DOI: 10.1016/j.molcel.2023.06.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/11/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Solute carrier spinster homolog 2 (SPNS2), one of only four known major facilitator superfamily (MFS) lysolipid transporters in humans, exports sphingosine-1-phosphate (S1P) across cell membranes. Here, we explore the synergistic effects of lipid binding and conformational dynamics on SPNS2's transport mechanism. Using mass spectrometry, we discovered that SPNS2 interacts preferentially with PI(4,5)P2. Together with functional studies and molecular dynamics (MD) simulations, we identified potential PI(4,5)P2 binding sites. Mutagenesis of proposed lipid binding sites and inhibition of PI(4,5)P2 synthesis reduce S1P transport, whereas the absence of the N terminus renders the transporter essentially inactive. Probing the conformational dynamics of SPNS2, we show how synergistic binding of PI(4,5)P2 and S1P facilitates transport, increases dynamics of the extracellular gate, and stabilizes the intracellular gate. Given that SPNS2 transports a key signaling lipid, our results have implications for therapeutic targeting and also illustrate a regulatory mechanism for MFS transporters.
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Affiliation(s)
- Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina Duerr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK; OMass Therapeutics, Ltd., Oxford OX4 2GX, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK.
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5
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Sauer DB, Marden JJ, Sudar JC, Song J, Mulligan C, Wang DN. Structural basis of ion - substrate coupling in the Na +-dependent dicarboxylate transporter VcINDY. Nat Commun 2022; 13:2644. [PMID: 35551191 PMCID: PMC9098524 DOI: 10.1038/s41467-022-30406-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.
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Affiliation(s)
- David B Sauer
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer J Marden
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Joseph C Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Jinmei Song
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA.
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA.
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6
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Sauer DB, Wang B, Sudar JC, Song J, Marden J, Rice WJ, Wang DN. The ups and downs of elevator-type di-/tricarboxylate membrane transporters. FEBS J 2022; 289:1515-1523. [PMID: 34403567 PMCID: PMC9832446 DOI: 10.1111/febs.16158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/16/2021] [Indexed: 01/13/2023]
Abstract
The divalent anion sodium symporter (DASS) family contains both sodium-driven anion cotransporters and anion/anion exchangers. The family belongs to a broader ion transporter superfamily (ITS), which comprises 24 families of transporters, including those of AbgT antibiotic efflux transporters. The human proteins in the DASS family play major physiological roles and are drug targets. We recently determined multiple structures of the human sodium-dependent citrate transporter (NaCT) and the succinate/dicarboxylate transporter from Lactobacillus acidophilus (LaINDY). Structures of both proteins show high degrees of structural similarity to the previously determined VcINDY fold. Conservation between these DASS protein structures and those from the AbgT family indicates that the VcINDY fold represents the overall protein structure for the entire ITS. The new structures of NaCT and LaINDY are captured in the inward- or outward-facing conformations, respectively. The domain arrangements in these structures agree with a rigid body elevator-type transport mechanism for substrate translocation across the membrane. Two separate NaCT structures in complex with a substrate or an inhibitor allowed us to explain the inhibition mechanism and propose a detailed classification scheme for grouping disease-causing mutations in the human protein. Structural understanding of multiple kinetic states of DASS proteins is a first step toward the detailed characterization of their entire transport cycle.
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Affiliation(s)
- David B. Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph C. Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jennifer Marden
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - William J. Rice
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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7
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Sauer DB, Song J, Wang B, Hilton JK, Karpowich NK, Mindell JA, Rice WJ, Wang DN. Structure and inhibition mechanism of the human citrate transporter NaCT. Nature 2021; 591:157-161. [PMID: 33597751 PMCID: PMC7933130 DOI: 10.1038/s41586-021-03230-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022]
Abstract
Citrate is most well-known as an intermediate in the TCA cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis 1–3. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic citrate concentration 4,5. Liver cells import citrate via the sodium-dependent citrate transporter NaCT (SLC13A5), and as a consequence this protein is a potential target for anti-obesity drugs. To understand the structural basis of its inhibition mechanism, we have determined cryo-electron microscopy structures of human NaCT in complex with citrate and with a small molecule inhibitor. These structures reveal how the inhibitor, bound at the same site as citrate, arrests the protein’s transport cycle. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish NaCT’s transport activity in the brain and thereby cause SLC13A5-Epilepsy in newborns 6–8.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Jacob K Hilton
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nathan K Karpowich
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.,Janssen Pharmaceuticals, Spring House, PA, USA
| | - Joseph A Mindell
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - William J Rice
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA. .,Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA.
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA. .,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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8
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Brawley DN, Sauer DB, Zheng X, Tate PM, Song J, Liu Z, Koide A, Koide S, Torres VJ, Wang DN, Traaseth NJ. Structure and Mechanism of the Multidrug Efflux Pump Nora. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife 2020; 9:e61350. [PMID: 32869741 PMCID: PMC7553777 DOI: 10.7554/elife.61350] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Jennifer J Marden
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolette Cocco
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
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Sauer DB, Wang DN. Predicting the optimal growth temperatures of prokaryotes using only genome derived features. Bioinformatics 2020; 35:3224-3231. [PMID: 30689741 DOI: 10.1093/bioinformatics/btz059] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/20/2018] [Accepted: 01/22/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Optimal growth temperature is a fundamental characteristic of all living organisms. Knowledge of this temperature is central to the study of a prokaryote, the thermal stability and temperature dependent activity of its genes, and the bioprospecting of its genome for thermally adapted proteins. While high throughput sequencing methods have dramatically increased the availability of genomic information, the growth temperatures of the source organisms are often unknown. This limits the study and technological application of these species and their genomes. Here, we present a novel method for the prediction of growth temperatures of prokaryotes using only genomic sequences. RESULTS By applying the reverse ecology principle that an organism's genome includes identifiable adaptations to its native environment, we can predict a species' optimal growth temperature with an accuracy of 5.17°C root-mean-square error and a coefficient of determination of 0.835. The accuracy can be further improved for specific taxonomic clades or by excluding psychrophiles. This method provides a valuable tool for the rapid calculation of organism growth temperature when only the genome sequence is known. AVAILABILITY AND IMPLEMENTATION Source code, genomes analyzed and features calculated are available at: https://github.com/DavidBSauer/OGT_prediction. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David B Sauer
- Department of Cell Biology, and The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
| | - Da-Neng Wang
- Department of Cell Biology, and The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
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Sauer DB, Karpowich NK, Wang DN. Bioinformatic Methods for the Rapid Identification of Thermostabilizing Mutants. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sauer DB, Zeng W, Canty J, Lam Y, Jiang Y. Sodium and potassium competition in potassium-selective and non-selective channels. Nat Commun 2014; 4:2721. [PMID: 24217363 PMCID: PMC3831281 DOI: 10.1038/ncomms3721] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/07/2013] [Indexed: 11/25/2022] Open
Abstract
Potassium channels selectively conduct K+, primarily to the exclusion of Na+, despite the fact that both ions can bind within the selectivity filter. Here we perform crystallographic titration and single-channel electrophysiology to examine the competition of Na+ and K+ binding within the filter of two NaK channel mutants; one is the potassium-selective NaK2K mutant and the other is the non-selective NaK2CNG, a CNG channel pore mimic. With high-resolution structures of these engineered NaK channel constructs, we explicitly describe the changes in K+ occupancy within the filter upon Na+ competition by anomalous diffraction. Our results demonstrate that the non-selective NaK2CNG still retains a K+-selective site at equilibrium, whereas the NaK2K channel filter maintains two high-affinity K+ sites. A double-barrier mechanism is proposed to explain K+ channel selectivity at low K+ concentrations. K+ channels are selective for K+ despite the fact that Na+ can bind and conduct through the selectivity filter. Sauer et al. show that a K+-selective NaK2K channel has two high-affinity K+-binding sites, whereas a non-selective NaK2CNG channel has one, and propose a double-barrier mechanism for ion selectivity.
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Affiliation(s)
- David B Sauer
- 1] Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9040, USA [2]
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Abstract
Sodium/calcium (Na(+)/Ca(2+)) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-exchange function of an NCX from Methanococcus jannaschii (NCX_Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca(2+) and three that likely bind Na(+). Two passageways allow for Na(+) and Ca(2+) access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX_Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX_Mj.
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Affiliation(s)
- Jun Liao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
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Hull MC, Sauer DB, Hovis JS. Influence of Lipid Chemistry on the Osmotic Response of Cell Membranes: Effect of Non-Bilayer Forming Lipids. J Phys Chem B 2004. [DOI: 10.1021/jp049845d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marshall C. Hull
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2018
| | - David B. Sauer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2018
| | - Jennifer S. Hovis
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2018
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Bechtel DB, Wilson JD, Eustace WD, Behnke KC, Whitaker T, Peterson GL, Sauer DB. Fate of Dwarf Bunt Fungus Teliospores During Milling of Wheat into Flour. Cereal Chem 1999. [DOI: 10.1094/cchem.1999.76.2.270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Donald B. Bechtel
- USDA-ARS, Grain Marketing and Production Research Center, Grain Marketing Research Laboratory, Manhattan, KS 66502
- Corresponding author. E-mail:
| | - Jeff D. Wilson
- USDA-ARS, Grain Marketing and Production Research Center, Grain Marketing Research Laboratory, Manhattan, KS 66502
| | - W. D. Eustace
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506
| | - Keith C. Behnke
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506
| | - Thomas Whitaker
- USDA-ARS, North Carolina State University, Raleigh, NC 27695
| | - Gary L. Peterson
- USDA-ARS, Foreign Disease-Weed Science Research, Fort Detrick, Frederick, MD 21702
| | - David B. Sauer
- USDA-ARS, Grain Marketing and Production Research Center, Grain Marketing Research Laboratory, Manhattan, KS 66502
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Abstract
Moulds or fungi that grow in grains and seeds during storage and transport cause germination decrease, visible mouldiness, discoloration, musty or sour odours, caking, chemical and nutritional changes, reduction in processing quality, and form of mycotoxins. These deteriorative changes affect the grade and price of grain and contribute to customer dissatisfaction when the grain is marketed. The respiration of grain and fungi results in a loss in dry matter as well as the production of heat and moisture which contribute to further spoilage. Net changes in nutritional value and the risk of mycotoxin contamination are difficult to predict because they depend on a complex interaction of factors such as temperature, moisture, storage time, fungal species composition, kind of grain, and previous storage history. Moisture is the most important variable determining the rate of deterioration caused by fungi, with temperature being the second major factor. Problems with deterioration of grain in export shipments are not a recent development. They are related primarily to grain moisture at loading, and also to the extent of previous mould invasion.
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Affiliation(s)
- D B Sauer
- U.S. Dept. of Agriculture, Manhattan, KS 66502
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Abstract
Alternariol and alternariol monomethyl ether are commonly associated with weathered grain sorghum. Production of these metabolites and altenuene by isolates of Alternaria alternata was evaluated on various sterile grain substrates. At 35% moisture content and 25 C, metabolite yields were highest on rice, intermediate on sorghums, and lowest on wheat and yellow corn. Fourteen-to 21-day cultures on milled rice were best in terms of ease of metabolite recovery, even though yields were higher on 28-day cultures of rough and brown rice. Metabolite production was reduced when rice was supplemented with yeast extract or yeast extract plus Czapek-Dox broth.
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