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Modak A, Kilic Z, Chattrakun K, Terry DS, Kalathur RC, Blanchard SC. Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. Annu Rev Biophys 2024; 53:427-453. [PMID: 39013028 DOI: 10.1146/annurev-biophys-070323-024308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.
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Affiliation(s)
- Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Kanokporn Chattrakun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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2
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Li J, Jo MH, Yan J, Hall T, Lee J, López-Sánchez U, Yan S, Ha T, Springer TA. Ligand binding initiates single-molecule integrin conformational activation. Cell 2024; 187:2990-3005.e17. [PMID: 38772370 PMCID: PMC11162317 DOI: 10.1016/j.cell.2024.04.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/21/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Integrins link the extracellular environment to the actin cytoskeleton in cell migration and adhesiveness. Rapid coordination between events outside and inside the cell is essential. Single-molecule fluorescence dynamics show that ligand binding to the bent-closed integrin conformation, which predominates on cell surfaces, is followed within milliseconds by two concerted changes, leg extension and headpiece opening, to give the high-affinity integrin conformation. The extended-closed integrin conformation is not an intermediate but can be directly accessed from the extended-open conformation and provides a pathway for ligand dissociation. In contrast to ligand, talin, which links the integrin β-subunit cytoplasmic domain to the actin cytoskeleton, modestly stabilizes but does not induce extension or opening. Integrin activation is thus initiated by outside-in signaling and followed by inside-out signaling. Our results further imply that talin binding is insufficient for inside-out integrin activation and that tensile force transmission through the ligand-integrin-talin-actin cytoskeleton complex is required.
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Affiliation(s)
- Jing Li
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Myung Hyun Jo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jiabin Yan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Taylor Hall
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joon Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Uriel López-Sánchez
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sophia Yan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Newton South High School, Newton, MA 02459, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Timothy A Springer
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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3
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Schmidt SG, Nygaard A, Mindell JA, Loland CJ. Exploring the K + binding site and its coupling to transport in the neurotransmitter:sodium symporter LeuT. eLife 2024; 12:RP87985. [PMID: 38271216 PMCID: PMC10945697 DOI: 10.7554/elife.87985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
The neurotransmitter:sodium symporters (NSSs) are secondary active transporters that couple the reuptake of substrate to the symport of one or two sodium ions. One bound Na+ (Na1) contributes to the substrate binding, while the other Na+ (Na2) is thought to be involved in the conformational transition of the NSS. Two NSS members, the serotonin transporter (SERT) and the Drosophila dopamine transporter (dDAT), also couple substrate uptake to the antiport of K+ by a largely undefined mechanism. We have previously shown that the bacterial NSS homologue, LeuT, also binds K+, and could therefore serve as a model protein for the exploration of K+ binding in NSS proteins. Here, we characterize the impact of K+ on substrate affinity and transport as well as on LeuT conformational equilibrium states. Both radioligand binding assays and transition metal ion FRET (tmFRET) yielded similar K+ affinities for LeuT. K+ binding was specific and saturable. LeuT reconstituted into proteoliposomes showed that intra-vesicular K+ dose-dependently increased the transport velocity of [3H]alanine, whereas extra-vesicular K+ had no apparent effect. K+ binding induced a LeuT conformation distinct from the Na+- and substrate-bound conformation. Conservative mutations of the Na1 site residues affected the binding of Na+ and K+ to different degrees. The Na1 site mutation N27Q caused a >10-fold decrease in K+ affinity but at the same time a ~3-fold increase in Na+ affinity. Together, the results suggest that K+ binding to LeuT modulates substrate transport and that the K+ affinity and selectivity for LeuT is sensitive to mutations in the Na1 site, pointing toward the Na1 site as a candidate site for facilitating the interaction with K+ in some NSSs.
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Affiliation(s)
- Solveig G Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Nygaard
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joseph A Mindell
- Membrane Transport Biophysics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A, Shoichet BK, Rudnick G. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Cell 2023; 186:2160-2175.e17. [PMID: 37137306 PMCID: PMC10306110 DOI: 10.1016/j.cell.2023.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/05/2023] [Accepted: 04/06/2023] [Indexed: 05/05/2023]
Abstract
The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.
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Affiliation(s)
- Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Anubha Seth
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Christian B Billesbølle
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Joao Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ramona M Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Kasturi Roy
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Bethlehem Bekele
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xi-Ping Huang
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danila Boytsov
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Vladimir M Pogorelov
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Bryan L Roth
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA.
| | - Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA.
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Iversen JF, Bohr SSR, Pinholt HD, Moses ME, Iversen L, Christensen SM, Hatzakis NS, Zhang M. Single-Particle Tracking of Thermomyces lanuginosus Lipase Reveals How Mutations in the Lid Region Remodel Its Diffusion. Biomolecules 2023; 13:biom13040631. [PMID: 37189378 DOI: 10.3390/biom13040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The function of most lipases is controlled by the lid, which undergoes conformational changes at a water–lipid interface to expose the active site, thus activating catalysis. Understanding how lid mutations affect lipases’ function is important for designing improved variants. Lipases’ function has been found to correlate with their diffusion on the substrate surface. Here, we used single-particle tracking (SPT), a powerful tool for deciphering enzymes’ diffusional behavior, to study Thermomyces lanuginosus lipase (TLL) variants with different lid structures in a laundry-like application condition. Thousands of parallelized recorded trajectories and hidden Markov modeling (HMM) analysis allowed us to extract three interconverting diffusional states and quantify their abundance, microscopic transition rates, and the energy barriers for sampling them. Combining those findings with ensemble measurements, we determined that the overall activity variation in the application condition is dependent on surface binding and lipase mobility when bound. Specifically, the L4 variant with a TLL-like lid and wild-type (WT) TLL displayed similar ensemble activity, but WT bound stronger to the surface than L4, while L4 had a higher diffusion coefficient and thus activity when bound to the surface. These mechanistic elements can only be de-convoluted by our combined assays. Our findings offer fresh perspectives on the development of the next iteration of enzyme-based detergent.
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Affiliation(s)
- Josephine F. Iversen
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Søren S.-R. Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Henrik D. Pinholt
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | - Nikos S. Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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6
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Piniella D, Zafra F. Functional crosstalk of the glycine transporter GlyT1 and NMDA receptors. Neuropharmacology 2023; 232:109514. [PMID: 37003571 DOI: 10.1016/j.neuropharm.2023.109514] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023]
Abstract
NMDA-type glutamate receptors (NMDARs) constitute one of the main glutamate (Glu) targets in the central nervous system and are involved in synaptic plasticity, which is the molecular substrate of learning and memory. Hypofunction of NMDARs has been associated with schizophrenia, while overstimulation causes neuronal death in neurodegenerative diseases or in stroke. The function of NMDARs requires coincidental binding of Glu along with other cellular signals such as neuronal depolarization, and the presence of other endogenous ligands that modulate their activity by allosterism. Among these allosteric modulators are zinc, protons and Gly, which is an obligatory co-agonist. These characteristics differentiate NMDARs from other receptors, and their structural bases have begun to be established in recent years. In this review we focus on the crosstalk between Glu and glycine (Gly), whose concentration in the NMDAR microenvironment is maintained by various Gly transporters that remove or release it into the medium in a regulated manner. The GlyT1 transporter is particularly involved in this task, and has become a target of great interest for the treatment of schizophrenia since its inhibition leads to an increase in synaptic Gly levels that enhances the activity of NMDARs. However, the only drug that has completed phase III clinical trials did not yield the expected results. Notwithstanding, there are additional drugs that continue to be investigated, and it is hoped that knowledge gained from the recently published 3D structure of GlyT1 may allow the rational design of more effective new drugs.
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Affiliation(s)
- Dolores Piniella
- Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain; IdiPAZ, Institute of Health Carlos III (ISCIII), Spain
| | - Francisco Zafra
- Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain; IdiPAZ, Institute of Health Carlos III (ISCIII), Spain.
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7
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Determining Ligand and Ion-Induced Conformational Changes in Serotonin Transporter with Its Fluorescent Substrates. Int J Mol Sci 2022; 23:ijms231810919. [PMID: 36142837 PMCID: PMC9503009 DOI: 10.3390/ijms231810919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/22/2023] Open
Abstract
Conformational changes are fundamental events in the transport mechanism. The serotonin transporter (SERT) catalyzes reuptake of the neurotransmitter serotonin after its release by serotonergic neurons and is the molecular target for antidepressant drugs and psychostimulants. Despite significant progress in characterizing the structure-function relationship of SERT, its conformational mechanism has not been fully understood. We present here a cell-based method for determining conformational changes in SERT with its fluorescent substrates by fluorescence imaging analysis. This method fluorometrically measures accessibility of strategically positioned cysteine residues in the substrate permeation pathway to calculate the rate constants of reactivity with MTS reagents in live or permeabilized cells. We validated this method by investigating ligand and ion-induced conformational changes in both the extracellular and cytoplasmic pathways of SERT. Furthermore, we applied this method for examining the influence of Cl- binding and vilazodone inhibition on SERT conformation. Our results showed that Cl- ion, in the presence of Na+, facilitates the conformational conversion from outward to inward open states, and that vilazodone binding stabilizes SERT in an outward open and inward-closed conformation. The present work provided insights into the conformational mechanism of SERT and also indicated that the cell-based fluorometric method is robust, straightforward to perform, and potentially applicable to any monoamine transporters in exploring the transport mechanism and mechanism of action of therapeutic agents for the treatment of several psychiatric disorders.
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8
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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9
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Abstract
SignificanceOuter membrane porins play a crucial role in processes as varied as energy production, photosynthesis, and nutrient transport. They act as the gatekeepers between a gram-negative bacterium and its environment. Understanding how these proteins fold and function is important in improving our understanding and control of these processes. Here we use single-molecule methods to help resolve the apparent differences between the fast folding expected on a molecular scale and the slow kinetics observed in ensemble measurements in the laboratory.
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10
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Chan MC, Procko E, Shukla D. Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation. ACS Chem Neurosci 2022; 13:933-945. [PMID: 35258286 DOI: 10.1021/acschemneuro.1c00714] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The reuptake of the neurotransmitter serotonin from the synaptic cleft by the serotonin transporter, SERT, is essential for proper neurological signaling. Biochemical studies have shown that Thr276 of transmembrane helix 5 is a site of PKG-mediated SERT phosphorylation, which has been proposed to shift the SERT conformational equilibria to promote inward-facing states, thus enhancing 5-HT transport. Recent structural and simulation studies have provided insights into the conformation transitions during substrate transport but have not shed light on SERT regulation via post-translational modifications. Using molecular dynamics simulations and Markov state models, we investigate how Thr276 phosphorylation impacts the SERT mechanism and its role in enhancing transporter stability and function. Our simulations show that Thr276 phosphorylation alters the hydrogen-bonding network involving residues on transmembrane helix 5. This in turn decreases the free energy barriers for SERT to transition to the inward-facing state, thus facilitating 5-HT import. The results provide atomistic insights into in vivo SERT regulation and can be extended to other pharmacologically important transporters in the solute carrier family.
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Affiliation(s)
- Matthew C. Chan
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Erik Procko
- Department of Biochemistry, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience Program, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
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11
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Chan MC, Selvam B, Young HJ, Procko E, Shukla D. The substrate import mechanism of the human serotonin transporter. Biophys J 2022; 121:715-730. [PMID: 35114149 PMCID: PMC8943754 DOI: 10.1016/j.bpj.2022.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/18/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
The serotonin transporter (SERT) initiates the reuptake of extracellular serotonin in the synapse to terminate neurotransmission. The cryogenic electron microscopy structures of SERT bound to ibogaine and the physiological substrate serotonin resolved in different states have provided a glimpse of the functional conformations at atomistic resolution. However, the conformational dynamics and structural transitions to intermediate states are not fully understood. Furthermore, the molecular basis of how serotonin is recognized and transported remains unclear. In this study, we performed unbiased microsecond-long simulations of the human SERT to investigate the structural dynamics to various intermediate states and elucidated the complete substrate import pathway. Using Markov state models, we characterized a sequential order of conformational-driven ion-coupled substrate binding and transport events and calculated the free energy barriers of conformation transitions associated with the import mechanism. We find that the transition from the occluded to inward-facing state is the rate-limiting step for substrate import and that the substrate decreases the free energy barriers to achieve the inward-facing state. Our study provides insights on the molecular basis of dynamics-driven ion-substrate recognition and transport of SERT that can serve as a model for other closely related neurotransmitter transporters.
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Affiliation(s)
- Matthew C Chan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Heather J Young
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Erik Procko
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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12
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Refai O, Aggarwal S, Cheng MH, Gichi Z, Salvino JM, Bahar I, Blakely RD, Mortensen OV. Allosteric Modulator KM822 Attenuates Behavioral Actions of Amphetamine in Caenorhabditis elegans through Interactions with the Dopamine Transporter DAT-1. Mol Pharmacol 2022; 101:123-131. [PMID: 34906999 PMCID: PMC8969146 DOI: 10.1124/molpharm.121.000400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Aberrant dopamine (DA) signaling is associated with several psychiatric disorders, such as autism, bipolar disorder, addiction, and Parkinson's disease, and several medications that target the DA transporter (DAT) can induce or treat these disorders. In addition, psychostimulants, such as cocaine and D-amphetamine (AMPH), rely on the competitive interactions with the transporter's substrate binding site to produce their rewarding effects. Agents that exhibit noncompetitive, allosteric modulation of DAT remain an important topic of investigation due to their potential therapeutic applications. We previously identified a novel allosteric modulator of human DAT, KM822, that can decrease the affinity of cocaine for DAT and attenuate cocaine-elicited behaviors; however, whether DAT is the sole mediator of KM822 actions in vivo is unproven given the large number of potential off-target sites. Here, we provide in silico and in vitro evidence that the allosteric site engaged by KM822 is conserved between human DAT and Caenorhabditis elegans DAT-1. KM822 binds to a similar pocket in DAT-1 as previously identified in human DAT. In functional dopamine uptake assays, KM822 affects the interaction between AMPH and DAT-1 by reducing the affinity of AMPH for DAT-1. Finally, through a combination of genetic and pharmacological in vivo approaches we provide evidence that KM822 diminishes the behavioral actions of AMPH on swimming-induced paralysis through a direct allosteric modulation of DAT-1. More broadly, our findings demonstrate allosteric modulation of DAT as a behavior modifying strategy and suggests that Caenorhabditis elegans can be operationalized to identify and investigate the interactions of DAT allosteric modulators. SIGNIFICANCE STATEMENT: We previously demonstrated that the dopamine transporter (DAT) allosteric modulator KM822 decreases cocaine affinity for human DAT. Here, using in silico and in vivo genetic approaches, we extend this finding to interactions with amphetamine, demonstrating evolutionary conservation of the DAT allosteric site. In Caenorhabditis elegans, we report that KM822 suppresses amphetamine behavioral effects via specific interactions with DAT-1. Our findings reveal Caenorhabditis elegans as a new tool to study allosteric modulation of DAT and its behavioral consequences.
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Affiliation(s)
- Osama Refai
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Shaili Aggarwal
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Mary Hongying Cheng
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Zayna Gichi
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Joseph M Salvino
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Ivet Bahar
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
| | - Ole V Mortensen
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida (O.R., Z.G., R.D.B.); Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida (O.R., R.D.B.); Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania (S.A., O.V.M.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (M.H.C., I.B.); and The Wistar Institute, Philadelphia, Pennsylvania (J.M.S.)
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13
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Abstract
Single molecule Förster resonance energy transfer (smFRET) is a unique biophysical approach for studying conformational dynamics in biomacromolecules. Photon-by-photon hidden Markov modeling (H2MM) is an analysis tool that can quantify FRET dynamics of single biomolecules, even if they occur on the sub-millisecond timescale. However, dye photophysical transitions intertwined with FRET dynamics may cause artifacts. Here, we introduce multi-parameter H2MM (mpH2MM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpH2MM to decouple FRET dynamics caused by conformational changes from photophysical transitions in confocal-based smFRET measurements of a DNA hairpin, the maltose binding protein, MalE, and the type-III secretion system effector, YopO, from Yersinia species, all exhibiting conformational dynamics ranging from the sub-second to microsecond timescales. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations and their origin. In this work, the authors demonstrate the application of multi-parameter photon-by-photon hidden Markov modeling (mpH2MM) on alternating laser excitation (ALEX)-based smFRET measurements. The utility of mpH2MM in identifying and quantifying dynamic biomolecular sub-populations is demonstrated in three different systems.
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14
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Szöllősi D, Stockner T. Sodium Binding Stabilizes the Outward-Open State of SERT by Limiting Bundle Domain Motions. Cells 2022; 11:cells11020255. [PMID: 35053371 PMCID: PMC8773566 DOI: 10.3390/cells11020255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
The human serotonin transporter (hSERT) removes the neurotransmitter serotonin from the synaptic cleft by reuptake into the presynaptic nerve terminal. A number of neurologic diseases are associated with dysfunction of the hSERT, and several medications for their treatment are hSERT blockers, including citalopram, fluoxetine, and paroxetine. The substrate transport is energized by the high concentration of external NaCl. We showed through molecular dynamics simulations that the binding of NaCl stabilized the hSERT in the substrate-binding competent conformation, which was characterized by an open access path to the substrate-binding site through the outer vestibule. Importantly, the binding of NaCl reduced the dynamics of the hSERT by decreasing the internal fluctuations of the bundle domain as well as the movement of the bundle domain relative to the scaffold domain. In contrast, the presence of only the bound chloride ion did not reduce the high domain mobility of the apo state.
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15
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Ciftci D, Martens C, Ghani VG, Blanchard SC, Politis A, Huysmans GHM, Boudker O. Linking function to global and local dynamics in an elevator-type transporter. Proc Natl Acad Sci U S A 2021; 118:e2025520118. [PMID: 34873050 PMCID: PMC8670510 DOI: 10.1073/pnas.2025520118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/24/2022] Open
Abstract
Transporters cycle through large structural changes to translocate molecules across biological membranes. The temporal relationships between these changes and function, and the molecular properties setting their rates, determine transport efficiency-yet remain mostly unknown. Using single-molecule fluorescence microscopy, we compare the timing of conformational transitions and substrate uptake in the elevator-type transporter GltPh We show that the elevator-like movements of the substrate-loaded transport domain across membranes and substrate release are kinetically heterogeneous, with rates varying by orders of magnitude between individual molecules. Mutations increasing the frequency of elevator transitions and reducing substrate affinity diminish transport rate heterogeneities and boost transport efficiency. Hydrogen deuterium exchange coupled to mass spectrometry reveals destabilization of secondary structure around the substrate-binding site, suggesting that increased local dynamics leads to faster rates of global conformational changes and confers gain-of-function properties that set transport rates.
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Affiliation(s)
- Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065
| | - Chloe Martens
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Vishnu G Ghani
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Argyris Politis
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Gerard H M Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY 10065
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16
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Sahai M, Opacka-Juffry J. Molecular mechanisms of action of stimulant novel psychoactive substances that target the high-affinity transporter for dopamine. Neuronal Signal 2021; 5:NS20210006. [PMID: 34888062 PMCID: PMC8630395 DOI: 10.1042/ns20210006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022] Open
Abstract
Drug misuse is a significant social and public health problem worldwide. Misused substances exert their neurobehavioural effects through changing neural signalling within the brain, many of them leading to substance dependence and addiction in the longer term. Among drugs with addictive liability, there are illicit classical stimulants such as cocaine and amphetamine, and their more recently available counterparts known as novel psychoactive substances (NPS). Stimulants normally increase dopamine availability in the brain, including the pathway implicated in reward-related behaviour. This pattern is observed in both animal and human brain. The main biological target of stimulants, both classical and NPS, is the dopamine transporter (DAT) implicated in the dopamine-enhancing effects of these drugs. This article aims at reviewing research on the molecular mechanisms underpinning the interactions between stimulant NPS, such as benzofurans, cathinones or piperidine derivatives and DAT, to achieve a greater understanding of the core phenomena that decide about the addictive potential of stimulant NPS. As the methodology is essential in the process of experimental research in this area, we review the applications of in vitro, in vivo and in silico approaches. The latter, including molecular dynamics, attracts the focus of the present review as the method of choice in molecular and atomistic investigations of the mechanisms of addiction of stimulant NPS. Research of this kind is of interest to not only scientists but also health professionals as updated knowledge of NPS, their modes of action and health risks, is needed to tackle the challenges posed by NPS misuse.
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Affiliation(s)
- Michelle A. Sahai
- School of Life and Health Sciences, University of Roehampton, London SW15 4JD, U.K
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17
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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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18
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Calugareanu D, Möller IR, Schmidt SG, Loland CJ, Rand KD. Probing the Impact of Temperature and Substrates on the Conformational Dynamics of the Neurotransmitter:Sodium symporter LeuT. J Mol Biol 2021; 434:167356. [PMID: 34780780 DOI: 10.1016/j.jmb.2021.167356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/21/2022]
Abstract
The crucial function of neurotransmitter:sodium symporters (NSS) in facilitating the reuptake of neurotransmitters into neuronal cells makes them attractive drug targets for treating multiple mental diseases. Due to the challenges in working with eukaryotic NSS proteins, LeuT, a prokaryotic amino acid transporter, has served as a model protein for studying structure-function relationships of NSS family proteins. With hydrogen-deuterium exchange mass spectrometry (HDX-MS), slow unfolding/refolding kinetics were identified in multiple regions of LeuT, suggesting that substrate translocation involves cooperative fluctuations of helical stretches. Earlier work has solely been performed at non-native temperatures (25 °C) for LeuT, which is evolutionarily adapted to function at high temperatures (85 - 95 °C). To address the effect of temperature on LeuT dynamics, we have performed HDX-MS experiments at elevated temperatures (45 °C and 60 °C). At these elevated temperatures, multiple regions in LeuT exhibited increased dynamics compared to 25 °C. Interestingly, coordinated slow unfolding/refolding of key regions could still be observed, though considerably faster. We have further investigated the conformational impact of binding the efficiently transported substrate alanine (Ala) relative to the much slower transported substrate leucine (Leu). Comparing the HDX of the Ala-bound versus Leu-bound state of LeuT, we observe distinct differences that could explain the faster transport rate (kcat) of Ala relative to Leu. Importantly, slow unfolding/refolding dynamics could still be observed in regions of Ala-bound LeuT . Overall, our work brings new insights into the conformational dynamics of LeuT and provides a better understanding of the transport mechanism of LeuT and possibly other transporters bearing the LeuT fold.
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Affiliation(s)
- Dionisie Calugareanu
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Solveig G Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark.
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19
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Kickinger S, Lie MEK, Suemasa A, Al-Khawaja A, Fujiwara K, Watanabe M, Wilhelmsen KS, Falk-Petersen CB, Frølund B, Shuto S, Ecker GF, Wellendorph P. Molecular Determinants and Pharmacological Analysis for a Class of Competitive Non-transported Bicyclic Inhibitors of the Betaine/GABA Transporter BGT1. Front Chem 2021; 9:736457. [PMID: 34595152 PMCID: PMC8476755 DOI: 10.3389/fchem.2021.736457] [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: 07/05/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
The betaine/GABA transporter 1 (BGT1) is a member of the GABA transporter (GAT) family with still elusive function, largely due to a lack of potent and selective tool compounds. Based on modeling, we here present the design, synthesis and pharmacological evaluation of five novel conformationally restricted cyclic GABA analogs related to the previously reported highly potent and selective BGT1 inhibitor (1S,2S,5R)-5-aminobicyclo[3.1.0]hexane-2-carboxylic acid (bicyclo-GABA). Using [3H]GABA radioligand uptake assays at the four human GATs recombinantly expressed in mammalian cell lines, we identified bicyclo-GABA and its N-methylated analog (2) as the most potent and selective BGT1 inhibitors. Additional pharmacological characterization in a fluorescence-based membrane potential assay showed that bicyclo-GABA and 2 are competitive inhibitors, not substrates, at BGT1, which was validated by a Schild analysis for bicyclo-GABA (pKB value of 6.4). To further elaborate on the selectivity profile both compounds were tested at recombinant α1β2γ2 GABAA receptors. Whereas bicyclo-GABA showed low micromolar agonistic activity, the N-methylated 2 was completely devoid of activity at GABAA receptors. To further reveal the binding mode of bicyclo-GABA and 2 binding hypotheses of the compounds were obtained from in silico-guided mutagenesis studies followed by pharmacological evaluation at selected BGT1 mutants. This identified the non-conserved BGT1 residues Q299 and E52 as the molecular determinants driving BGT1 activity and selectivity. The binding mode of bicyclo-GABA was further validated by the introduction of activity into the corresponding GAT3 mutant L314Q (38 times potency increase cf. wildtype). Altogether, our data reveal the molecular determinants for the activity of bicyclic GABA analogs, that despite their small size act as competitive inhibitors of BGT1. These compounds may serve as valuable tools to selectively and potently target BGT1 in order to decipher its elusive pharmacological role in the brain and periphery such as the liver and kidneys.
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Affiliation(s)
- Stefanie Kickinger
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Pharmaceutical Science, University of Vienna, Vienna, Austria
| | - Maria E K Lie
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Akihiro Suemasa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Anas Al-Khawaja
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Koichi Fujiwara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kristine S Wilhelmsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina B Falk-Petersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bente Frølund
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Gerhard F Ecker
- Department of Pharmaceutical Science, University of Vienna, Vienna, Austria
| | - Petrine Wellendorph
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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20
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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21
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Chloride-dependent conformational changes in the GlyT1 glycine transporter. Proc Natl Acad Sci U S A 2021; 118:2017431118. [PMID: 33658361 DOI: 10.1073/pnas.2017431118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1,000-fold by Cl- We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine, and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homolog indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide an unexpected insight into the role of Cl- in this family of transporters.
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22
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Moses ME, Lund PM, Bohr SSR, Iversen JF, Kæstel-Hansen J, Kallenbach AS, Iversen L, Christensen SM, Hatzakis NS. Single-Molecule Study of Thermomyces lanuginosus Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33704-33712. [PMID: 34235926 DOI: 10.1021/acsami.1c08809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lipases comprise one of the major enzyme classes in biotechnology with applications within, e.g., baking, brewing, biocatalysis, and the detergent industry. Understanding the mechanisms of lipase function and regulation is therefore important to facilitate the optimization of their function by protein engineering. Advances in single-molecule studies in model systems have provided deep mechanistic insights on lipase function, such as the existence of functional states, their dependence on regulatory cues, and their correlation to activity. However, it is unclear how these observations translate to enzyme behavior in applied settings. Here, single-molecule tracking of individual Thermomyces lanuginosus lipase (TLL) enzymes in a detergency application system allowed real-time direct observation of spatiotemporal localization, and thus diffusional behavior, of TLL enzymes on a lard substrate. Parallelized imaging of thousands of individual enzymes allowed us to observe directly the existence and quantify the abundance and interconversion kinetics between three diffusional states that we recently provided evidence to correlate with function. We observe redistribution of the enzyme's diffusional pattern at the lipid-water interface as well as variations in binding efficiency in response to surfactants and calcium, demonstrating that detergency effectors can drive the sampling of lipase functional states. Our single-molecule results combined with ensemble activity assays and enzyme surface binding efficiency readouts allowed us to deconvolute how application conditions can significantly alter protein functional dynamics and/or surface binding, both of which underpin enzyme performance. We anticipate that our results will inspire further efforts to decipher and integrate the dynamic nature of lipases, and other enzymes, in the design of new biotechnological solutions.
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Affiliation(s)
- Matias E Moses
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Philip M Lund
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Josephine F Iversen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Lars Iversen
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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23
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Wu C, Shan Y, Wang S, Liu F. Dynamically probing ATP-dependent RNA helicase A-assisted RNA structure conversion using single molecule fluorescence resonance energy transfer. Protein Sci 2021; 30:1157-1168. [PMID: 33837988 DOI: 10.1002/pro.4081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/08/2021] [Indexed: 12/16/2022]
Abstract
RNA helicase A (RHA) as a member of DExH-box subgroup of helicase superfamily II, participates in diverse biological processes involved in RNA metabolism in organisms, and these RNA-mediated biological processes rely on RNA structure conversion. However, how RHA regulate the RNA structure conversion was still unknown. In order to unveil the mechanism of RNA structure conversion mediated by RHA, single molecule fluorescence resonance energy transfer was adopted to in our assay, and substrates RNA were from internal ribosome entry site of foot-and-mouth disease virus genome. We first found that the RNA structure conversion by RHA against thermodynamic equilibrium in vitro, and the process of dsRNA YZ converted to dsRNA XY through a tripartite intermediate state. In addition, the rate of the RNA structure conversion and the distribution of dsRNA YZ and XY were affected by ATP concentrations. Our study provides real-time insight into ATP-dependent RHA-assisted RNA structure conversion at the single molecule level, the mechanism displayed by RHA may help in understand how RHA contributes to many biological functions, and the basic mechanistic features illustrated in our work also underlay more complex protein-assisted RNA structure conversions.
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Affiliation(s)
- Chengcheng Wu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Yanke Shan
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China.,Computational Optics Laboratory, Jiangnan University, Wuxi, China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, China
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24
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Szöllősi D, Stockner T. Investigating the Mechanism of Sodium Binding to SERT Using Direct Simulations. Front Cell Neurosci 2021; 15:673782. [PMID: 34040506 PMCID: PMC8141550 DOI: 10.3389/fncel.2021.673782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
The serotonin transporter (SERT) terminates neurotransmission by transporting serotonin from the synapse into the pre-synaptic nerve terminal. Altered SERT function leads to several neurological diseases including depression, anxiety, mood disorders, and attention deficit hyperactivity disorders (ADHD). Accordingly SERT is the target for their pharmacological treatments, but also targeted by multiple drugs of abuse. Transport of serotonin by SERT is energized by the transmembrane electrochemical gradient of sodium. We used extensive molecular dynamics simulations to investigate the process of sodium binding to SERT, which is the first step in the transport cycle that leads to serotonin uptake. Comparing data from 51 independent simulations, we find a remarkably well-defined path for sodium entry and could identify two transient binding sites, while observing binding kinetics that are comparable to experimental data. Importantly, the structure and dynamics of the sodium binding sites indicate that sodium binding is accompanied by an induced-fit mechanism that leads to new conformations and reduces local dynamics.
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Affiliation(s)
- Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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25
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Meinke C, Quinlan MA, Paffenroth KC, Harrison FE, Fenollar-Ferrer C, Katamish RM, Stillman I, Ramamoorthy S, Blakely RD. Serotonin Transporter Ala276 Mouse: Novel Model to Assess the Neurochemical and Behavioral Impact of Thr276 Phosphorylation In Vivo. Neurochem Res 2021; 47:37-60. [PMID: 33830406 DOI: 10.1007/s11064-021-03299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/21/2021] [Accepted: 03/17/2021] [Indexed: 11/30/2022]
Abstract
The serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressants and psychostimulants. Human SERT coding variants have been identified in subjects with obsessive-compulsive disorder (OCD) and autism spectrum disorder (ASD) that impact transporter phosphorylation, cell surface trafficking and/or conformational dynamics. Prior to an initial description of a novel mouse line expressing the non-phosphorylatable SERT substitution Thr276Ala, we review efforts made to elucidate the structure and conformational dynamics of SERT with a focus on research implicating phosphorylation at Thr276 as a determinant of SERT conformational dynamics. Using the high-resolution structure of human SERT in inward- and outward-open conformations, we explore the conformation dependence of SERT Thr276 exposure, with results suggesting that phosphorylation is likely restricted to an inward-open conformation, consistent with prior biochemical studies. Assessment of genotypes from SERT/Ala276 heterozygous matings revealed a deviation from Mendelian expectations, with reduced numbers of Ala276 offspring, though no genotype differences were seen in growth or physical appearance. Similarly, no genotype differences were evident in midbrain or hippocampal 5-HT levels, midbrain and hippocampal SERT mRNA or midbrain protein levels, nor in midbrain synaptosomal 5-HT uptake kinetics. Behaviorally, SERT Ala276 homozygotes appeared normal in measures of anxiety and antidepressant-sensitive stress coping behavior. However, these mice displayed sex-dependent alterations in repetitive and social interactions, consistent with circuit-dependent requirements for Thr276 phosphorylation underlying these behaviors. Our findings indicate the utility of SERT Ala276 mice in evaluation of developmental, functional and behavioral consequences of regulatory SERT phosphorylation in vivo.
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Affiliation(s)
- Carina Meinke
- International Max Planck Research School for Brain and Behavior, Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA.,Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | - Meagan A Quinlan
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | | | - Fiona E Harrison
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cristina Fenollar-Ferrer
- Laboratories of Molecular Genetics and Molecular Biology, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Rania M Katamish
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | - Isabel Stillman
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | | | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA. .,Florida Atlantic University Brain Institute, Rm 109, MC-17, 5353 Parkside Dr, Jupiter, FL, 35348, USA.
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26
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Quick M, Dwivedi M, Padan E. Insight into the direct interaction of Na + with NhaA and mechanistic implications. Sci Rep 2021; 11:7045. [PMID: 33782459 PMCID: PMC8007835 DOI: 10.1038/s41598-021-86318-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/05/2021] [Indexed: 11/21/2022] Open
Abstract
Na+/H+ antiporters comprise a family of membrane proteins evolutionarily conserved in all kingdoms of life that are essential in cellular ion homeostasis. While several human homologues have long been drug targets, NhaA of Escherichia coli has become the paradigm for this class of secondary active transporters as NhaA crystals provided insight in the structure of this molecular machine. However, structural data revealing the composition of the binding site for Na+ (or its surrogate Li+) is missing, representing a bottleneck in our understanding of the correlation between the structure and function of NhaA. Here, by adapting the scintillation proximity assay (SPA) for direct determination of Na+ binding to NhaA, we revealed that (i) NhaA is well adapted as the main antiporter for Na+ homeostasis in Escherichia coli and possibly in other bacteria as the cytoplasmic Na+ concentration is similar to the Na+ binding affinity of NhaA, (ii) experimental conditions affect NhaA-mediated cation binding, (iii) in addition to Na+ and Li+, the halide Tl+ interacts with NhaA, (iv) whereas acidic pH inhibits maximum binding of Na+ to NhaA, partial Na+ binding by NhaA is independent of the pH, an important novel insight into the effect of pH on NhaA cation binding.
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Affiliation(s)
- Matthias Quick
- Department of Psychiatry and Center for Molecular Recognition, Columbia University Vagelos College of Physicians and Surgeons, and New York State Psychiatric Institute, New York, NY, 10032, USA.
| | - Manish Dwivedi
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.,Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Etana Padan
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.
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27
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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28
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Tassis K, Vietrov R, de Koning M, de Boer M, Gouridis G, Cordes T. Single-molecule studies of conformational states and dynamics in the ABC importer OpuA. FEBS Lett 2021; 595:717-734. [PMID: 33314056 DOI: 10.1002/1873-3468.14026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/02/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022]
Abstract
The current model of active transport via ABC importers is mostly based on structural, biochemical and genetic data. We here establish single-molecule Förster resonance energy transfer (smFRET) assays to monitor the conformational states and heterogeneity of the osmoregulatory type I ABC importer OpuA from Lactococcus lactis. We present data probing both intradomain distances that elucidate conformational changes within the substrate-binding domain (SBD) OpuAC, and interdomain distances between SBDs or transmembrane domains. Using this methodology, we studied ligand-binding mechanisms, as well as ATP and glycine betaine dependences of conformational changes. Our work expands the scope of smFRET investigations towards a class of so far unstudied ABC importers, and paves the way for a full understanding of their transport cycle in the future.
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Affiliation(s)
- Konstantinos Tassis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Ruslan Vietrov
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Matthijs de Koning
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Belgium.,Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Heraklion-Crete, Greece
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Martinsried, Germany
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29
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Khan JA, Sohail A, Jayaraman K, Szöllősi D, Sandtner W, Sitte HH, Stockner T. The Amino Terminus of LeuT Changes Conformation in an Environment Sensitive Manner. Neurochem Res 2020; 45:1387-1398. [PMID: 31858375 PMCID: PMC7260283 DOI: 10.1007/s11064-019-02928-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/21/2022]
Abstract
Neurotransmitter:sodium symporters are highly expressed in the human brain and catalyze the uptake of substrate through the plasma membrane by using the electrochemical gradient of sodium as the energy source. The bacterial homolog LeuT, a small amino acid transporter isolated from the bacteria Aquifex aeolicus, is the founding member of the family and has been crystallized in three conformations. The N-terminus is structurally well defined and strongly interacts with the transporter core in the outward-facing conformations. However, it could not be resolved in the inward-facing conformation, which indicates enhanced mobility. Here we investigate conformations and dynamics of the N-terminus, by combining molecular dynamics simulations with experimental verification using distance measurements and accessibility studies. We found strongly increased dynamics of the N-terminus, but also that helix TM1A is subject to enhanced mobility. TM1A moves towards the transporter core in the membrane environment, reaching a conformation that is closer to the structure of LeuT with wild type sequence, indicating that the mutation introduced to create the inward-facing structure might have altered the position of helix TM1A. The mobile N-terminus avoids entering the open vestibule of the inward-facing state, as accessibility studies do not show any reduction of quenching by iodide of a fluorophore attached to the N-terminus.
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Affiliation(s)
- Jawad A Khan
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Azmat Sohail
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Kumaresan Jayaraman
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Harald H Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr. 13a, 1090, Vienna, Austria.
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30
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Zhekova HR, Sakuma T, Johnson R, Concilio SC, Lech PJ, Zdravkovic I, Damergi M, Suksanpaisan L, Peng KW, Russell SJ, Noskov S. Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). J Chem Inf Model 2020; 60:1652-1665. [PMID: 32134653 DOI: 10.1021/acs.jcim.9b01114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human sodium iodide symporter (hNIS) is a theranostic reporter gene which concentrates several clinically approved SPECT and PET radiotracers and plays an essential role for the synthesis of thyroid hormones as an iodide transporter in the thyroid gland. Development of hNIS mutants which could enhance translocation of the desired imaging ions is currently underway. Unfortunately, it is hindered by lack of understanding of the 3D organization of hNIS and its relation to anion transport. There are no known crystal structures of hNIS in any of its conformational states. Homology modeling can be very effective in such situations; however, the low sequence identity between hNIS and relevant secondary transporters with available experimental structures makes the choice of a template and the generation of 3D models nontrivial. Here, we report a combined application of homology modeling and molecular dynamics refining of the hNIS structure in its semioccluded state. The modeling was based on templates from the LeuT-fold protein family and was done with emphasis on the refinement of the substrate-ion binding pocket. The consensus model developed in this work is compared to available biophysical and biochemical experimental data for a number of different LeuT-fold proteins. Some functionally important residues contributing to the formation of putative binding sites and permeation pathways for the cotransported Na+ ions and I- substrate were identified. The model predictions were experimentally tested by generation of mutant versions of hNIS and measurement of relative (to WT hNIS) 125I- uptake of 35 hNIS variants.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Toshie Sakuma
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Ryan Johnson
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Susanna C Concilio
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Patrycja J Lech
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Igor Zdravkovic
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mirna Damergi
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Kah-Whye Peng
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Stephen J Russell
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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31
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X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release. Nat Commun 2020; 11:1005. [PMID: 32081981 PMCID: PMC7035281 DOI: 10.1038/s41467-020-14735-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na+/substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na+ binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.
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32
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Shiref H, Bergman S, Clivio S, Sahai MA. The fine art of preparing membrane transport proteins for biomolecular simulations: Concepts and practical considerations. Methods 2020; 185:3-14. [PMID: 32081744 PMCID: PMC10062712 DOI: 10.1016/j.ymeth.2020.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 10/25/2022] Open
Abstract
Molecular dynamics (MD) simulations have developed into an invaluable tool in bimolecular research, due to the capability of the method in capturing molecular events and structural transitions that describe the function as well as the physiochemical properties of biomolecular systems. Due to the progressive development of more efficient algorithms, expansion of the available computational resources, as well as the emergence of more advanced methodologies, the scope of computational studies has increased vastly over time. We now have access to a multitude of online databases, software packages, larger molecular systems and novel ligands due to the phenomenon of emerging novel psychoactive substances (NPS). With so many advances in the field, it is understandable that novices will no doubt find it challenging setting up a protein-ligand system even before they run their first MD simulation. These initial steps, such as homology modelling, ligand docking, parameterization, protein preparation and membrane setup have become a fundamental part of the drug discovery pipeline, and many areas of biomolecular sciences benefit from the applications provided by these technologies. However, there still remains no standard on their usage. Therefore, our aim within this review is to provide a clear overview of a variety of concepts and methodologies to consider, providing a workflow for a case study of a membrane transport protein, the full-length human dopamine transporter (hDAT) in complex with different stimulants, where MD simulations have recently been applied successfully.
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Affiliation(s)
- Hana Shiref
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK
| | - Shana Bergman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | | | - Michelle A Sahai
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK.
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33
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Thompson CM, Chao CK. VGLUT substrates and inhibitors: A computational viewpoint. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183175. [PMID: 31923412 DOI: 10.1016/j.bbamem.2020.183175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023]
Abstract
The vesicular glutamate transporters (VGLUTs) bind and move glutamate (Glu) from the cytosol into the lumen of synaptic vesicles using a H+-electrochemical gradient (ΔpH and Δψ) generated by the vesicular H+-ATPase. VGLUTs show very low Glu binding and to date, no three-dimensional structure has been elucidated. Prior studies have attempted to identify the key residues involved in binding VGLUT substrates and inhibitors using homology models and docking experiments. Recently, the inward and outward oriented crystal structures of d-galactonate transporter (DgoT) emerged as possible structure templates for VGLUT. In this review, a new homology model for VGLUT2 based on DgoT has been developed and used to conduct docking experiments to identify and differentiate residues and binding orientations involved in ligand interactions. This review describes small molecule-ligand interactions including docking using a VGLUT2 homology model derived from DgoT.
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Affiliation(s)
- Charles M Thompson
- Center for Structural and Functional Neurosciences, Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, MT 59812, United States.
| | - Chih-Kai Chao
- Center for Structural and Functional Neurosciences, Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, MT 59812, United States
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34
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Bozzi AT, McCabe AL, Barnett BC, Gaudet R. Transmembrane helix 6b links proton and metal release pathways and drives conformational change in an Nramp-family transition metal transporter. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49881-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Bozzi AT, McCabe AL, Barnett BC, Gaudet R. Transmembrane helix 6b links proton and metal release pathways and drives conformational change in an Nramp-family transition metal transporter. J Biol Chem 2019; 295:1212-1224. [PMID: 31882536 DOI: 10.1074/jbc.ra119.011336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
The natural resistance-associated macrophage protein (Nramp) family encompasses transition metal and proton cotransporters that are present in many organisms from bacteria to humans. Recent structures of Deinococcus radiodurans Nramp (DraNramp) in multiple conformations revealed the intramolecular rearrangements required for alternating access of the metal-binding site to the external or cytosolic environment. Here, using recombinant proteins and metal transport and cysteine accessibility assays, we demonstrate that two parallel cytoplasm-accessible networks of conserved hydrophilic residues in DraNramp, one lining the wide intracellular vestibule for metal release and the other forming a narrow proton transport pathway, are essential for metal transport. We further show that mutagenic or posttranslational modifications of transmembrane helix (TM) 6b, which structurally links these two pathways, impede normal conformational cycling and metal transport. TM6b contains two highly conserved histidines, His232 and His237 We found that different mutagenic perturbations of His232, just below the metal-binding site along the proton exit route, differentially affect DraNramp's conformational state, suggesting that His232 serves as a pivot point for conformational changes. In contrast, any replacement of His237, lining the metal exit route, locked the transporter in a transport-inactive outward-closed state. We conclude that these two histidines, and TM6b more broadly, help trigger the bulk rearrangement of DraNramp to the inward-open state upon metal binding and facilitate return of the empty transporter to an outward-open state upon metal release.
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Affiliation(s)
- Aaron T Bozzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Anne L McCabe
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Benjamin C Barnett
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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36
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Li J, Zhao Z, Tajkhorshid E. Locking Two Rigid-body Bundles in an Outward-Facing Conformation: The Ion-coupling Mechanism in a LeuT-fold Transporter. Sci Rep 2019; 9:19479. [PMID: 31862903 PMCID: PMC6925253 DOI: 10.1038/s41598-019-55722-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/02/2019] [Indexed: 01/26/2023] Open
Abstract
Secondary active transporters use electrochemical gradient of ions to fuel the "uphill" translocation of the substrate following the alternating-access model. The coupling of ions to conformational dynamics of the protein remains one of the least characterized aspects of the transporter function. We employ extended molecular dynamics (MD) simulations to examine the Na+-binding effects on the structure and dynamics of a LeuT-fold, Na+-coupled secondary transporter (Mhp1) in its major conformational states, i.e., the outward-facing (OF) and inward-facing (IF) states, as well as on the OF ↔ IF state transition. Microsecond-long, unbiased MD simulations illustrate that Na+ stabilizes an OF conformation favorable for substrate association, by binding to a highly conserved site at the interface between the two helical bundles and restraining their relative position and motion. Furthermore, a special-protocol biased simulation for state transition suggests that Na+ binding hinders the OF ↔ IF transition. These synergistic Na+-binding effects allosterically couple the ion and substrate binding sites and modify the kinetics of state transition, collectively increasing the lifetime of an OF conformation with high substrate affinity, thereby facilitating substrate recruitment from a low-concentration environment. Based on the similarity between our findings for Mhp1 and experimental reports on LeuT, we propose that this model may represent a general Na+-coupling mechanism among LeuT-fold transporters.
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Affiliation(s)
- Jing Li
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, United States
| | - Zhiyu Zhao
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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37
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Quantifying secondary transport at single-molecule resolution. Nature 2019; 575:528-534. [PMID: 31723269 DOI: 10.1038/s41586-019-1747-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/07/2019] [Indexed: 01/07/2023]
Abstract
Secondary active transporters, which are vital for a multitude of physiological processes, use the energy of electrochemical ion gradients to power substrate transport across cell membranes1,2. Efforts to investigate their mechanisms of action have been hampered by their slow transport rates and the inherent limitations of ensemble methods. Here we quantify the activity of individual MhsT transporters, which are representative of the neurotransmitter:sodium symporter family of secondary transporters3, by imaging the transport of individual substrate molecules across lipid bilayers at both single- and multi-turnover resolution. We show that MhsT is active only when physiologically oriented and that the rate-limiting step of the transport cycle varies with the nature of the transported substrate. These findings are consistent with an extracellular allosteric substrate-binding site that modulates the rate-limiting aspects of the transport mechanism4,5, including the rate at which the transporter returns to an outward-facing state after the transported substrate is released.
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38
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Bohr SSR, Lund PM, Kallenbach AS, Pinholt H, Thomsen J, Iversen L, Svendsen A, Christensen SM, Hatzakis NS. Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition. Sci Rep 2019; 9:16169. [PMID: 31700110 PMCID: PMC6838188 DOI: 10.1038/s41598-019-52539-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022] Open
Abstract
Lipases are interfacially activated enzymes that catalyze the hydrolysis of ester bonds and constitute prime candidates for industrial and biotechnological applications ranging from detergent industry, to chiral organic synthesis. As a result, there is an incentive to understand the mechanisms underlying lipase activity at the molecular level, so as to be able to design new lipase variants with tailor-made functionalities. Our understanding of lipase function primarily relies on bulk assay averaging the behavior of a high number of enzymes masking structural dynamics and functional heterogeneities. Recent advances in single molecule techniques based on fluorogenic substrate analogues revealed the existence of lipase functional states, and furthermore so how they are remodeled by regulatory cues. Single particle studies of lipases on the other hand directly observed diffusional heterogeneities and suggested lipases to operate in two different modes. Here to decipher how mutations in the lid region controls Thermomyces lanuginosus lipase (TLL) diffusion and function we employed a Single Particle Tracking (SPT) assay to directly observe the spatiotemporal localization of TLL and rationally designed mutants on native substrate surfaces. Parallel imaging of thousands of individual TLL enzymes and HMM analysis allowed us to observe and quantify the diffusion, abundance and microscopic transition rates between three linearly interconverting diffusional states for each lipase. We proposed a model that correlate diffusion with function that allowed us to predict that lipase regulation, via mutations in lid region or product inhibition, primarily operates via biasing transitions to the active states.
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Affiliation(s)
- Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philip M Lund
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Amalie S Kallenbach
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Henrik Pinholt
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Lars Iversen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S, Krogshøjsvej 36, DK 2880, Bagværd, Denmark
| | | | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, Thorvaldsensvej 40, University of Copenhagen, Frederiksberg C, 1871, Denmark.
- NovoNordisk center for protein research, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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Dudev T, Mazmanian K, Weng WH, Grauffel C, Lim C. Free and Bound Therapeutic Lithium in Brain Signaling. Acc Chem Res 2019; 52:2960-2970. [PMID: 31556294 DOI: 10.1021/acs.accounts.9b00389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lithium, a first-line therapy for bipolar disorder, is effective in preventing suicide and new depressive/manic episodes. Yet, how this beguilingly simple monocation with only two electrons could yield such profound therapeutic effects remains unclear. An in-depth understanding of lithium's mechanisms of actions would help one to develop better treatments limiting its adverse side effects and repurpose lithium for treating traumatic brain injury and chronic neurodegenerative diseases. In this Account, we begin with a comparison of the physicochemical properties of Li+ and its key native rivals, Na+ and Mg2+, to provide physical grounds for their competition in protein binding sites. Next, we review the abnormal signaling pathways and proteins found in bipolar patients, who generally have abnormally high intracellular Na+ and Ca2+ concentrations, high G-protein levels, and hyperactive phosphatidylinositol signaling and glycogen synthase kinase-3β (GSK3β) activity. We briefly summarize experimental findings on how lithium, at therapeutic doses, modulates these abnormal signaling pathways and proteins. Following this survey, we address the following aspects of lithium's therapeutic actions: (1) Can Li+ displace Na+ from the allosteric Na+-binding sites in neurotransmitter transporters and G-protein coupled receptors (GPCRs); if so, how would this affect the host protein's function? (2) Why are certain Mg2+-dependent enzymes targeted by Li+? (3) How does Li+ binding to Mg2+-bound ATP/GTP (denoted as NTP) in solution affect the cofactor's conformation and subsequent recognition by the host protein? (4) How do NTP-Mg-Li complexes modulate the properties of the respective cellular receptors and signal-transducing proteins? We show that Li+ may displace Na+ from allosteric Na+-binding sites in certain GPCRs and stabilize inactive conformations, preventing these receptors from relaying signal to the respective G-proteins. It may also displace Mg2+ in enzymes containing highly cationic Mg2+-binding sites such as GSK3β, but not in enzymes containing Mg2+-binding sites with low or zero charge. We further show that Li+ binding to Mg2+-NTP in water does not alter the NTP conformation, which is locked by all three phosphates binding to Mg2+. However, bound lithium in the form of [NTP-Mg-Li]2- dianions can activate or inhibit the host protein depending on the NTP-binding pocket's shape, which determines the metal-binding mode: The ATP-binding pocket's shape in the P2X receptor is complementary to the native ATP-Mg solution conformation and nicely fits [ATP-Mg-Li]2-. However, since the ATP βγ phosphates bind Li+, bimetallic [ATP-Mg-Li]2- may be more resistant to hydrolysis than the native cofactor, enabling ATP to reside longer in the binding site and elicit a prolonged P2X response. In contrast, the elongated GTP-binding pockets in G-proteins allow only two GTP phosphates to bind Mg2+, so the GTP conformation is no longer "triply-locked". Consequently, Li+ binding to GTP-Mg can significantly alter the native cofactor's structure, lowering the activated G-protein level, thus attenuating hyperactive G-protein-mediated signaling in bipolar patients. In summary, we have presented a larger "connected" picture of lithium's diverse effects based on its competition as a free monocation with native cations or as a phosphate-bound polyanionic complex modulating the host protein function.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Wei-Hsiang Weng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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40
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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41
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Rudnick G, Sandtner W. Serotonin transport in the 21st century. J Gen Physiol 2019; 151:1248-1264. [PMID: 31570504 PMCID: PMC6829555 DOI: 10.1085/jgp.201812066] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/24/2019] [Indexed: 12/16/2022] Open
Abstract
Rudnick and Sandtner review the history of serotonin transporter research in light of structural and electrophysiological advances. Serotonin (5-hydroxytryptamine [5-HT]) is accumulated within nerve endings by the serotonin transporter (SERT), which terminates its extracellular action and provides cytoplasmic 5-HT for refilling of synaptic vesicles. SERT is the target for many antidepressant medications as well as psychostimulants such as cocaine and ecstasy (3,4-methylenedioxymethamphetamine). SERT belongs to the SLC6 family of ion-coupled transporters and is structurally related to several other transporter families. SERT was studied in the 1970s and 1980s using membrane vesicles isolated from blood platelets. These studies led to a proposed stoichiometry of transport that has been challenged by high-resolution structures of SERT and its homologues and by studies of SERT electrophysiology. Here, we review the original evidence alongside more recent structural and electrophysiological evidence. A self-consistent picture emerges with surprising insights into the ion fluxes that accompany 5-HT transport.
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Affiliation(s)
- Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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42
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Joseph D, Pidathala S, Mallela AK, Penmatsa A. Structure and Gating Dynamics of Na +/Cl - Coupled Neurotransmitter Transporters. Front Mol Biosci 2019; 6:80. [PMID: 31555663 PMCID: PMC6742698 DOI: 10.3389/fmolb.2019.00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022] Open
Abstract
Neurotransmitters released at the neural synapse through vesicle exocytosis are spatiotemporally controlled by the action of neurotransmitter transporters. Integral membrane proteins of the solute carrier 6 (SLC6) family are involved in the sodium and chloride coupled uptake of biogenic amine neurotransmitters including dopamine, serotonin, noradrenaline and inhibitory neurotransmitters including glycine and γ-amino butyric acid. This ion-coupled symport works through a well-orchestrated gating of substrate through alternating-access, which is mediated through movements of helices that resemble a rocking-bundle. A large array of commercially prescribed drugs and psychostimulants selectively target neurotransmitter transporters thereby modulating their levels in the synaptic space. Drug-induced changes in the synaptic neurotransmitter levels can be used to treat depression or neuropathic pain whereas in some instances prolonged usage can lead to habituation. Earlier structural studies of bacterial neurotransmitter transporter homolog LeuT and recent structure elucidation of the Drosophila dopamine transporter (dDAT) and human serotonin transporter (hSERT) have yielded a wealth of information in understanding the transport and inhibition mechanism of neurotransmitter transporters. Computational studies based on the structures of dDAT and hSERT have shed light on the dynamics of varied components of these molecular gates in affecting the uphill transport of neurotransmitters. This review seeks to address structural dynamics of neurotransmitter transporters at the extracellular and intracellular gates and the effect of inhibitors on the ligand-binding pocket. We also delve into the effect of additional factors including lipids and cytosolic domains that influence the translocation of neurotransmitters across the membrane.
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Affiliation(s)
- Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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43
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LeVine MV, Terry DS, Khelashvili G, Siegel ZS, Quick M, Javitch JA, Blanchard SC, Weinstein H. The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor. Proc Natl Acad Sci U S A 2019; 116:15947-15956. [PMID: 31324743 PMCID: PMC6689989 DOI: 10.1073/pnas.1903020116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. Results from many structural, functional, and computational studies on LeuT, a bacterial NSS homolog, have provided critical insight into the mechanism of sodium-coupled transport, but the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of molecular dynamics simulations, single-molecule fluorescence resonance energy transfer (smFRET) imaging, and measurements of Na+ binding and substrate transport that reveals an allosteric substrate specificity mechanism. In this mechanism, residues F259 and I359 in the substrate binding pocket couple the binding of substrate to Na+ release from the Na2 site by allosterically modulating the stability of a partially open, inward-facing state. We propose a model for transport selectivity in which residues F259 and I359 act as a volumetric sensor that inhibits the transport of bulky amino acids.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Zarek S Siegel
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Matthias Quick
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
- Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
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44
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Song S, Wang H, Sun M, Tang J, Zheng B, Wang X, Tan YW. Reactive oxygen species-mediated BIN2 activity revealed by single-molecule analysis. THE NEW PHYTOLOGIST 2019; 223:692-704. [PMID: 30597572 DOI: 10.1111/nph.15669] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 12/21/2018] [Indexed: 05/28/2023]
Abstract
Much evidence has shown that reactive oxygen species (ROS) regulate several plant hormone signaling cascades, but little is known about the real-time kinetics and the underlying molecular mechanisms of the target proteins in the brassinosteroid (BR) signaling pathway. In this study, we used single-molecule techniques to investigate the true signaling timescales of the major BR signaling components BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINOSTEROID INSENSITIVE 2 (BIN2) of Arabidopsis thaliana. The rate constants of BIN2 associating with ATP and phosphorylating BES1 were determined to be 0.7 ± 0.4 mM-1 s-1 and 2.3 ± 1.4 s-1 , respectively. Interestingly, we found that the interaction of BIN2 and BES1 was oxygen-dependent, and oxygen can directly modify BIN2. The activity of BIN2 was switched on via modification of specific cysteine (Cys) residues, including C59, C95, C99 and C162. The mutation of these Cys residues inhibited the BR signaling outputs. These findings demonstrate the power of using single-molecule techniques to study the dynamic interactions of signaling components, which is difficult to be discovered by conventional physiological and biochemical methods.
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Affiliation(s)
- Song Song
- State Key Laboratory of Surface Physics, Collaborative Innovation Center for Genetics and Development, Department of Physics, Fudan University, Shanghai, 200433, China
| | - Haijiao Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengyuan Sun
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jie Tang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xuelu Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Collaborative Innovation Center for Genetics and Development, Department of Physics, Fudan University, Shanghai, 200433, China
- Multiscale Research Institute for Complex Systems, Fudan University, Shanghai, 200438, China
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45
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Nielsen AK, Möller IR, Wang Y, Rasmussen SGF, Lindorff-Larsen K, Rand KD, Loland CJ. Substrate-induced conformational dynamics of the dopamine transporter. Nat Commun 2019; 10:2714. [PMID: 31221956 PMCID: PMC6586795 DOI: 10.1038/s41467-019-10449-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 05/09/2019] [Indexed: 02/02/2023] Open
Abstract
The dopamine transporter is a member of the neurotransmitter:sodium symporters (NSSs), which are responsible for termination of neurotransmission through Na+-driven reuptake of neurotransmitter from the extracellular space. Experimental evidence elucidating the coordinated conformational rearrangements related to the transport mechanism has so far been limited. Here we probe the global Na+- and dopamine-induced conformational dynamics of the wild-type Drosophila melanogaster dopamine transporter using hydrogen-deuterium exchange mass spectrometry. We identify Na+- and dopamine-induced changes in specific regions of the transporter, suggesting their involvement in protein conformational transitions. Furthermore, we detect ligand-dependent slow cooperative fluctuations of helical stretches in several domains of the transporter, which could be a molecular mechanism that assists in the transporter function. Our results provide a framework for understanding the molecular mechanism underlying the function of NSSs by revealing detailed insight into the state-dependent conformational changes associated with the alternating access model of the dopamine transporter.
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Affiliation(s)
- Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Ingvar R Möller
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark.
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark.
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smFRET Probing Reveals Substrate-Dependent Conformational Dynamics of E. coli Multidrug MdfA. Biophys J 2019; 116:2296-2303. [PMID: 31146923 DOI: 10.1016/j.bpj.2019.04.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 11/21/2022] Open
Abstract
Bacterial multidrug-resistance transporters of the major facilitator superfamily are distinguished by their extraordinary ability to bind structurally diverse substrates, thus serving as a highly efficient tool to protect cells from multiple toxic substances present in their environment, including antibiotic drugs. However, details of the dynamic conformational changes of the transport cycle involved remain to be elucidated. Here, we used the single-molecule fluorescence resonance energy transfer technique to investigate the conformational behavior of the Escherichia coli multidrug transporter MdfA under conditions of different substrates, pH, and alkali metal ions. Our data show that different substrates exhibit distinct effects on both the conformational distribution and transition rate between two major conformations. Although the cationic substrate tetraphenylphosphonium favors the outward-facing conformation, it has less effect on the transition rate. In contrast, binding of the electroneutral substrate chloramphenicol tends to stabilize the inward-facing conformation and decreases the transition rate. Therefore, our study supports the notion that the MdfA transporter uses distinct mechanisms to transport electroneutral and cationic substrates.
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47
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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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48
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Niello M, Cintulova D, Hellsberg E, Jäntsch K, Holy M, Ayatollahi LH, Cozzi NV, Freissmuth M, Sandtner W, Ecker GF, Mihovilovic MD, Sitte HH. para-Trifluoromethyl-methcathinone is an allosteric modulator of the serotonin transporter. Neuropharmacology 2019; 161:107615. [PMID: 31028773 DOI: 10.1016/j.neuropharm.2019.04.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 11/15/2022]
Abstract
The transporters for dopamine (DAT) and serotonin (SERT) are important targets in the treatment of psychiatric disorders including major depression, anxiety and attention-deficit hyperactivity disorder. Drugs acting at these transporters can act as inhibitors or as releasers. In addition, it has been recently appreciated that some compounds are less efficacious releasers than amphetamine. Thus, they are classified as partial releasers. Compounds can act on both SERT and DAT or display exquisite selectivity for either SERT or DAT, but the structural basis for selectivity is poorly understood. The trifluoromethyl-substitution of methcathinone in the para-position has been shown to dramatically shift the selectivity of methcathinone (MCAT) towards SERT. Here, we examined MCAT, para-trifluoromethyl-methcathinone (pCF3MCAT) and other analogues to understand (i) the determinants of selectivity and (ii) the effects of the para-CF3-substitution of MCAT on the transport cycle. We systematically tested different para-substituted MCATs by biochemical, computational and electrophysiological approaches: addition of the pCF3group, but not of other substituents with larger van der Waal's volume, lipophilicity or polarity, converted the DAT-selective MCAT into a SERT-selective partial releaser. Electrophysiological and superfusion experiments, together with kinetic modelling, showed that pCF3MCAT, but not MCAT, trapped a fraction of SERTs in an inactive state by occupying the S2-site. These findings define a new mechanism of action for partial releasers, which is distinct from the other two known binding modes underlying partial release. Our observations highlight the fact that the substrate permeation pathway of monoamine transporters supports multiple binding modes, which can be exploited for drug design. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Marco Niello
- Institute of Pharmacology, Medical University, Vienna, Austria
| | | | - Eva Hellsberg
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Kathrin Jäntsch
- Institute of Pharmacology, Medical University, Vienna, Austria
| | - Marion Holy
- Institute of Pharmacology, Medical University, Vienna, Austria
| | | | - Nicholas V Cozzi
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | | | - Walter Sandtner
- Institute of Pharmacology, Medical University, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | | | - Harald H Sitte
- Institute of Pharmacology, Medical University, Vienna, Austria.
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Möller IR, Slivacka M, Nielsen AK, Rasmussen SGF, Gether U, Loland CJ, Rand KD. Conformational dynamics of the human serotonin transporter during substrate and drug binding. Nat Commun 2019; 10:1687. [PMID: 30976000 PMCID: PMC6459873 DOI: 10.1038/s41467-019-09675-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/22/2019] [Indexed: 12/24/2022] Open
Abstract
The serotonin transporter (SERT), a member of the neurotransmitter:sodium symporter family, is responsible for termination of serotonergic signaling by re-uptake of serotonin (5-HT) into the presynaptic neuron. Its key role in synaptic transmission makes it a major drug target, e.g. for the treatment of depression, anxiety and post-traumatic stress. Here, we apply hydrogen-deuterium exchange mass spectrometry to probe the conformational dynamics of human SERT in the absence and presence of known substrates and targeted drugs. Our results reveal significant changes in dynamics in regions TM1, EL3, EL4, and TM12 upon binding co-transported ions (Na+/K+) and ligand-mediated changes in TM1, EL3 and EL4 upon binding 5-HT, the drugs S-citalopram, cocaine and ibogaine. Our results provide a comprehensive direct view of the conformational response of SERT upon binding both biologically relevant substrate/ions and ligands of pharmaceutical interest, thus advancing our understanding of the structure-function relationship in SERT.
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Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marika Slivacka
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ulrik Gether
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark.
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Ponzoni L, Zhang S, Cheng MH, Bahar I. Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0177. [PMID: 29735731 PMCID: PMC5941172 DOI: 10.1098/rstb.2017.0177] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
The LeuT-fold superfamily includes secondary active transporters from different functional families, which share a common tertiary structure, despite having a remarkably low sequence similarity. By identifying the common structural and dynamical features upon principal component analysis of a comprehensive ensemble of 90 experimentally resolved structures and anisotropic network model evaluation of collective motions, we provide a unified point of view for understanding the reasons why this particular fold has been selected by evolution to accomplish such a broad spectrum of functions. The parallel identification of conserved sequence features, localized at specific sites of transmembrane helices, sheds light on the role of broken helices (TM1 and TM6 in LeuT) in promoting ion/substrate binding and allosteric interconversion between the outward- and inward-facing conformations of transporters. Finally, the determination of the dynamics landscape for the structural ensemble provides a promising framework for the classification of transporters based on their dynamics, and the characterization of the collective movements that favour multimerization.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Luca Ponzoni
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - She Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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