1
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Li HZ, Pike ACW, Lotsaris I, Chi G, Hansen JS, Lee SC, Rödström KEJ, Bushell SR, Speedman D, Evans A, Wang D, He D, Shrestha L, Nasrallah C, Burgess-Brown NA, Vandenberg RJ, Dafforn TR, Carpenter EP, Sauer DB. Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Nat Commun 2024; 15:5503. [PMID: 38951531 PMCID: PMC11217458 DOI: 10.1038/s41467-024-48921-x] [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: 05/24/2023] [Accepted: 05/16/2024] [Indexed: 07/03/2024] Open
Abstract
Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes that link substrate release and opening of the cytoplasmic gate and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.
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Affiliation(s)
- Huanyu Z Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashley C W Pike
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Irina Lotsaris
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Karin E J Rödström
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon R Bushell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Speedman
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Evans
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dong Wang
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Didi He
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leela Shrestha
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chady Nasrallah
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert J Vandenberg
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
| | | | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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2
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Stary D, Bajda M. Taurine and Creatine Transporters as Potential Drug Targets in Cancer Therapy. Int J Mol Sci 2023; 24:ijms24043788. [PMID: 36835201 PMCID: PMC9964810 DOI: 10.3390/ijms24043788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Cancer cells are characterized by uncontrolled growth, proliferation, and impaired apoptosis. Tumour progression could be related to poor prognosis and due to this fact, researchers have been working on novel therapeutic strategies and antineoplastic agents. It is known that altered expression and function of solute carrier proteins from the SLC6 family could be associated with severe diseases, including cancers. These proteins were noticed to play important physiological roles through transferring nutrient amino acids, osmolytes, neurotransmitters, and ions, and many of them are necessary for survival of the cells. Herein, we present the potential role of taurine (SLC6A6) and creatine (SLC6A8) transporters in cancer development as well as therapeutic potential of their inhibitors. Experimental data indicate that overexpression of analyzed proteins could be connected with colon or breast cancers, which are the most common types of cancers. The pool of known inhibitors of these transporters is limited; however, one ligand of SLC6A8 protein is currently tested in the first phase of clinical trials. Therefore, we also highlight structural aspects useful for ligand development. In this review, we discuss SLC6A6 and SLC6A8 transporters as potential biological targets for anticancer agents.
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Affiliation(s)
- Dorota Stary
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688 Cracow, Poland
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 16 St., 31-530 Cracow, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9 St., 30-688 Cracow, Poland
- Correspondence:
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3
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Anderson CMH, Edwards N, Watson AK, Althaus M, Thwaites DT. Reshaping the Binding Pocket of the Neurotransmitter:Solute Symporter (NSS) Family Transporter SLC6A14 (ATB 0,+) Selectively Reduces Access for Cationic Amino Acids and Derivatives. Biomolecules 2022; 12:biom12101404. [PMID: 36291613 PMCID: PMC9599917 DOI: 10.3390/biom12101404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
SLC6A14 (ATB0,+) is unique among SLC proteins in its ability to transport 18 of the 20 proteinogenic (dipolar and cationic) amino acids and naturally occurring and synthetic analogues (including anti-viral prodrugs and nitric oxide synthase (NOS) inhibitors). SLC6A14 mediates amino acid uptake in multiple cell types where increased expression is associated with pathophysiological conditions including some cancers. Here, we investigated how a key position within the core LeuT-fold structure of SLC6A14 influences substrate specificity. Homology modelling and sequence analysis identified the transmembrane domain 3 residue V128 as equivalent to a position known to influence substrate specificity in distantly related SLC36 and SLC38 amino acid transporters. SLC6A14, with and without V128 mutations, was heterologously expressed and function determined by radiotracer solute uptake and electrophysiological measurement of transporter-associated current. Substituting the amino acid residue occupying the SLC6A14 128 position modified the binding pocket environment and selectively disrupted transport of cationic (but not dipolar) amino acids and related NOS inhibitors. By understanding the molecular basis of amino acid transporter substrate specificity we can improve knowledge of how this multi-functional transporter can be targeted and how the LeuT-fold facilitates such diversity in function among the SLC6 family and other SLC amino acid transporters.
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Affiliation(s)
- Catriona M. H. Anderson
- School of Natural & Environmental Sciences, Faculty of Science, Engineering & Agriculture, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Correspondence: (C.M.H.A.); (D.T.T.)
| | - Noel Edwards
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew K. Watson
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mike Althaus
- School of Natural & Environmental Sciences, Faculty of Science, Engineering & Agriculture, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Natural Sciences & Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53359 Rheinbach, Germany
| | - David T. Thwaites
- Biosciences Institute, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (C.M.H.A.); (D.T.T.)
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4
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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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5
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Xue W, Fu T, Zheng G, Tu G, Zhang Y, Yang F, Tao L, Yao L, Zhu F. Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters. Curr Med Chem 2020; 27:3830-3876. [DOI: 10.2174/0929867325666181009123218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023]
Abstract
Background:
The human Monoamine Transporters (hMATs), primarily including hSERT,
hNET and hDAT, are important targets for the treatment of depression and other behavioral disorders
with more than the availability of 30 approved drugs.
Objective:
This paper is to review the recent progress in the binding mode and inhibitory mechanism of
hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor
design and discovery. The Structure-Activity Relationship (SAR) and the selectivity for hit/lead compounds
to hMATs that are evaluated by in vitro and in vivo experiments will be highlighted.
Methods:
PubMed and Web of Science databases were searched for protein-ligand interaction, novel
inhibitors design and synthesis studies related to hMATs.
Results:
Literature data indicate that since the first crystal structure determinations of the homologous
bacterial Leucine Transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental
structures or computational models has been accumulated that now defines a substantial degree
of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs
inhibitors have been discovered by medicinal chemistry with significant help from computational models.
Conclusion:
The reported new compounds act on hMATs as well as the structures of the transporters
complexed with diverse ligands by either experiment or computational modeling have shed light on the
poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies
will greatly promote the Structure-Based Drug Design (SBDD) of structurally novel scaffolds with high
activity and selectivity for hMATs.
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Affiliation(s)
- Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Guoxun Zheng
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Yang Zhang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Lixia Yao
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, United States
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
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6
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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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7
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Hellsberg E, Ecker GF, Stary-Weinzinger A, Forrest LR. A structural model of the human serotonin transporter in an outward-occluded state. PLoS One 2019; 14:e0217377. [PMID: 31251747 PMCID: PMC6599148 DOI: 10.1371/journal.pone.0217377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
The human serotonin transporter hSERT facilitates the reuptake of its endogenous substrate serotonin from the synaptic cleft into presynaptic neurons after signaling. Reuptake regulates the availability of this neurotransmitter and therefore hSERT plays an important role in balancing human mood conditions. In 2016, the first 3D structures of this membrane transporter were reported in an inhibitor-bound, outward-open conformation. These structures revealed valuable information about interactions of hSERT with antidepressant drugs. Nevertheless, the question remains how serotonin facilitates the specific conformational changes that open and close pathways from the synapse and to the cytoplasm as required for transport. Here, we present a serotonin-bound homology model of hSERT in an outward-occluded state, a key intermediate in the physiological cycle, in which the interactions with the substrate are likely to be optimal. Our approach uses two template structures and includes careful refinement and comprehensive computational validation. According to microsecond-long molecular dynamics simulations, this model exhibits interactions between the gating residues in the extracellular pathway, and these interactions differ from those in an outward-open conformation of hSERT bound to serotonin. Moreover, we predict several features of this state by monitoring the intracellular gating residues, the extent of hydration, and, most importantly, protein-ligand interactions in the central binding site. The results illustrate common and distinct characteristics of these two transporter states and provide a starting point for future investigations of the transport mechanism in hSERT.
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Affiliation(s)
- Eva Hellsberg
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | | | - Lucy R. Forrest
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States of America
- * E-mail:
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8
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Navratna V, Gouaux E. Insights into the mechanism and pharmacology of neurotransmitter sodium symporters. Curr Opin Struct Biol 2019; 54:161-170. [PMID: 30921707 DOI: 10.1016/j.sbi.2019.03.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/17/2022]
Abstract
Neurotransmitter sodium symporters (NSS) belong to the SLC6 family of solute carriers and play an essential role in neurotransmitter homeostasis throughout the body. In the past decade, structural studies employing bacterial orthologs of NSSs have provided insight into the mechanism of neurotransmitter transport. While the overall architecture of SLC6 transporters is conserved among species, in comparison to the bacterial homologs, the eukaryotic SLC6 family members harbor differences in amino acid sequence and molecular structure, which underpins their functional and pharmacological diversity, as well as their ligand specificity. Here, we review the structures and mechanisms of eukaryotic NSSs, focusing on the molecular basis for ligand recognition and on transport mechanism.
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Affiliation(s)
- Vikas Navratna
- Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, United States; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR, United States.
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9
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Abstract
The small intestine mediates the absorption of amino acids after ingestion of protein and sustains the supply of amino acids to all tissues. The small intestine is an important contributor to plasma amino acid homeostasis, while amino acid transport in the large intestine is more relevant for bacterial metabolites and fluid secretion. A number of rare inherited disorders have contributed to the identification of amino acid transporters in epithelial cells of the small intestine, in particular cystinuria, lysinuric protein intolerance, Hartnup disorder, iminoglycinuria, and dicarboxylic aminoaciduria. These are most readily detected by analysis of urine amino acids, but typically also affect intestinal transport. The genes underlying these disorders have all been identified. The remaining transporters were identified through molecular cloning techniques to the extent that a comprehensive portrait of functional cooperation among transporters of intestinal epithelial cells is now available for both the basolateral and apical membranes. Mouse models of most intestinal transporters illustrate their contribution to amino acid homeostasis and systemic physiology. Intestinal amino acid transport activities can vary between species, but these can now be explained as differences of amino acid transporter distribution along the intestine. © 2019 American Physiological Society. Compr Physiol 9:343-373, 2019.
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Affiliation(s)
- Stefan Bröer
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Stephen J Fairweather
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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10
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The LeuT-fold neurotransmitter:sodium symporter MhsT has two substrate sites. Proc Natl Acad Sci U S A 2018; 115:E7924-E7931. [PMID: 30082383 DOI: 10.1073/pnas.1717444115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Crystal structures of the neurotransmitter:sodium symporter MhsT revealed occluded inward-facing states with one substrate (Trp) bound in the primary substrate (S1) site and a collapsed extracellular vestibule, which in LeuT contains the second substrate (S2) site. In n-dodecyl-β-d-maltoside, the detergent used to prepare MhsT for crystallization, the substrate-to-protein binding stoichiometry was determined by using scintillation proximity to be 1 Trp:MhsT. Here, using the same experimental approach, as well as equilibrium dialysis, we report that in n-decyl-β-d-maltoside, or after reconstitution in lipid, MhsT, like LeuT, can simultaneously bind two Trp substrate molecules. Trp binding to the S2 site sterically blocks access to a substituted Cys at position 33 in the S2 site, as well as access to the deeper S1 site. Mutation of either the S1 or S2 site disrupts transport, consistent with previous studies in LeuT showing that substrate binding to the S2 site is an essential component of the transport mechanism.
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11
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Navratna V, Tosh DK, Jacobson KA, Gouaux E. Thermostabilization and purification of the human dopamine transporter (hDAT) in an inhibitor and allosteric ligand bound conformation. PLoS One 2018; 13:e0200085. [PMID: 29965988 PMCID: PMC6028122 DOI: 10.1371/journal.pone.0200085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
The human dopamine transporter (hDAT) plays a major role in dopamine homeostasis and regulation of neurotransmission by clearing dopamine from the extracellular space using secondary active transport. Dopamine is an essential monoamine chemical messenger that regulates reward seeking behavior, motor control, hormonal release, and emotional response in humans. Psychostimulants such as cocaine primarily target the central binding site of hDAT and lock the transporter in an outward-facing conformation, thereby inhibiting dopamine reuptake. The inhibition of dopamine reuptake leads to accumulation of dopamine in the synapse causing heightened signaling. In addition, hDAT is implicated in various neurological disorders and disease-associated neurodegeneration. Despite its significance, the structural studies of hDAT have proven difficult. Instability of hDAT in detergent micelles has been a limiting factor in its successful biochemical, biophysical, and structural characterization. To overcome this hurdle, we identified ligands that stabilize hDAT in detergent micelles. We then screened ~200 single residue mutants of hDAT using a high-throughput scintillation proximity assay and identified a thermostable variant (I248Y). Here we report a robust strategy to overexpress and successfully purify a thermostable variant of hDAT in an inhibitor and allosteric ligand bound conformation.
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Affiliation(s)
- Vikas Navratna
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Dilip K. Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon, United States of America
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12
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Bai X, Moraes TF, Reithmeier RAF. Structural biology of solute carrier (SLC) membrane transport proteins. Mol Membr Biol 2018; 34:1-32. [PMID: 29651895 DOI: 10.1080/09687688.2018.1448123] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human solute carriers (SLCs) comprise over 400 different transporters, organized into 65 families ( http://slc.bioparadigms.org/ ) based on their sequence homology and transport function. SLCs are responsible for transporting extraordinarily diverse solutes across biological membranes, including inorganic ions, amino acids, lipids, sugars, neurotransmitters and drugs. Most of these membrane proteins function as coupled symporters (co-transporters) utilizing downhill ion (H+ or Na+) gradients as the driving force for the transport of substrate against its concentration gradient into cells. Other members work as antiporters (exchangers) that typically contain a single substrate-binding site with an alternating access mode of transport, while a few members exhibit channel-like properties. Dysfunction of SLCs is correlated with numerous human diseases and therefore they are potential therapeutic drug targets. In this review, we identified all of the SLC crystal structures that have been determined, most of which are from prokaryotic species. We further sorted all the SLC structures into four main groups with different protein folds and further discuss the well-characterized MFS (major facilitator superfamily) and LeuT (leucine transporter) folds. This review provides a systematic analysis of the structure, molecular basis of substrate recognition and mechanism of action in different SLC family members.
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Affiliation(s)
- Xiaoyun Bai
- a Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Trevor F Moraes
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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13
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Reith MEA, Jones KT, Zhen J, Topiol S. Latch and trigger role for R445 in DAT transport explains molecular basis of DTDS. Bioorg Med Chem Lett 2017; 28:470-475. [PMID: 29258773 DOI: 10.1016/j.bmcl.2017.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 01/12/2023]
Abstract
A recent study reports on five different mutations as sources of dopamine transporter (DAT) deficiency syndrome (DTDS). One of these mutations, R445C, is believed to be located on the intracellular side of DAT distal to the primary (S1) or secondary (S2) sites to which substrate binding is understood to occur. Thus, the molecular mechanism by which the R445C mutation results in DAT transport deficiency has eluded explanation. However, the recently reported X-ray structures of the endogenous amine transporters for dDAT and hSERT revealed the presence of a putative salt bridge between R445 and E428 suggesting a possible mechanism. To evaluate whether the R445C effect is a result of a salt bridge interaction, the mutants R445E, E428R, and the double mutant E428R/R445E were generated. The single mutants R445E and E428R displayed loss of binding and transport properties of the substrate [3H]DA and inhibitor [3H]CFT at the cell surface while the double mutant E428R/R445E, although nonfunctional, restored [3H]DA and [3H]CFT binding affinity to that of WT. Structure based analyses of these results led to a model wherein R445 plays a dual role in normal DAT function. R445 acts as a component of a latch in its formation of a salt bridge with E428 which holds the primary substrate binding site (S1) in place and helps enforce the inward closed protein state. When this salt bridge is broken, R445 acts as a trigger which disrupts a local polar network and leads to the release of the N-terminus from its position inducing the inward closed state to one allowing the inward open state. In this manner, both the loss of binding and transport properties of the R445C variant are explained.
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Affiliation(s)
- Maarten E A Reith
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA; Department Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Kymry T Jones
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Juan Zhen
- Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Sid Topiol
- 3D-2drug, LLC, P.O. Box 184, Fair Lawn, NJ, USA.
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14
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Krout D, Pramod AB, Dahal RA, Tomlinson MJ, Sharma B, Foster JD, Zou MF, Boatang C, Newman AH, Lever JR, Vaughan RA, Henry LK. Inhibitor mechanisms in the S1 binding site of the dopamine transporter defined by multi-site molecular tethering of photoactive cocaine analogs. Biochem Pharmacol 2017; 142:204-215. [PMID: 28734777 DOI: 10.1016/j.bcp.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints. Understanding the molecular mechanisms governing the pharmacological inhibition of DAT is therefore key for understanding the requisite interactions for behavioral modulation and addiction. Previously, we leveraged complementary computational docking, mutagenesis, peptide mapping, and substituted cysteine accessibility strategies to identify the specific adduction site and binding pose for the crosslinkable, photoactive cocaine analog, RTI 82, which contains a photoactive azide attached at the 2β position of the tropane pharmacophore. Here, we utilize similar methodology with a different cocaine analog N-[4-(4-azido-3-I-iodophenyl)-butyl]-2-carbomethoxy-3-(4-chlorophenyl)tropane, MFZ 2-24, where the photoactive azide is attached to the tropane nitrogen. In contrast to RTI 82, which crosslinked into residue Phe319 of transmembrane domain (TM) 6, our findings show that MFZ 2-24 adducts to Leu80 in TM1 with modeling and biochemical data indicating that MFZ 2-24, like RTI 82, occupies the central S1 binding pocket with the (+)-charged tropane ring nitrogen coordinating with the (-)-charged carboxyl side chain of Asp79. The superimposition of the tropane ring in the three-dimensional binding poses of these two distinct ligands provides strong experimental evidence for cocaine binding to DAT in the S1 site and the importance of the tropane moiety in competitive mechanisms of DA uptake inhibition. These findings set a structure-function baseline for comparison of typical and atypical DAT inhibitors and how their interactions with DAT could lead to the loss of cocaine-like behaviors.
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Affiliation(s)
- Danielle Krout
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Akula Bala Pramod
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Rejwi Acharya Dahal
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Michael J Tomlinson
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Babita Sharma
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Mu-Fa Zou
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Comfort Boatang
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Amy Hauck Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - John R Lever
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; Department of Radiology and Radiopharmaceutical Sciences Institute, University of Missouri, Columbia, MO 65211, USA
| | - Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
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15
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Sohail A, Jayaraman K, Venkatesan S, Gotfryd K, Daerr M, Gether U, Loland CJ, Wanner KT, Freissmuth M, Sitte HH, Sandtner W, Stockner T. The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput Biol 2016; 12:e1005197. [PMID: 27835643 PMCID: PMC5105988 DOI: 10.1371/journal.pcbi.1005197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/12/2016] [Indexed: 12/27/2022] Open
Abstract
Human neurotransmitter transporters are found in the nervous system terminating synaptic signals by rapid removal of neurotransmitter molecules from the synaptic cleft. The homologous transporter LeuT, found in Aquifex aeolicus, was crystallized in different conformations. Here, we investigated the inward-open state of LeuT. We compared LeuT in membranes and micelles using molecular dynamics simulations and lanthanide-based resonance energy transfer (LRET). Simulations of micelle-solubilized LeuT revealed a stable and widely open inward-facing conformation. However, this conformation was unstable in a membrane environment. The helix dipole and the charged amino acid of the first transmembrane helix (TM1A) partitioned out of the hydrophobic membrane core. Free energy calculations showed that movement of TM1A by 0.30 nm was driven by a free energy difference of ~15 kJ/mol. Distance measurements by LRET showed TM1A movements, consistent with the simulations, confirming a substantially different inward-open conformation in lipid bilayer from that inferred from the crystal structure. Crystal structures of the bacterial small amino acid transporter LeuT provided structural evidence for the alternating access model. Thereby, these structures shaped our understanding of the mechanisms underlying substrate translocation by neurotransmitter transporters. However, it has been questioned, if the crystallized inward-open conformation of LeuT can exist in the membrane environment. Here we show that, while stable in detergent micelles, the inward-open conformation of LeuT is of high energy and undergoes structural readjustments. We use a multi-faceted approach including molecular dynamics simulations, scintillation proximity assays, free energy calculations and apply for the first time lanthanide resonance energy transfer measurements to verify the in silico predictions. In silico and in vitro approaches using the same conditions allowed us to combine the macroscopic experimental data with microscopic all atom results from simulations to identify the underlying driving forces: partitioning of charged and polar groups from the hydrophobic membrane interior to the hydrophilic environment. We propose that the inward-facing state shows a much smaller movement of TM1A, but large enough to create an access path to the S1 substrate binding site from the vestibule.
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Affiliation(s)
- Azmat Sohail
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kumaresan Jayaraman
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Santhoshkannan Venkatesan
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kamil Gotfryd
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
- University of Copenhagen, Faculty of Health Sciences Denmark, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Markus Daerr
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Ulrik Gether
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Claus J. Loland
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Klaus T. Wanner
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Michael Freissmuth
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Harald H. Sitte
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
- * E-mail:
| | - Walter Sandtner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
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16
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Andersen J, Ladefoged LK, Kristensen TNB, Munro L, Grouleff J, Stuhr-Hansen N, Kristensen AS, Schiøtt B, Strømgaard K. Interrogating the Molecular Basis for Substrate Recognition in Serotonin and Dopamine Transporters with High-Affinity Substrate-Based Bivalent Ligands. ACS Chem Neurosci 2016; 7:1406-1417. [PMID: 27425420 DOI: 10.1021/acschemneuro.6b00164] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The transporters for the neurotransmitters serotonin and dopamine (SERT and DAT, respectively) are targets for drugs used in the treatment of mental disorders and widely used drugs of abuse. Studies of prokaryotic homologues have advanced our structural understanding of SERT and DAT, but it still remains enigmatic whether the human transporters contain one or two high-affinity substrate binding sites. We have designed and employed 24 bivalent ligands possessing a highly systematic combination of substrate moieties (serotonin and/or dopamine) and aliphatic or poly(ethylene glycol) spacers to reveal insight into substrate recognition in SERT and DAT. An optimized bivalent ligand comprising two serotonin moieties binds SERT with 3,800-fold increased affinity compared to that of serotonin, suggesting that the human transporters have two distinct substrate binding sites. We show that the bivalent ligands are inhibitors of SERT and an experimentally validated docking model suggests that the bivalent compounds bind with one substrate moiety in the central binding site (the S1 site), whereas the other substrate moiety binds in a distinct binding site (the S2 site). A systematic study of nonconserved SERT/DAT residues surrounding the proposed binding region showed that nonconserved binding site residues do not contribute to selective recognition of substrates in SERT or DAT. This study provides novel insight into the molecular basis for substrate recognition in human transporters and provides an improved foundation for the development of new drugs targeting SERT and DAT.
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Affiliation(s)
- Jacob Andersen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lucy Kate Ladefoged
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Trine N. Bjerre Kristensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lachlan Munro
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Julie Grouleff
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Nicolai Stuhr-Hansen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Anders S. Kristensen
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Birgit Schiøtt
- Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kristian Strømgaard
- Department
of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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17
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Khelashvili G, Schmidt SG, Shi L, Javitch JA, Gether U, Loland CJ, Weinstein H. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290. J Biol Chem 2016; 291:19786-99. [PMID: 27474737 DOI: 10.1074/jbc.m116.731455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K(+) ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na(+) Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K(+) binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na(+) ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na(+) in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu(290), either charged or neutral, point to the Glu(290) protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a "water gate" opens through coordinated motions of residues Leu(25), Tyr(108), and Phe(253) The resulting water channel enables the binding/dissociation of the Na(+) and K(+) ions that are prevalent, respectively, in the extracellular and intracellular environments.
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Affiliation(s)
- George Khelashvili
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065,
| | - Solveig Gaarde Schmidt
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224
| | - Jonathan A Javitch
- the Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, and
| | - Ulrik Gether
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Harel Weinstein
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065
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18
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Khelashvili G, Stanley N, Sahai MA, Medina J, LeVine MV, Shi L, De Fabritiis G, Weinstein H. Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus. ACS Chem Neurosci 2015; 6:1825-37. [PMID: 26255829 PMCID: PMC4653762 DOI: 10.1021/acschemneuro.5b00179] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
![]()
We
present the dynamic mechanism of concerted motions in a full-length
molecular model of the human dopamine transporter (hDAT), a member
of the neurotransmitter/sodium symporter (NSS) family, involved in
state-to-state transitions underlying function. The findings result
from an analysis of unbiased atomistic molecular dynamics simulation
trajectories (totaling >14 μs) of the hDAT molecule immersed
in lipid membrane environments with or without phosphatidylinositol
4,5-biphosphate (PIP2) lipids. The N-terminal region of
hDAT (N-term) is shown to have an essential mechanistic role in correlated
rearrangements of specific structural motifs relevant to state-to-state
transitions in the hDAT. The mechanism involves PIP2-mediated
electrostatic interactions between the N-term and the intracellular
loops of the transporter molecule. Quantitative analyses of collective
motions in the trajectories reveal that these interactions correlate
with the inward-opening dynamics of hDAT and are allosterically coupled
to the known functional sites of the transporter. The observed large-scale
motions are enabled by specific reconfiguration of the network of
ionic interactions at the intracellular end of the protein. The isomerization
to the inward-facing state in hDAT is accompanied by concomitant movements
in the extracellular vestibule and results in the release of an Na+ ion from the Na2 site and destabilization of the substrate
dopamine in the primary substrate binding S1 site. The dynamic mechanism
emerging from the findings highlights the involvement of the PIP2-regulated interactions between the N-term and the intracellular
loop 4 in the functionally relevant conformational transitions that
are also similar to those found to underlie state-to-state transitions
in the leucine transporter (LeuT), a prototypical bacterial homologue
of the NSS.
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Affiliation(s)
- George Khelashvili
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Nathaniel Stanley
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Michelle A. Sahai
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Jaime Medina
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Michael V. LeVine
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Lei Shi
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
- HRH
Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Gianni De Fabritiis
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Harel Weinstein
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
- HRH
Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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19
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Billesbølle CB, Krüger MB, Shi L, Quick M, Li Z, Stolzenberg S, Kniazeff J, Gotfryd K, Mortensen JS, Javitch JA, Weinstein H, Loland CJ, Gether U. Substrate-induced unlocking of the inner gate determines the catalytic efficiency of a neurotransmitter:sodium symporter. J Biol Chem 2015; 290:26725-38. [PMID: 26363074 DOI: 10.1074/jbc.m115.677658] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/06/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) mediate reuptake of neurotransmitters from the synaptic cleft and are targets for several therapeutics and psychostimulants. The prokaryotic NSS homologue, LeuT, represents a principal structural model for Na(+)-coupled transport catalyzed by these proteins. Here, we used site-directed fluorescence quenching spectroscopy to identify in LeuT a substrate-induced conformational rearrangement at the inner gate conceivably leading to formation of a structural intermediate preceding transition to the inward-open conformation. The substrate-induced, Na(+)-dependent change required an intact primary substrate-binding site and involved increased water exposure of the cytoplasmic end of transmembrane segment 5. The findings were supported by simulations predicting disruption of an intracellular interaction network leading to a discrete rotation of transmembrane segment 5 and the adjacent intracellular loop 2. The magnitude of the spectroscopic response correlated inversely with the transport rate for different substrates, suggesting that stability of the intermediate represents an unrecognized rate-limiting barrier in the NSS transport mechanism.
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Affiliation(s)
- Christian B Billesbølle
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Mie B Krüger
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- Department of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10065
| | - Matthias Quick
- Center for Molecular Recognition and Departments of Psychiatry and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032
| | - Zheng Li
- Department of Physiology and Biophysics and
| | | | - Julie Kniazeff
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kamil Gotfryd
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jonas S Mortensen
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jonathan A Javitch
- Center for Molecular Recognition and Departments of Psychiatry and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032 Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, and
| | - Harel Weinstein
- Department of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10065
| | - Claus J Loland
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ulrik Gether
- From the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark,
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20
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Functional mechanisms of neurotransmitter transporters regulated by lipid-protein interactions of their terminal loops. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1765-74. [PMID: 25847498 DOI: 10.1016/j.bbamem.2015.03.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 01/28/2023]
Abstract
The physiological functions of neurotransmitter:sodium symporters (NSS) in reuptake of neurotransmitters from the synapse into the presynaptic nerve have been shown to be complemented by their involvement, together with non-plasma membrane neurotransmitter transporters, in the reverse transport of substrate (efflux) in response to psychostimulants. Recent experimental evidence implicates highly anionic phosphatidylinositol 4,5-biphosphate (PIP(2)) lipids in such functions of the serotonin (SERT) and dopamine (DAT) transporters. Thus, for both SERT and DAT, neurotransmitter efflux has been shown to be strongly regulated by the presence of PIP(2) lipids in the plasma membrane, and the electrostatic interaction of the N-terminal region of DAT with the negatively charged PIP(2) lipids. We examine the experimentally established phenotypes in a structural context obtained from computational modeling based on recent crystallographic data. The results are shown to set the stage for a mechanistic understanding of physiological actions of neurotransmitter transporters in the NSS family of membrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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21
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Khelashvili G, Doktorova M, Sahai MA, Johner N, Shi L, Weinstein H. Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes. Proteins 2015; 83:952-69. [PMID: 25739722 DOI: 10.1002/prot.24792] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/05/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Abstract
The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N-terminal segment. Here we report a computational model of the N-term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N-term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 μs). Combining MD simulations with continuum mean-field modeling we found that the N-term engages with lipid membranes through electrostatic interactions with the charged lipids PIP2 (phosphatidylinositol 4,5-Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N-term implicated in such interactions and show that differential modes of N-term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure-based studies that will elucidate the mechanistic role of the N-term in DAT function.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, 10065
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22
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Gournas C, Evangelidis T, Athanasopoulos A, Mikros E, Sophianopoulou V. The Aspergillus nidulans proline permease as a model for understanding the factors determining substrate binding and specificity of fungal amino acid transporters. J Biol Chem 2015; 290:6141-55. [PMID: 25572393 DOI: 10.1074/jbc.m114.612069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amino acid uptake in fungi is mediated by general and specialized members of the yeast amino acid transporter (YAT) family, a branch of the amino acid polyamine organocation (APC) transporter superfamily. PrnB, a highly specific l-proline transporter, only weakly recognizes other Put4p substrates, its Saccharomyces cerevisiae orthologue. Taking advantage of the high sequence similarity between the two transporters, we combined molecular modeling, induced fit docking, genetic, and biochemical approaches to investigate the molecular basis of this difference and identify residues governing substrate binding and specificity. We demonstrate that l-proline is recognized by PrnB via interactions with residues within TMS1 (Gly(56), Thr(57)), TMS3 (Glu(138)), and TMS6 (Phe(248)), which are evolutionary conserved in YATs, whereas specificity is achieved by subtle amino acid substitutions in variable residues. Put4p-mimicking substitutions in TMS3 (S130C), TMS6 (F252L, S253G), TMS8 (W351F), and TMS10 (T414S) broadened the specificity of PrnB, enabling it to recognize more efficiently l-alanine, l-azetidine-2-carboxylic acid, and glycine without significantly affecting the apparent Km for l-proline. S253G and W351F could transport l-alanine, whereas T414S, despite displaying reduced proline uptake, could transport l-alanine and glycine, a phenotype suppressed by the S130C mutation. A combination of all five Put4p-ressembling substitutions resulted in a functional allele that could also transport l-alanine and glycine, displaying a specificity profile impressively similar to that of Put4p. Our results support a model where residues in these positions determine specificity by interacting with the substrates, acting as gating elements, altering the flexibility of the substrate binding core, or affecting conformational changes of the transport cycle.
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Affiliation(s)
- Christos Gournas
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
| | - Thomas Evangelidis
- the School of Pharmacy, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Alexandros Athanasopoulos
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
| | - Emmanuel Mikros
- the School of Pharmacy, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Vicky Sophianopoulou
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
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23
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Dahal RA, Pramod AB, Sharma B, Krout D, Foster JD, Cha JH, Cao J, Newman AH, Lever JR, Vaughan RA, Henry LK. Computational and biochemical docking of the irreversible cocaine analog RTI 82 directly demonstrates ligand positioning in the dopamine transporter central substrate-binding site. J Biol Chem 2014; 289:29712-27. [PMID: 25179220 PMCID: PMC4207985 DOI: 10.1074/jbc.m114.571521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/09/2014] [Indexed: 12/20/2022] Open
Abstract
The dopamine transporter (DAT) functions as a key regulator of dopaminergic neurotransmission via re-uptake of synaptic dopamine (DA). Cocaine binding to DAT blocks this activity and elevates extracellular DA, leading to psychomotor stimulation and addiction, but the mechanisms by which cocaine interacts with DAT and inhibits transport remain incompletely understood. Here, we addressed these questions using computational and biochemical methodologies to localize the binding and adduction sites of the photoactivatable irreversible cocaine analog 3β-(p-chlorophenyl)tropane-2β-carboxylic acid, 4'-azido-3'-iodophenylethyl ester ([(125)I]RTI 82). Comparative modeling and small molecule docking indicated that the tropane pharmacophore of RTI 82 was positioned in the central DA active site with an orientation that juxtaposed the aryliodoazide group for cross-linking to rat DAT Phe-319. This prediction was verified by focused methionine substitution of residues flanking this site followed by cyanogen bromide mapping of the [(125)I]RTI 82-labeled mutants and by the substituted cysteine accessibility method protection analyses. These findings provide positive functional evidence linking tropane pharmacophore interaction with the core substrate-binding site and support a competitive mechanism for transport inhibition. This synergistic application of computational and biochemical methodologies overcomes many uncertainties inherent in other approaches and furnishes a schematic framework for elucidating the ligand-protein interactions of other classes of DA transport inhibitors.
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Affiliation(s)
- Rejwi Acharya Dahal
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Akula Bala Pramod
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Babita Sharma
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Danielle Krout
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - James D Foster
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Joo Hwan Cha
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Jianjing Cao
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Amy Hauck Newman
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - John R Lever
- the Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, Missouri 65201, and the Department of Radiology, Radiopharmaceutical Sciences Institute, and Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri 65211
| | - Roxanne A Vaughan
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
| | - L Keith Henry
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
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24
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A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters. Nat Struct Mol Biol 2014; 21:1006-12. [PMID: 25282149 DOI: 10.1038/nsmb.2894] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Neurotransmitter/sodium symporters (NSSs) terminate synaptic signal transmission by Na+-dependent reuptake of released neurotransmitters. Key conformational states have been reported for the bacterial homolog LeuT and an inhibitor-bound Drosophila dopamine transporter. However, a coherent mechanism of Na+-driven transport has not been described. Here, we present two crystal structures of MhsT, an NSS member from Bacillus halodurans, in occluded inward-facing states with bound Na+ ions and L-tryptophan, providing insight into the cytoplasmic release of Na+. The switch from outward- to inward-oriented states is centered on the partial unwinding of transmembrane helix 5, facilitated by a conserved GlyX9Pro motif that opens an intracellular pathway for water to access the Na2 site. We propose a mechanism, based on our structural and functional findings, in which solvation through the TM5 pathway facilitates Na+ release from Na2 and the transition to an inward-open state.
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25
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Simmons KJ, Jackson SM, Brueckner F, Patching SG, Beckstein O, Ivanova E, Geng T, Weyand S, Drew D, Lanigan J, Sharples DJ, Sansom MSP, Iwata S, Fishwick CWG, Johnson AP, Cameron AD, Henderson PJF. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1. EMBO J 2014; 33:1831-44. [PMID: 24952894 PMCID: PMC4195764 DOI: 10.15252/embj.201387557] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.
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Affiliation(s)
- Katie J Simmons
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Scott M Jackson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Florian Brueckner
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simon G Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, AZ, USA Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ekaterina Ivanova
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Tian Geng
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simone Weyand
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK
| | - Joseph Lanigan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Sharples
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - So Iwata
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Colin W G Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - A Peter Johnson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alexander D Cameron
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK School of Life Sciences, University of Warwick, Coventry, UK
| | - Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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26
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Thomas JR, Gedeon PC, Madura JD. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins 2014; 82:2289-302. [PMID: 24753369 DOI: 10.1002/prot.24588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/29/2014] [Accepted: 04/10/2014] [Indexed: 01/28/2023]
Abstract
The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.
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Affiliation(s)
- James R Thomas
- Department of Chemistry and Biochemistry and the Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania; Mylan School of Pharmacy, Duquesne University, Pittsburgh, Pennsylvania
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27
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LeVine MV, Weinstein H. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol 2014; 10:e1003603. [PMID: 24785005 PMCID: PMC4006702 DOI: 10.1371/journal.pcbi.1003603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/24/2014] [Indexed: 11/23/2022] Open
Abstract
Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems. We developed the new information theory-based analysis framework presented here, NbIT analysis, for the study of allosteric mechanisms in biomolecular systems from Molecular Dynamics trajectories. The illustrative application of NbIT to the analysis of the occluded state in the bacterial transporter LeuT, produced a quantitative representation of the allosteric behavior, and identified intramolecular channels that enable the long-distance information transmission. Our findings, identifying the roles of specific residues in the communication of the allosteric information, were validated by the recognition of residues that have been previously shown to play functional roles in this very well studied system. In addition, we show that application of NbIT analysis leads to the discrimination of functional roles by differentiating between residues that are essential to the dynamics within functional sites (e.g., the substrate binding sites), and residues whose role is to communicate between such functional sites. These results demonstrate that the information theoretical analysis presented here is a powerful tool for quantifying complex allosteric behavior in biomolecular systems and for identifying the crucial components underlying those behaviors.
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Affiliation(s)
- Michael V. LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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28
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Loland CJ. The use of LeuT as a model in elucidating binding sites for substrates and inhibitors in neurotransmitter transporters. Biochim Biophys Acta Gen Subj 2014; 1850:500-10. [PMID: 24769398 DOI: 10.1016/j.bbagen.2014.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 01/24/2023]
Abstract
BACKGROUND The mammalian neurotransmitter transporters are complex proteins playing a central role in synaptic transmission between neurons by rapid reuptake of neurotransmitters. The proteins which transport dopamine, noradrenaline and serotonin belong to the Neurotransmitter:Sodium Symporters (NSS). Due to their important role, dysfunctions are associated with several psychiatric and neurological diseases and they also serve as targets for a wide range of therapeutic and illicit drugs. Despite the central physiological and pharmacological importance, direct evidence on structure-function relationships on mammalian NSS proteins has so far been unsuccessful. The crystal structure of the bacterial NSS protein, LeuT, has been a turning point in structural investigations. SCOPE OF REVIEW To provide an update on what is known about the binding sites for substrates and inhibitors in the LeuT. The different binding modes and binding sites will be discussed with special emphasis on the possible existence of a second substrate binding site. It is the goal to give an insight into how investigations on ligand binding in LeuT have provided basic knowledge about transporter conformations and translocation mechanism which can pave the road for a deeper understanding of drug binding and function of the mammalian transporters. MAJOR CONCLUSIONS The LeuT is a suitable model for the structural investigation of NSS proteins including the possible location of drug binding sites. It is still debated whether the LeuT is a suitable model for the molecular mechanisms behind substrate translocation. GENERAL SIGNIFICANCE Structure and functional aspects of NSS proteins are central for understanding synaptic transmission. With the purification and crystallization of LeuT as well as the dopamine transporter from Drosophila melanogaster, the application of biophysical methods such as fluorescence spectroscopy, neutron- or x-ray scattering and NMR for understanding its function becomes increasingly available. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Claus J Loland
- Molecular Neuropharmacology Laboratory, Department of Neuroscience and Pharmacology, The Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
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29
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Usami Y, Uemura S, Mochizuki T, Morita A, Shishido F, Inokuchi JI, Abe F. Functional mapping and implications of substrate specificity of the yeast high-affinity leucine permease Bap2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1719-29. [PMID: 24699373 DOI: 10.1016/j.bbamem.2014.03.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 11/29/2022]
Abstract
Leucine is a major amino acid in nutrients and proteins and is also an important precursor of higher alcohols during brewing. In Saccharomyces cerevisiae, leucine uptake is mediated by multiple amino acid permeases, including the high-affinity leucine permease Bap2. Although BAP2 transcription has been extensively analyzed, the mechanisms by which a substrate is recognized and moves through the permease remain unknown. Recently, we determined 15 amino acid residues required for Tat2-mediated tryptophan import. Here we introduced homologous mutations into Bap2 amino acid residues and showed that 7 residues played a role in leucine import. Residues I109/G110/T111 and E305 were located within the putative α-helix break in TMD1 and TMD6, respectively, according to the structurally homologous Escherichia coli arginine/agmatine antiporter AdiC. Upon leucine binding, these α-helix breaks were assumed to mediate a conformational transition in Bap2 from an outward-open to a substrate-binding occluded state. Residues Y336 (TMD7) and Y181 (TMD3) were located near I109 and E305, respectively. Bap2-mediated leucine import was inhibited by some amino acids according to the following order of severity: phenylalanine, leucine>isoleucine>methionine, tyrosine>valine>tryptophan; histidine and asparagine had no effect. Moreover, this order of severity clearly coincided with the logP values (octanol-water partition coefficients) of all amino acids except tryptophan. This result suggests that the substrate partition efficiency to the buried Bap2 binding pocket is the primary determinant of substrate specificity rather than structural amino acid side chain recognition.
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Affiliation(s)
- Yuki Usami
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Satsohi Uemura
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Takahiro Mochizuki
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Asami Morita
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Fumi Shishido
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Pharmaceutical University, Sendai, Japan
| | - Jin-ichi Inokuchi
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Pharmaceutical University, Sendai, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan; Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
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30
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Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model 2014; 54:933-43. [PMID: 24521202 PMCID: PMC3982395 DOI: 10.1021/ci400742s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The serotonin (5-hydroxytryptamine, 5-HT) transporter (SERT) plays an essential role in the termination of serotonergic neurotransmission by removing 5-HT from the synaptic cleft into the presynaptic neuron. It is also of pharmacological importance being targeted by antidepressants and psychostimulant drugs. Here, five commercial databases containing approximately 3.24 million drug-like compounds have been screened using a combination of two-dimensional (2D) fingerprint-based and three-dimensional (3D) pharmacophore-based screening and flexible docking into multiple conformations of the binding pocket detected in an outward-open SERT homology model. Following virtual screening (VS), selected compounds were evaluated using in vitro screening and full binding assays and an in silico hit-to-lead (H2L) screening was performed to obtain analogues of the identified compounds. Using this multistep VS/H2L approach, 74 active compounds, 46 of which had K(i) values of ≤1000 nM, belonging to 16 structural classes, have been identified, and multiple compounds share no structural resemblance with known SERT binders.
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Affiliation(s)
- Mari Gabrielsen
- Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway , 9037 Tromsø, Norway
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31
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Neurotransmitter transporters: structure meets function. Structure 2014; 21:694-705. [PMID: 23664361 DOI: 10.1016/j.str.2013.03.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/15/2013] [Accepted: 03/06/2013] [Indexed: 12/22/2022]
Abstract
At synapses, sodium-coupled transporters remove released neurotransmitters, thereby recycling them and maintaining a low extracellular concentration of the neurotransmitter. The molecular mechanism underlying sodium-coupled neurotransmitter uptake is not completely understood. Several structures of homologs of human neurotransmitter transporters have been solved with X-ray crystallography. These crystal structures have spurred a plethora of computational and experimental work to elucidate the molecular mechanism underlying sodium-coupled transport. Here, we compare the structures of GltPh, a glutamate transporter homolog, and LeuT, a homolog of neurotransmitter transporters for the biogenic amines and inhibitory molecules GABA and glycine. We relate these structures to data obtained from experiments and computational simulations, to draw conclusions about the mechanism of uptake by sodium-coupled neurotransmitter transporters. Here, we propose how sodium and substrate binding is coupled and how binding of sodium and substrate opens and closes the gates in these transporters, thereby leading to an efficient coupled transport.
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32
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Felts B, Pramod AB, Sandtner W, Burbach N, Bulling S, Sitte HH, Henry LK. The two Na+ sites in the human serotonin transporter play distinct roles in the ion coupling and electrogenicity of transport. J Biol Chem 2013; 289:1825-40. [PMID: 24293367 DOI: 10.1074/jbc.m113.504654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Neurotransmitter transporters of the SLC6 family of proteins, including the human serotonin transporter (hSERT), utilize Na(+), Cl(-), and K(+) gradients to induce conformational changes necessary for substrate translocation. Dysregulation of ion movement through monoamine transporters has been shown to impact neuronal firing potentials and could play a role in pathophysiologies, such as depression and anxiety. Despite multiple crystal structures of prokaryotic and eukaryotic SLC transporters indicating the location of both (or one) conserved Na(+)-binding sites (termed Na1 and Na2), much remains uncertain in regard to the movements and contributions of these cation-binding sites in the transport process. In this study, we utilize the unique properties of a mutation of hSERT at a single, highly conserved asparagine on TM1 (Asn-101) to provide several lines of evidence demonstrating mechanistically distinct roles for Na1 and Na2. Mutations at Asn-101 alter the cation dependence of the transporter, allowing Ca(2+) (but not other cations) to functionally replace Na(+) for driving transport and promoting 5-hydroxytryptamine (5-HT)-dependent conformational changes. Furthermore, in two-electrode voltage clamp studies in Xenopus oocytes, both Ca(2+) and Na(+) illicit 5-HT-induced currents in the Asn-101 mutants and reveal that, although Ca(2+) promotes substrate-induced current, it does not appear to be the charge carrier during 5-HT transport. These findings, in addition to functional evaluation of Na1 and Na2 site mutants, reveal separate roles for Na1 and Na2 and provide insight into initiation of the translocation process as well as a mechanism whereby the reported SERT stoichiometry can be obtained despite the presence of two putative Na(+)-binding sites.
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Affiliation(s)
- Bruce Felts
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203 and
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33
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Extracellular loop 3 of the noradrenaline transporter contributes to substrate and inhibitor selectivity. Naunyn Schmiedebergs Arch Pharmacol 2013; 387:95-107. [PMID: 24081522 DOI: 10.1007/s00210-013-0923-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
The human noradrenaline transporter (NET) and 5-hydroxytryptamine (5-HT) transporter (SERT) are inhibited by antidepressants and psychoactive drugs such as cocaine. Both substrates and inhibitors bind in the transmembrane core of the protein, but molecular divergence at the binding site is not sufficient to account for the NET-selective and SERT-selective inhibition of the antidepressants, desipramine and citalopram, respectively. We considered that the poorly conserved third extracellular loop may contribute to these differences. We substituted single amino acid residues of the third extracellular loop in NET for equivalents from SERT, transiently transfected COS-7 cells with WT NET, 13 mutant NETs and WT SERT, and measured [(3)H]noradrenaline uptake, [(3)H]nisoxetine binding and [(3)H]5-HT uptake. Mutants F299W, Y300Q, R301K and K303L, at the C-terminal end of EL3, all showed significantly decreased [(3)H]nisoxetine binding, indicative of a reduced cell surface expression. Most mutants differed little, if at all, from WT NET regarding [(3)H]noradrenaline uptake; however, the I297P mutant showed no significant uptake activity despite intact cell surface expression, and the A293F mutant showed a significantly slower transporter turnover than WT NET in addition to [(3)H]5-HT uptake that was significantly greater than that of WT NET. The A293F mutation also decreased desipramine potency and increased the inhibition of [(3)H]noradrenaline uptake by citalopram compared to WT NET. These results suggest that the third extracellular loop allosterically regulates the ability of the transmembrane domains to transport substrates and bind inhibitors and thus contributes to the selectivity of substrates and antidepressants for NET and SERT.
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Khelashvili G, LeVine MV, Shi L, Quick M, Javitch JA, Weinstein H. The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site. J Am Chem Soc 2013; 135:14266-75. [PMID: 23980525 PMCID: PMC3788620 DOI: 10.1021/ja405984v] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Structural and functional properties of integral membrane proteins are often studied in detergent micellar environments (proteomicelles), but how such proteomicelles form and organize is not well understood. This makes it difficult to evaluate the relationship between the properties of the proteins measured in such a detergent-solubilized form and under native conditions. To obtain mechanistic information about this relationship for the leucine transporter (LeuT), a prokaryotic homologue of the mammalian neurotransmitter/sodium symporters (NSSs), we studied the properties of proteomicelles formed by n-dodecyl-β,D-maltopyranoside (DDM) detergent. Extensive atomistic molecular dynamics simulations of different protein/detergent/water number ratios revealed the formation of a proteomicelle characterized by a constant-sized shell of detergents surrounding LeuT protecting its transmembrane segments from unfavorable hydrophobic/hydrophilic exposure. Regardless of the DDM content in the simulated system, this shell consisted of a constant number of DDM molecules (∼120 measured at a 4 Å cutoff distance from LeuT). In contrast, the overall number of DDMs in the proteomicelle (aggregation number) was found to depend on the detergent concentration, reaching a saturation value of 226±17 DDMs in the highest concentration regime simulated. Remarkably, we found that at high detergent-to-protein ratios we observed two independent ways of DDM penetration into LeuT, both leading to a positioning of the DDM molecule in the second substrate (S2) binding site of LeuT. Consonant with several recent experimental studies demonstrating changes in functional properties of membrane proteins due to detergent, our findings highlight how the environment in which the membrane proteins are examined may affect the outcome and interpretation of their mechanistic features.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC) , New York, New York 10065, United States
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Pramod AB, Foster J, Carvelli L, Henry LK. SLC6 transporters: structure, function, regulation, disease association and therapeutics. Mol Aspects Med 2013; 34:197-219. [PMID: 23506866 DOI: 10.1016/j.mam.2012.07.002] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/03/2012] [Indexed: 02/08/2023]
Abstract
The SLC6 family of secondary active transporters are integral membrane solute carrier proteins characterized by the Na(+)-dependent translocation of small amino acid or amino acid-like substrates. SLC6 transporters, which include the serotonin, dopamine, norepinephrine, GABA, taurine, creatine, as well as amino acid transporters, are associated with a number of human diseases and disorders making this family a critical target for therapeutic development. In addition, several members of this family are directly involved in the action of drugs of abuse such as cocaine, amphetamines, and ecstasy. Recent advances providing structural insight into this family have vastly accelerated our ability to study these proteins and their involvement in complex biological processes.
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Affiliation(s)
- Akula Bala Pramod
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, United States
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36
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Kanda N, Abe F. Structural and functional implications of the yeast high-affinity tryptophan permease Tat2. Biochemistry 2013; 52:4296-307. [PMID: 23768406 DOI: 10.1021/bi4004638] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tryptophan is hydrophobic, bulky, and the rarest amino acid found in nutrients. Accordingly, the import machinery can be specialized evolutionarily. Our previous study in Saccharomyces cerevisiae demonstrated that tryptophan import by the high-affinity tryptophan permease Tat2 is accompanied by a large volume increase during substrate import. Nevertheless, the mechanisms by which the permease mediates tryptophan recognition and permeation remain to be elucidated. Here we determined amino acid residues essential for Tat2-mediated tryptophan import. By means of random mutagenesis in combination with site-directed mutagenesis based on crystallographic studies of the Escherichia coli arginine/agmatine antiporter AdiC, we identified 15 amino acid residues in the Tat2 transmembrane domains (TMDs) 1, -3, -5, -8, and -10, which are responsible for tryptophan uptake. T98, Y167, and E286 were assumed to form the central cavity in Tat2. G97/T98 and E286 were located within the putative α-helix break in TMD1 and TMD6, respectively, which are highly conserved among yeast amino acid permeases and bacterial solute transporters. Given the conformational change in AdiC upon substrate binding, G97/T98 and E286 of Tat2 were assumed to mediate a structural shift from an outward-open to a tryptophan-bound-occluded structure upon tryptophan binding, and T320, V322, and F324 became stabilized in TMD7. Such dynamic structural changes may account for the large volume increase associated with tryptophan import occurring concomitantly with a movement of water molecules from the tryptophan binding site. We also propose the working hypothesis that E286 mediates the proton influx that is coupled to tryptophan import.
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Affiliation(s)
- Naoko Kanda
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
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37
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Mondal S, Khelashvili G, Shi L, Weinstein H. The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT. Chem Phys Lipids 2013; 169:27-38. [PMID: 23376428 PMCID: PMC3631462 DOI: 10.1016/j.chemphyslip.2013.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 12/27/2022]
Abstract
Many observations of the role of the membrane in the function and organization of transmembrane (TM) proteins have been explained in terms of hydrophobic mismatch between the membrane and the inserted protein. For a quantitative investigation of this mechanism in the lipid-protein interactions of functionally relevant conformations adopted by a multi-TM segment protein, the bacterial leucine transporter (LeuT), we employed a novel method, Continuum-Molecular Dynamics (CTMD), that quantifies the energetics of hydrophobic mismatch by combining the elastic continuum theory of membrane deformations with an atomistic level description of the radially asymmetric membrane-protein interface from MD simulations. LeuT has been serving as a model for structure-function studies of the mammalian neurotransmitter:sodium symporters (NSSs), such as the dopamine and serotonin transporters, which are the subject of intense research in the field of neurotransmission. The membrane models in which LeuT was embedded for these studies were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid, or 3:1 mixture of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) lipids. The results show that deformation of the host membrane alone is not sufficient to alleviate the hydrophobic mismatch at specific residues of LeuT. The calculations reveal significant membrane thinning and water penetration due to the specific local polar environment produced by the charged K288 of TM7 in LeuT, that is membrane-facing deep inside the hydrophobic milieu of the membrane. This significant perturbation is shown to result in unfavorable polar-hydrophobic interactions at neighboring hydrophobic residues in TM1a and TM7. We show that all the effects attributed to the K288 residue (membrane thinning, water penetration, and the unfavorable polar-hydrophobic interactions at TM1a and TM7), are abolished in calculations with the K288A mutant. The involvement of hydrophobic mismatch is somewhat different in the functionally distinct conformations (outward-open, occluded, inward-open) of LeuT, and the differences are shown to connect to structural elements (e.g., TM1a) known to play key roles in transport. This finding suggests a mechanistic hypothesis for the enhanced transport activity observed for the K288A mutant, suggesting that the unfavorable hydrophobic-hydrophilic interactions hinder the motion of TM1a in the functionally relevant conformational transition to the inward-open state. Various extents of such unfavorable interactions, involving exposure to the lipid environment of adjacent hydrophobic and polar residues, are common in multi-segment transmembrane proteins, and must be considered to affect functionally relevant conformational transitions.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065
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Shaikh S, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry 2013; 52:569-87. [PMID: 23298176 PMCID: PMC3560430 DOI: 10.1021/bi301086x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
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Affiliation(s)
- Saher
A. Shaikh
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jing Li
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Giray Enkavi
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhijian Huang
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
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Harder D, Fotiadis D. Measuring substrate binding and affinity of purified membrane transport proteins using the scintillation proximity assay. Nat Protoc 2012; 7:1569-78. [PMID: 22864198 DOI: 10.1038/nprot.2012.090] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The scintillation proximity assay (SPA) is a rapid radioligand binding assay. Upon binding of radioactively labeled ligands (here L-[(3)H]arginine or D-[(3)H]glucose) to acceptor proteins immobilized on fluoromicrospheres (containing the scintillant), a light signal is stimulated and measured. The application of SPA to purified, detergent-solubilized membrane transport proteins allows substrate-binding properties to be assessed (e.g., substrate specificity and affinity), usually within 1 d. Notably, the SPA makes it possible to study specific transporters without interference from other cellular components, such as endogenous transporters. Reconstitution of the target transporter into proteoliposomes is not required. The SPA procedure allows high sample throughput and simple sample handling without the need for washing or separation steps: components are mixed in one well and the signal is measured directly after incubation. Therefore, the SPA is an excellent tool for high-throughput screening experiments, e.g., to search for substrates and inhibitors, and it has also recently become an attractive tool for drug discovery.
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Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
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40
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Role of the irreplaceable residues in the LacY alternating access mechanism. Proc Natl Acad Sci U S A 2012; 109:12438-42. [PMID: 22802658 DOI: 10.1073/pnas.1210684109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Few side chains in the galactoside/H(+) symporter LacY (lactose permease of Escherichia coli) are irreplaceable for an alternating access mechanism in which sugar binding induces closing of the cytoplasmic cavity and reciprocal opening of a periplasmic cavity. In this study, each irreplaceable residue was mutated individually, and galactoside-induced opening or closing of periplasmic or cytoplasmic cavities was probed by site-directed alkylation. Mutation of Glu126 (helix IV) or Arg144 (helix V), which are essential for sugar binding, completely blocks sugar-induced periplasmic opening as expected. Remarkably, however, replacement of Glu269 (helix VIII), His322 (helix X), or Tyr236 (helix VII) causes spontaneous opening of the periplasmic cavity in the absence of sugar and decreased closing of the cytoplasmic cavity in the presence of galactoside. In contrast, mutation of Arg302 (helix IX) or Glu325 (helix X) has no such effect, and sugar binding induces normal opening and closing of periplasmic and cytoplasmic cavities. Possibly, Glu269, His322, and Tyr236 act in concert to coordinate opening and closing of the cavities by binding water, which also acts as a cofactor in H(+) translocation. Mutation of the triad results in loss of the bound water, which destabilizes LacY, and the cavities open and close in an uncoordinated manner. Thus, the triad mutants exhibit poor affinity for sugar, and galactoside/H(+) symport is abolished as well.
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Merchant BA, Madura JD. Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. J Mol Graph Model 2012; 38:1-12. [PMID: 23079638 DOI: 10.1016/j.jmgm.2012.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/30/2012] [Accepted: 05/04/2012] [Indexed: 11/18/2022]
Abstract
The dopamine transporter (DAT) facilitates the regulation of synaptic neurotransmitter levels. As a target for therapeutic and illicit psycho-stimulant drugs like antidepressants and cocaine, DAT has been studied intensively. Despite a wealth of mutational and physiological data regarding DAT, the structure remains unsolved and details of the transport mechanism, binding sites and conformational changes remain debated. A bacterial homolog of DAT, the leucine transporter (LeuT(Aa)) has been used as a template and framework for modeling and understanding DAT. Free energy profiles obtained from Multi-Configuration Thermodynamic Integration simulations allowed us to correctly identify the primary and secondary binding pockets of LeuT(Aa). A comparison of free energy profiles for dopamine and cocaine in DAT suggests that the binding site of cocaine is located in a secondary pocket, not the primary substrate site. Two recurring primary pathways for intracellular substrate release from the primary pocket are identified in both transporters using the Random Acceleration Molecular Dynamics method. One pathway appears to follow transmembranes (TMs) 1a and 6b while the other pathway follows along TMs 6b and 8. Interestingly, we observe that a single sodium ion is co-transported with leucine during both simulation types.
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Affiliation(s)
- Bonnie A Merchant
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, USA
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