2019
A Novel Bromine-Containing Paroxetine Analogue Provides Mechanistic Clues for Binding Ambiguity at the Central Primary Binding Site of the Serotonin Transporter
Slack RD, Abramyan AM, Tang H, Meena S, Davis BA, Bonifazi A, Giancola JB, Deschamps JR, Naing S, Yano H, Singh SK, Newman AH, Shi L. A Novel Bromine-Containing Paroxetine Analogue Provides Mechanistic Clues for Binding Ambiguity at the Central Primary Binding Site of the Serotonin Transporter. ACS Chemical Neuroscience 2019, 10: 3946-3952. PMID: 31424193, PMCID: PMC8272913, DOI: 10.1021/acschemneuro.9b00375.Peer-Reviewed Original Research
2018
Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics
Abramyan AM, Slack RD, Meena S, Davis BA, Newman AH, Singh SK, Shi L. Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics. Neuropharmacology 2018, 161: 107411. PMID: 30391505, PMCID: PMC6494725, DOI: 10.1016/j.neuropharm.2018.10.040.Peer-Reviewed Original ResearchNeurotransmitter Transporter Conformational Dynamics using HDX-MS and Molecular Dynamics Simulation
Bradshaw R, Nagarajan A, Adhikary S, Deredge D, Wintrode P, Singh S, Forrest L. Neurotransmitter Transporter Conformational Dynamics using HDX-MS and Molecular Dynamics Simulation. Biophysical Journal 2018, 114: 207a. DOI: 10.1016/j.bpj.2017.11.1161.Peer-Reviewed Original Research
2017
Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer
Adhikary S, Deredge DJ, Nagarajan A, Forrest LR, Wintrode PL, Singh SK. Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e1786-e1795. PMID: 28223522, PMCID: PMC5347597, DOI: 10.1073/pnas.1613293114.Peer-Reviewed Original ResearchConceptsSodium symportersMembrane proteinsMammalian membrane proteinsConformational mechanismIntegral membrane proteinsPhospholipid bilayer nanodiscsSolution spectroscopyDetergent-solubilized stateExtracellular loop 2Site-specific labelingSmall molecule neurotransmittersBilayer nanodiscsHydrogen-deuterium exchangeX-ray crystallographyCysteine accessibilityConformational dynamicsMembrane mimicsMolecular dynamics simulationsLoop 2Endogenous cysteineHelices 1ALeuTLipid bilayersProteinSymporter
2016
Mechanism of Paroxetine (Paxil) Inhibition of the Serotonin Transporter
Davis BA, Nagarajan A, Forrest LR, Singh SK. Mechanism of Paroxetine (Paxil) Inhibition of the Serotonin Transporter. Scientific Reports 2016, 6: 23789. PMID: 27032980, PMCID: PMC4817154, DOI: 10.1038/srep23789.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesCells, CulturedChickensCocaineDopamine Plasma Membrane Transport ProteinsDrosophila melanogasterDrosophila ProteinsModels, MolecularMolecular ConformationMolecular Docking SimulationParoxetineProtein ConformationRadioligand AssaySelective Serotonin Reuptake InhibitorsSequence AlignmentSequence Homology, Amino AcidSerotoninSerotonin Plasma Membrane Transport ProteinsConceptsIntegral membrane proteinsDrosophila melanogaster dopamine transporterSERT homology modelMembrane proteinsSerotonin transporterMolecular insightsHomology modelIon gradientsFlux assaysTransportersSERT substratesPotassium ion gradientSignificant clinical attentionPresynaptic neuronsDopamine transporterProteinUnfavorable movementSitesSynaptic serotoninBindingSubstrateAssaysRadioligand bindingInhibitorsPotent selective serotonin reuptake inhibitor
2015
Cryo-EM: Spinning the Micelles Away
Singh SK, Sigworth FJ. Cryo-EM: Spinning the Micelles Away. Structure 2015, 23: 1561. PMID: 26331455, PMCID: PMC4901521, DOI: 10.1016/j.str.2015.08.001.Peer-Reviewed Original ResearchChapter Nine Biophysical Approaches to the Study of LeuT, a Prokaryotic Homolog of Neurotransmitter Sodium Symporters
Singh SK, Pal A. Chapter Nine Biophysical Approaches to the Study of LeuT, a Prokaryotic Homolog of Neurotransmitter Sodium Symporters. Methods In Enzymology 2015, 557: 167-198. PMID: 25950965, PMCID: PMC4818570, DOI: 10.1016/bs.mie.2015.01.002.Peer-Reviewed Original ResearchConceptsMultiple integral membrane proteinsSolute carrier 6 (SLC6) familyNeurotransmitter sodium symportersIntegral membrane proteinsAmino acid symporterDependent neurotransmitter transportersEukaryotic counterpartsSodium symportersProkaryotic homologAcid symporterLeuT structureMembrane proteinsNeurotransmitter transportersBiophysical approachesLeuTHomology modelingMechanism of transportSecondary transportAmino acidsLipid bilayersSignificant transportersMechanistic paradigmMolecular dynamics simulationsSymporterProteinCarboxyl Residues Required for Transport by a Vesicular Monoamine Transporter Homolog from Brevibacillus Brevis (BbMAT)
Vergara-Jaque A, Yaffe D, Shuster Y, Listov D, Meena S, Singh S, Schuldiner S, Forrest L. Carboxyl Residues Required for Transport by a Vesicular Monoamine Transporter Homolog from Brevibacillus Brevis (BbMAT). Biophysical Journal 2015, 108: 462a. DOI: 10.1016/j.bpj.2014.11.2522.Peer-Reviewed Original Research
2014
Functionally Important Carboxyls in a Bacterial Homologue of the Vesicular Monoamine Transporter (VMAT)*
Yaffe D, Vergara-Jaque A, Shuster Y, Listov D, Meena S, Singh SK, Forrest LR, Schuldiner S. Functionally Important Carboxyls in a Bacterial Homologue of the Vesicular Monoamine Transporter (VMAT)*. Journal Of Biological Chemistry 2014, 289: 34229-34240. PMID: 25336661, PMCID: PMC4256354, DOI: 10.1074/jbc.m114.607366.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsArginineBacterial ProteinsBiogenic MonoaminesBrevibacillusCarrier ProteinsDrug Resistance, BacterialEscherichia coliEvolution, MolecularGene ExpressionHistidineModels, MolecularMolecular Sequence DataProtein FoldingRatsRecombinant ProteinsSequence AlignmentStructural Homology, ProteinStructure-Activity RelationshipSubstrate SpecificitySynaptic TransmissionVesicular Monoamine Transport ProteinsConceptsBacterial multidrug transportersMultidrug transporterBacterial homologueVesicular monoamine transporterRat vesicular monoamine transporterMonoamine transportersPreliminary biochemical characterizationMammalian transportersTransmembrane helicesMammalian counterpartsTransmembrane segmentsMammalian organismsEvolutionary aspectsMajor facilitatorBiochemical characterizationImportant carboxylB. brevisHomology modelBiochemical studiesTransportersHomologuesCarboxyl residuesAntibiotic resistanceOrganismsNeurotransportersStructure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter
Fenollar-Ferrer C, Stockner T, Schwarz TC, Pal A, Gotovina J, Hofmaier T, Jayaraman K, Adhikary S, Kudlacek O, Mehdipour AR, Tavoulari S, Rudnick G, Singh SK, Konrat R, Sitte HH, Forrest LR. Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter. Biochemistry 2014, 53: 5444-5460. PMID: 25093911, PMCID: PMC4147951, DOI: 10.1021/bi500637f.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCircular DichroismCytoplasmFluorescence Resonance Energy TransferHumansMagnetic Resonance SpectroscopyModels, MolecularMolecular Sequence DataProtein ConformationProtein FoldingProtein Structure, SecondaryProtein Structure, TertiarySerotonin Plasma Membrane Transport ProteinsConceptsTerminal domainStructures of homologuesYellow fluorescent protein tagProtein-protein interactionsFluorescent protein tagsFluorescence resonance energy transfer signalN-terminal domainCarboxy-terminal endHelix-breaking residuesCyan fluorescent proteinEnergy transfer signalHuman serotonin transporterNSS familyConformational cycleCircular dichroism spectroscopyProtein tagsCytoplasmic segmentRegulatory interactionsTransmembrane regionUptake of neurotransmittersInteraction partnersRegulatory mechanismsSerotonin transporterBiophysical approachesFluorescent proteinCorrection to Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay
Nasr M, Singh S. Correction to Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay. Biochemistry 2014, 53: 1239-1239. PMCID: PMC4090034, DOI: 10.1021/bi500089c.Peer-Reviewed Original Research
2013
Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay
Nasr ML, Singh SK. Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay. Biochemistry 2013, 53: 4-6. PMID: 24344975, PMCID: PMC4062192, DOI: 10.1021/bi401412e.Peer-Reviewed Original ResearchConceptsMembrane transportersPhospholipid bilayer nanodiscsNative cell membranesSecondary transportersScintillation proximityBilayer nanodiscsDetergent solubilizationCell membraneLipid vesiclesTransportersNanodiscsScreening effortsBackground interferenceLeuTProteinVesiclesPowerful techniqueBindingMembraneReconstitutionRadioligand bindingSolubilizationInterferencePotential challengesProximity
2009
Crystal structure and association behaviour of the GluR2 amino‐terminal domain
Jin R, Singh SK, Gu S, Furukawa H, Sobolevsky AI, Zhou J, Jin Y, Gouaux E. Crystal structure and association behaviour of the GluR2 amino‐terminal domain. The EMBO Journal 2009, 28: 1812-1823. PMID: 19461580, PMCID: PMC2699365, DOI: 10.1038/emboj.2009.140.Peer-Reviewed Original ResearchConceptsAmino-terminal domainLigand-gated ion channel proteinsReceptor assemblyModular domain architectureIon channel proteinsFast excitatory neurotransmissionSame subfamilyMolecular basisReceptor subfamiliesChannel proteinsMolecular processesSubfamiliesAMPA receptor GluR1Ionotropic glutamate receptorsCrystal structureExcitatory neurotransmissionAssemblyGlutamate receptorsPropose mechanismsReceptorsSubunitsDomainProteinAssemblagesNMDA receptors
2008
A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation
Singh SK, Piscitelli CL, Yamashita A, Gouaux E. A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation. Science 2008, 322: 1655-1661. PMID: 19074341, PMCID: PMC2832577, DOI: 10.1126/science.1166777.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid Transport SystemsAmino AcidsBacterial ProteinsBinding SitesBinding, CompetitiveBiological TransportCrystallizationCrystallography, X-RayHydrogen BondingHydrophobic and Hydrophilic InteractionsKineticsLeucineLigandsModels, BiologicalModels, MolecularProtein ConformationProtein Structure, TertiarySodiumSymportersTryptophanConceptsNeurotransmitter sodium symportersPrimary substrate siteAmino acid substratesSodium symportersSecondary transportersExtracellular gateSubstrate passageLeucine transporterArginine 30Substrate transportCellular membranesConformational changesAcid substratesConformational statesSubstrate siteFunctional studiesIon gradientsLeuTWeak binding sitesTransportersBinding sitesSmall moleculesCompetitive inhibitorConformationTrp complexLeuT: A prokaryotic stepping stone on the way to a eukaryotic neurotransmitter transporter structure
Singh SK. LeuT: A prokaryotic stepping stone on the way to a eukaryotic neurotransmitter transporter structure. Channels 2008, 2: 380-389. PMID: 19066470, DOI: 10.4161/chan.2.5.6904.Peer-Reviewed Original ResearchConceptsSodium binding siteSolute carrier 6 (SLC6) familyIntegral membrane proteinsStructure/function studiesBinding sitesCrystal structureEukaryotic counterpartsAccurate homology modelsTransporter structureBacterial membersMembrane proteinsNutrient uptakeSequence identityMolecular insightsConformational changesHomology modelSecondary transportLeuTNeurotransmitter clearanceLipid bilayersSolute moleculesBiochemical dataFunction studiesIon bindingCrucial roleStructural models of inhibition in neurotransmitter sodium symporters
Singh S, Gouaux J. Structural models of inhibition in neurotransmitter sodium symporters. The FASEB Journal 2008, 22: 254.2-254.2. DOI: 10.1096/fasebj.22.1_supplement.254.2.Peer-Reviewed Original ResearchNeurotransmitter sodium symportersSodium symportersNovel noncompetitive inhibitorsX-ray crystallographyAtomic-level insightsSteady-state kinetic dataLeucine transporterSteady-state kineticsMolecular principlesRational designSmall moleculesIon gradientsKinetic dataDissociation assaysAddictive compoundInhibitor actionCritical roleNoncompetitive modeStructural paradigmSymporterNoncompetitive inhibitorAllosteric antagonistsGlial cytoplasmSynaptic transmissionLeuT
2007
Antidepressant binding site in a bacterial homologue of neurotransmitter transporters
Singh SK, Yamashita A, Gouaux E. Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 2007, 448: 952-956. PMID: 17687333, DOI: 10.1038/nature06038.Peer-Reviewed Original Research
2006
S3h1-2 Crystal structure of a bacterial homolog of Na^+/Cl^- -dependent neurotransmitter transporters(S3-h1: "Structural Aspects of Channel and Transporter Proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)
Yamashita A, Singh S, Kawate T, Jin Y, Gouaux E. S3h1-2 Crystal structure of a bacterial homolog of Na^+/Cl^- -dependent neurotransmitter transporters(S3-h1: "Structural Aspects of Channel and Transporter Proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006). Seibutsu Butsuri 2006, 46: s139. DOI: 10.2142/biophys.46.s139_4.Peer-Reviewed Original Research
2005
Subunit arrangement and function in NMDA receptors
Furukawa H, Singh SK, Mancusso R, Gouaux E. Subunit arrangement and function in NMDA receptors. Nature 2005, 438: 185-192. PMID: 16281028, DOI: 10.1038/nature04089.Peer-Reviewed Original ResearchConceptsHeteromeric ion channelsNR1-NR2AMammalian central nervous systemSlow channel openingChannel openingHeterodimer interfaceTransduction cascadeIon channel openingSubunit arrangementSubunit interfaceIon channelsNR2 subunitsReceptor functionChannel deactivationNMDA receptorsNMDA receptor functionReceptorsExcitatory neurotransmissionFunctional unitsCentral nervous systemNR1GlutamateGlycineNervous systemHeterodimersCrystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters
Yamashita A, Singh SK, Kawate T, Jin Y, Gouaux E. Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters. Nature 2005, 437: 215-223. PMID: 16041361, DOI: 10.1038/nature03978.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacteriaBacterial ProteinsBinding SitesBiological TransportChloridesCrystallography, X-RayHydrophobic and Hydrophilic InteractionsLeucineMembrane Transport ProteinsModels, MolecularMolecular Sequence DataNeurotransmitter AgentsSequence AlignmentSodiumStructure-Activity RelationshipWaterConceptsBacterial homologueProtein coreDependent neurotransmitter transportersTransmembrane helicesTransmembrane segmentsAquifex aeolicusUptake of neurotransmittersSubstrate bindingNeurotransmitter transportersMain-chain atomsMembrane bilayerDependent transportersElectrochemical gradientIon binding siteTransportersHelix dipole