2025
BPS2025 - Anti-tuberculosis drug bedaquiline ameliorates calcium-induced mitochondrial permeability transition by inhibiting the ATP synthase leak channel
Kumar A, Smith E, Mezghani I, Eedarapalli S, Wu Y, Amjad E, Park H, Mnatsakanyan N. BPS2025 - Anti-tuberculosis drug bedaquiline ameliorates calcium-induced mitochondrial permeability transition by inhibiting the ATP synthase leak channel. Biophysical Journal 2025, 124: 447a. DOI: 10.1016/j.bpj.2024.11.2381.Peer-Reviewed Original Research
2024
Passing Behavior of Oligonucleotides through a Stacked DNA Nanochannel with Featured Path Design
Zhang R, Xiang Y, Yang Y. Passing Behavior of Oligonucleotides through a Stacked DNA Nanochannel with Featured Path Design. Journal Of The American Chemical Society 2024, 146: 17122-17130. PMID: 38861703, DOI: 10.1021/jacs.4c02734.Peer-Reviewed Original Research
2022
β-cell deletion of the PKm1 and PKm2 isoforms of pyruvate kinase in mice reveals their essential role as nutrient sensors for the KATP channel
Foster HR, Ho T, Potapenko E, Sdao SM, Huang SM, Lewandowski SL, VanDeusen HR, Davidson SM, Cardone RL, Prentki M, Kibbey RG, Merrins MJ. β-cell deletion of the PKm1 and PKm2 isoforms of pyruvate kinase in mice reveals their essential role as nutrient sensors for the KATP channel. ELife 2022, 11: e79422. PMID: 35997256, PMCID: PMC9444242, DOI: 10.7554/elife.79422.Peer-Reviewed Original ResearchConceptsPyruvate kinaseATP/ADPCytosolic ATP/ADPAmino acidsPKM2 isoformPK isoformsPlasma membraneNutrient sensorNutrient responsesPEP carboxykinasePKM1Mitochondrial sourcesPKM2Channel closureEssential roleInsulin secretionDifferential responsePK activityKinaseMembrane depolarizationIsoformsDeletionATPKey roleADPThe nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release
Gray S, Cao W, Montpetit B, De La Cruz EM. The nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release. Nucleic Acids Research 2022, 50: 3998-4011. PMID: 35286399, PMCID: PMC9023272, DOI: 10.1093/nar/gkac164.Peer-Reviewed Original ResearchConceptsNuclear pore complexRNA exportDEAD-box protein Dbp5ATPase cycleDbp5's ATPase activityDEAD (Asp-Glu-Ala-Asp) box protein 5Pore complexDbp5ATP bindingATPase cyclingNucleotide stateCytoplasmic faceGle1Pool of ATPADP-PiGene expressionProtein 5Mechanistic understandingNucleoporinsNup159ATPase activityATP dissociationATPPi releasePi release rate
2021
The nucleotide binding affinities of two critical conformations of Escherichia coli ATP synthase
Li Y, Valdez NA, Mnatsakanyan N, Weber J. The nucleotide binding affinities of two critical conformations of Escherichia coli ATP synthase. Archives Of Biochemistry And Biophysics 2021, 707: 108899. PMID: 33991499, PMCID: PMC8278868, DOI: 10.1016/j.abb.2021.108899.Peer-Reviewed Original ResearchConceptsATP synthaseCritical conformationEscherichia coli ATP synthaseRotary catalytic mechanismCatalytic dwell stateCatalytic mechanismAerobic energy metabolismΓ subunitCysteine mutationsTryptophan fluorescenceDwell stateDisulfide bondsEnergetic functionEnergy metabolismCatalytic siteSynthaseCatalytic dwellAffinity changesATPEnzymeAffinityConformationSubunitsMutationsSites
2020
The new role of F1Fo ATP synthase in mitochondria-mediated neurodegeneration and neuroprotection
Mnatsakanyan N, Jonas EA. The new role of F1Fo ATP synthase in mitochondria-mediated neurodegeneration and neuroprotection. Experimental Neurology 2020, 332: 113400. PMID: 32653453, PMCID: PMC7877222, DOI: 10.1016/j.expneurol.2020.113400.Peer-Reviewed Original ResearchConceptsMitochondrial inner membraneATP synthaseInner membraneOxidative phosphorylationF1Fo-ATP synthaseUnique rotational mechanismMitochondrial inner membrane potentialEfficient cellular metabolismInner membrane potentialMitochondrial permeability transition porePermeability transition poreUnique regulatorAbundant proteinsNew roleCellular metabolismCell lifeProton translocationATP synthesisTransition poreCell survivalElectrochemical gradientCertain pathophysiological conditionsSynthaseATPMembrane potentialCellular Mechanisms of Metabolic Remodeling During Fluid Sheer Stress-Induced Metastasis
Dunn T, Brown S, Mnatsakanyan N, Jonas E, Yonghyun K, Park H. Cellular Mechanisms of Metabolic Remodeling During Fluid Sheer Stress-Induced Metastasis. Current Developments In Nutrition 2020, 4: nzaa044_021. PMCID: PMC7258028, DOI: 10.1093/cdn/nzaa044_021.Peer-Reviewed Original ResearchATP synthaseC subunitBreast cancer cellsMDA-MB-231 cellsMetabolic remodelingCancer cellsCellular mechanismsEnergy metabolismKey enzyme complexMitochondrial energy metabolismMDA-MB-231 breast cancer cellsMDA-MB-231 human breast cancer cellsCell divisionMitochondrial remodelingEnzyme complexHuman breast cancer cellsATP productionMetastatic phenotypeActive transport systemUncoupler FCCPMitochondrial ATPProtein levelsIntracellular ATPATPAbundanceChaperonin-assisted protein folding: a chronologue
Horwich AL, Fenton WA. Chaperonin-assisted protein folding: a chronologue. Quarterly Reviews Of Biophysics 2020, 53: e4. PMID: 32070442, DOI: 10.1017/s0033583519000143.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino AcidsAnimalsCarbon DioxideChaperoninsCytosolDimerizationHeat-Shock ProteinsHumansHydrophobic and Hydrophilic InteractionsKineticsMiceMitochondriaMutationNeurosporaProtein ConformationProtein DenaturationProtein FoldingRibonuclease, PancreaticRibulose-Bisphosphate CarboxylaseSurface PropertiesTemperature
2019
Altered allostery of the left flipper domain underlies the weak ATP response of rat P2X5 receptors
Sun L, Liu Y, Wang J, Huang L, Yang Y, Cheng X, Fan Y, Zhu M, Liang H, Tian Y, Wang H, Guo C, Yu Y. Altered allostery of the left flipper domain underlies the weak ATP response of rat P2X5 receptors. Journal Of Biological Chemistry 2019, 294: 19589-19603. PMID: 31727741, PMCID: PMC6926468, DOI: 10.1074/jbc.ra119.009959.Peer-Reviewed Original ResearchConceptsFuture transgenic studiesFull-length variantATP responseTransmembrane domainTransgenic studiesMammalian speciesP2X5 receptorsAllosteryPathological functionsSingle replacementSingle-channel recordingsSkeletal muscleExon 10Molecular modelingFunctional subtypesATPResiduesNervous systemP2X5ReceptorsDomainMammalsSpeciesTM2Lack of knowledge
2018
Flipping ATP to AMPlify Kinase Functions
Sheetz JB, Lemmon MA. Flipping ATP to AMPlify Kinase Functions. Cell 2018, 175: 641-642. PMID: 30340038, PMCID: PMC6421561, DOI: 10.1016/j.cell.2018.10.011.Peer-Reviewed Original ResearchRIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization
Devarkar S, Schweibenz B, Wang C, Marcotrigiano J, Patel S. RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization. Molecular Cell 2018, 72: 355-368.e4. PMID: 30270105, PMCID: PMC6434538, DOI: 10.1016/j.molcel.2018.08.021.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateAortic DiseasesCell LineDEAD Box Protein 58DEAD-box RNA HelicasesDental Enamel HypoplasiaFemaleHEK293 CellsHumansHydrolysisKineticsMetacarpusMuscular DiseasesOdontodysplasiaOsteoporosisProtein BindingReceptors, Antigen, T-CellReceptors, ImmunologicRibosomesRNARNA, Double-StrandedSignal TransductionVascular CalcificationConceptsRIG-ISelf-RNARNA discriminationMechanism of RIG-I activationRIG-I oligomerizationC-terminal domainActivation of RIG-IRIG-I activationTransient-state kineticsAutoinhibited stateBind ATPATP bindingDNA polymeraseDsRNAOligomeric complexesConstitutive signalingKinetic proofreadingStem regionATPase activityT cell receptorRNACell receptorsFast off rateATPTranslocation
2017
The Krebs Cycle Enzyme Isocitrate Dehydrogenase 3A Couples Mitochondrial Metabolism to Synaptic Transmission
Ugur B, Bao H, Stawarski M, Duraine LR, Zuo Z, Lin YQ, Neely GG, Macleod GT, Chapman ER, Bellen HJ. The Krebs Cycle Enzyme Isocitrate Dehydrogenase 3A Couples Mitochondrial Metabolism to Synaptic Transmission. Cell Reports 2017, 21: 3794-3806. PMID: 29281828, PMCID: PMC5747319, DOI: 10.1016/j.celrep.2017.12.005.Peer-Reviewed Original ResearchConceptsSynaptic vesiclesKrebs cycle enzymeRole of metabolitesC2 domainPlasma membraneMitochondrial metabolismSynaptic transmissionMetabolic regulationCycle enzymesSynaptic roleAlpha-ketoglutarateSyt1ΑKGNeurodegenerative disordersDependent processesRegulationMetabolitesIDH3ASynaptotagmin1Multiple levelsFliesRoleFusionVesiclesATPReconstructed Serine 288 in the Left Flipper Region of the Rat P2X7 Receptor Stabilizes Nonsensitized States
Ishchenko Y, Novosolova N, Khafizov K, Bart G, Timonina A, Fayuk D, Skorinkin A, Giniatullin R. Reconstructed Serine 288 in the Left Flipper Region of the Rat P2X7 Receptor Stabilizes Nonsensitized States. Biochemistry 2017, 56: 3394-3402. PMID: 28616989, DOI: 10.1021/acs.biochem.7b00258.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionAnimalsBinding SitesBiological Transport, ActiveComputer SimulationFluorescent DyesHEK293 CellsHumansKineticsLigandsModels, MolecularPatch-Clamp TechniquesPoint MutationProtein Interaction Domains and MotifsProtein StabilityPurinergic P2X Receptor AgonistsPurinergic P2X Receptor AntagonistsRatsReceptors, Purinergic P2X7Recombinant ProteinsSerineConceptsRat P2X7 receptorP2X7 receptorSerine 288Novel phenotypesCorresponding residuesPosition 288MM ATPHuman P2X7 receptorMolecular modeling dataF288Agonist bindingATPReceptor statesP2X receptorsReceptor desensitizationPhenotypeATP concentrationFast deactivation ratesResiduesReceptorsKey roleS applicationMutantsSerineWT valuesIdentification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders
Puleo DE, Kucera K, Hammarén H, Ungureanu D, Newton AS, Silvennoinen O, Jorgensen WL, Schlessinger J. Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders. ACS Medicinal Chemistry Letters 2017, 8: 618-621. PMID: 28626521, PMCID: PMC5467198, DOI: 10.1021/acsmedchemlett.7b00153.Peer-Reviewed Original ResearchSmall molecule bindersJAK2 pseudokinase domainKinase foldTyrosine kinase domainNovel pharmacological opportunitiesPseudokinase domainKinase domainJAK-STATJAK2 proteinTop hitsMicromolar affinityPharmacological opportunitiesHyperactivation stateProteinATPJH2JAK2 V617FRecent evidencePseudokinaseMutantsJAKDomainHematopoiesisPathwayStructural approach
2016
Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress
Pontes MH, Yeom J, Groisman EA. Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress. Molecular Cell 2016, 64: 480-492. PMID: 27746019, PMCID: PMC5500012, DOI: 10.1016/j.molcel.2016.05.008.Peer-Reviewed Original ResearchConceptsSynthesis of ribosomesAmino acid abundanceExpression of proteinsPromotes TranslationAvailability of ATPRibosomal componentsRegulatory circuitsTranslational arrestCytosolic MgRRNA geneProtein synthesisRibosomesATP levelsLevels of ATPATP amountATPDivalent cationsMutantsTranscriptionNegative chargeGenesLow Mg2TranslationProteinAbundanceThe Mitochondrial Permeability Transition Pore and ATP Synthase
Beutner G, Alavian K, Jonas EA, Porter GA. The Mitochondrial Permeability Transition Pore and ATP Synthase. Handbook Of Experimental Pharmacology 2016, 240: 21-46. PMID: 27590224, PMCID: PMC7439278, DOI: 10.1007/164_2016_5.BooksConceptsPermeability transition poreElectron transport chainATP synthaseGeneration of ATPMitochondrial permeability transition poreATP generationTransition poreCell deathC subunit ringMitochondrial ATP generationFo subunitsEmbryonic mouse heartPTP openingTransport chainOxidative phosphorylationEquivalents NADHMature cellsSynthasePhysiologic roleMouse heartsATPRecent studiesPhosphorylationSubunitsFADH2
2015
Mitochondrial ROS Signaling in Organismal Homeostasis
Shadel GS, Horvath TL. Mitochondrial ROS Signaling in Organismal Homeostasis. Cell 2015, 163: 560-569. PMID: 26496603, PMCID: PMC4634671, DOI: 10.1016/j.cell.2015.10.001.Peer-Reviewed Original ResearchConceptsReactive oxygen speciesOrganismal homeostasisMitochondrial ROS signalingMitochondrial reactive oxygen speciesAdaptive physiological responsesROS signalingCellular differentiationMitochondrial oxygen consumptionOxidative phosphorylationPhysiological responsesOxygen speciesCentral roleHomeostasisEukaryotesOrganic fuel moleculesPhosphorylationMitochondriaMoleculesSignalingSpeciesATPDifferentiationPathwayGreater understandingRoleWhen Too Much ATP Is Bad for Protein Synthesis
Pontes MH, Sevostyanova A, Groisman EA. When Too Much ATP Is Bad for Protein Synthesis. Journal Of Molecular Biology 2015, 427: 2586-2594. PMID: 26150063, PMCID: PMC4531837, DOI: 10.1016/j.jmb.2015.06.021.Peer-Reviewed Original ResearchConceptsProtein synthesisStructure of ribosomesEnergy-dependent activitiesATP levelsRibosome productionCellular processesTranslation initiationCytoplasmic membraneEssential enzymeCellular ATPEnergy currencyLiving cellsATPCellsDivalent cationsCrucial roleTriphosphateRibosomesAminoacylationOrganismsNon-physiological increaseCofactorEnzymeBiochemistryCommon divalent cationsForm and Function in Cells of the Brain
Levitan I, Kaczmarek L. Form and Function in Cells of the Brain. 2015, 23-38. DOI: 10.1093/med/9780199773893.003.0002.Chapters
2014
Contribution of sodium channels to lamellipodial protrusion and Rac1 and ERK1/2 activation in ATP‐stimulated microglia
Persson A, Estacion M, Ahn H, Liu S, Stamboulian‐Platel S, Waxman SG, Black JA. Contribution of sodium channels to lamellipodial protrusion and Rac1 and ERK1/2 activation in ATP‐stimulated microglia. Glia 2014, 62: 2080-2095. PMID: 25043721, DOI: 10.1002/glia.22728.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAnimalsAnimals, NewbornBrainCell MovementCells, CulturedEnzyme ActivationEnzyme InhibitorsGene Expression RegulationMembrane PotentialsMiceMice, TransgenicMicrogliaMitogen-Activated Protein Kinase 3NAV1.6 Voltage-Gated Sodium ChannelPseudopodiarac1 GTP-Binding ProteinRatsRats, Sprague-DawleySignal TransductionSodium Channel BlockersConceptsActin-rich membrane protrusionsStream signaling cascadesAccumulation of Rac1Modulation of Rac1Sodium channel activityChannel activitySodium channelsP38α/βCellular polarizationMembrane protrusionsSignal transductionLamellipodial protrusionCellular pathwaysSignaling cascadesCoordinated processCytoskeletal elementsMembrane adhesionRac1Dependent pathwayPhosphorylated ERK1/2Central nervous systemATPERK1/2ATP stimulationActivated state
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