2022
Identification of substrates of palmitoyl protein thioesterase 1 highlights roles of depalmitoylation in disulfide bond formation and synaptic function
Gorenberg EL, Tieze S, Yücel B, Zhao HR, Chou V, Wirak GS, Tomita S, Lam TT, Chandra SS. Identification of substrates of palmitoyl protein thioesterase 1 highlights roles of depalmitoylation in disulfide bond formation and synaptic function. PLOS Biology 2022, 20: e3001590. PMID: 35358180, PMCID: PMC9004782, DOI: 10.1371/journal.pbio.3001590.Peer-Reviewed Original ResearchConceptsPalmitoyl-protein thioesterase 1Disulfide bond formationNeuronal ceroid lipofuscinosisPosttranslational modificationsRole of PPT1Identification of substratesResin-assisted captureEnzyme palmitoyl-protein thioesterase 1Synaptic adhesion moleculesNeurodegenerative diseasesMature proteinMitochondrial proteinsMolecular dissectionPutative substratesDepalmitoylationKnockout mouse brainFunction mutationsStringent screenMolecular pathwaysSynapse functionDisulfide bondsProteinDevastating neurodegenerative diseaseDisease mechanismsSynaptic function
2018
Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase
Wang Z, Kim MS, Martinez-Ferrando I, Koleske A, Pandey A, Cole P. Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase. Biochemistry 2018, 57: 1390-1398. PMID: 29341593, PMCID: PMC5906802, DOI: 10.1021/acs.biochem.7b01158.Peer-Reviewed Original ResearchConceptsProtein kinaseNonreceptor tyrosine kinases AblMass spectrometry-based quantitative proteomicsNovel putative substratesTyrosine kinase AblCellular tyrosine phosphorylationExtracellular growth factorsChemical rescue approachIntracellular signal transductionQuantitative phosphoproteomicsUnanticipated functionCellular physiologyGrowth factorPhosphorylation sitesPutative substratesDirect substrateDownstream substratesSignal transductionReceptor kinaseQuantitative proteomicsTyrosine phosphorylationActive Abl kinasesAbl kinaseChemical rescueKinase
2015
Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication
Avey D, Tepper S, Li W, Turpin Z, Zhu F. Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication. PLOS Pathogens 2015, 11: e1004993. PMID: 26133373, PMCID: PMC4489790, DOI: 10.1371/journal.ppat.1004993.Peer-Reviewed Original ResearchMeSH KeywordsBlotting, WesternCell LineGene Expression Regulation, ViralGene Knockout TechniquesHerpesviridae InfectionsHerpesvirus 8, HumanHost-Parasite InteractionsHumansImmediate-Early ProteinsImmunoprecipitationMass SpectrometryPhosphorylationProteomicsReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRibosomal Protein S6 Kinases, 90-kDaTransfectionVirus ReplicationConceptsKaposi's sarcoma-associated herpesvirusKSHV lytic replicationProgeny virion productionKSHV ORF45Putative substratesRSK activityExtracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathwayGene expressionEfficient KSHV lytic replicationLytic replicationP90 ribosomal S6 kinaseMitogen-activated protein kinase pathwayRSK-dependent phosphorylationHost cell machineryRibosomal S6 kinaseProtein kinase pathwayVirion productionActivation of RSKComplex secondary structureKSHV lytic gene expressionTranscriptional regulatorsDifferential phosphorylationLytic gene expressionCellular genesCell machinery
2012
Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae *
Henriksen P, Wagner SA, Weinert BT, Sharma S, Bačinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C. Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae *. Molecular & Cellular Proteomics 2012, 11: 1510-1522. PMID: 22865919, PMCID: PMC3494197, DOI: 10.1074/mcp.m112.017251.Peer-Reviewed Original ResearchConceptsAcetylation sitesLysine acetylationS. cerevisiaeUnicellular eukaryotic model organismBudding yeast Saccharomyces cerevisiaeRegulatory roleBroader regulatory scopeProtein synthesisEukaryotic model organismYeast Saccharomyces cerevisiaePost-translational modificationsLysine acetylation sitesImportant regulatory roleChromatin organizationLysine acetyltransferasesModel organismsWide analysisPutative substratesRegulatory domainCritical regulatory domainsHistone H2BAcetylated proteinsProtein foldingSaccharomyces cerevisiaeBioinformatics analysis
2007
Use of a Chemical Genetic Technique To Identify Myosin IIB as a Substrate of the Abl-Related Gene (Arg) Tyrosine Kinase
Boyle SN, Koleske AJ. Use of a Chemical Genetic Technique To Identify Myosin IIB as a Substrate of the Abl-Related Gene (Arg) Tyrosine Kinase. Biochemistry 2007, 46: 11614-11620. PMID: 17892306, DOI: 10.1021/bi701119s.Peer-Reviewed Original ResearchConceptsPutative substratesMyosin IIBGene Tyrosine KinaseUnnatural ATP analoguesProtein substrate specificityPhosphotyrosine-containing proteinsSer/ThrAbl/ArgChemical-genetic techniqueCell morphogenesisKinase substrateDirect substrateFamily kinasesTyrosine phosphorylationSubstrate specificityGenetic techniquesNucleotide specificityMolecular mechanismsTyrosine kinaseK-252aUnexpected high levelATP analogGene kinaseKinaseABLDissecting kinase signaling pathways
Boyle SN, Koleske AJ. Dissecting kinase signaling pathways. Drug Discovery Today 2007, 12: 717-724. PMID: 17826684, DOI: 10.1016/j.drudis.2007.07.019.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, MonoclonalAntibodies, Monoclonal, HumanizedAntineoplastic AgentsBenzamidesDrug Delivery SystemsHumansImatinib MesylateLapatinibNeoplasmsPhosphoproteinsPhosphorylationPiperazinesProtein Kinase InhibitorsProtein KinasesProteomicsPyrimidinesQuinazolinesSignal TransductionTrastuzumabConceptsSame protein substrateProtein Kinase SignalingKinase substratePutative substratesProtein substratesKinase signalingProtein kinaseMultiple kinasesPhysiological substratesKinaseHuman diseasesDrug targetsPhysiological relevanceSubstrate interactionsKinase inhibitorsPathwaySignalingSubstrateNeurological disordersInteractionHallmarkInhibitorsTarget
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