2018
Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq
Carlyle B, Kitchen RR, Zhang J, Wilson R, Lam T, Rozowsky JS, Williams KR, Sestan N, Gerstein M, Nairn AC. Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. Journal Of Proteome Research 2018, 17: 3431-3444. PMID: 30125121, PMCID: PMC6392456, DOI: 10.1021/acs.jproteome.8b00310.Peer-Reviewed Original ResearchConceptsRNA-seqProteomic dataGene expressionLiquid chromatography-tandem mass spectrometry proteomicsTandem mass spectrometry proteomicsHigh-throughput proteomic dataTranscriptomic profiling methodsDistinct amino acid sequencesTranscript-level expressionAmino acid sequenceMass spectrometry proteomicsHEK293 cell culturesTranslatome dataMost genesProfound functional implicationsProtein isoformsAlternate isoformsGene productsAcid sequenceCellular controlBiosynthetic stateGeneration of peptidesCell typesFunctional relevanceFunctional implications
2000
The Dopamine/D1 Receptor Mediates the Phosphorylation and Inactivation of the Protein Tyrosine Phosphatase STEP via a PKA-Dependent Pathway
Paul S, Snyder G, Yokakura H, Picciotto M, Nairn A, Lombroso P. The Dopamine/D1 Receptor Mediates the Phosphorylation and Inactivation of the Protein Tyrosine Phosphatase STEP via a PKA-Dependent Pathway. Journal Of Neuroscience 2000, 20: 5630-5638. PMID: 10908600, PMCID: PMC6772528, DOI: 10.1523/jneurosci.20-15-05630.2000.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAnimalsCatalytic DomainCorpus StriatumCyclic AMP-Dependent Protein KinasesEnzyme ActivationIn Vitro TechniquesMaleMolecular Sequence DataNeuronsPhosphoproteinsPhosphorus RadioisotopesPhosphorylationProtein Tyrosine PhosphatasesProtein Tyrosine Phosphatases, Non-ReceptorRatsRats, Sprague-DawleyReceptors, Dopamine D1Signal TransductionConceptsProtein tyrosine phosphatase familyCAMP-dependent protein kinaseTryptic phosphopeptide mappingPotential phosphorylation sitesUnique N-terminalProtein-protein interactionsMembrane-associated proteinsRole of phosphorylationTyrosine phosphatase familyAmino acid sequenceSite-directed mutagenesisAmino acid sequencingPKA-dependent pathwayTyrosine phosphatase STEPPhosphatase familyPhosphopeptide mappingPhosphorylation sitesAlternative splicingSubcellular compartmentsProtein kinaseTerminal domainEquivalent residuesCytosolic proteinsSpecific residuesAcid sequence
1999
Molecular identification of human G-substrate, a possible downstream component of the cGMP-dependent protein kinase cascade in cerebellar Purkinje cells
Endo S, Suzuki M, Sumi M, Nairn A, Morita R, Yamakawa K, Greengard P, Ito M. Molecular identification of human G-substrate, a possible downstream component of the cGMP-dependent protein kinase cascade in cerebellar Purkinje cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 2467-2472. PMID: 10051666, PMCID: PMC26808, DOI: 10.1073/pnas.96.5.2467.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBrainCerebellumCloning, MolecularCyclic GMP-Dependent Protein KinasesDatabases as TopicExpressed Sequence TagsHumansMolecular Sequence DataNerve Tissue ProteinsPurkinje CellsRabbitsRecombinant ProteinsRNA, MessengerSequence AlignmentSequence Homology, Amino AcidTranscription, GeneticConceptsAmino acid sequenceProtein phosphatase 1G-substrateAcid sequencePhosphatase 1Deduced amino acid sequenceRadiation hybrid panel analysisProtein phosphatase 2APutative phosphorylation sitesCGMP-dependent protein kinaseProtein kinase cascadeProtein phosphatase inhibitorSequence tag databaseSites of phosphorylationVitro translation productsHuman brain libraryCGMP-dependent proteinAcid-soluble proteinsApparent molecular massSDS/PAGEPhosphatase 2AThr-35Kinase cascadePhosphorylation sitesTag database
1997
Phosphorylation of Alzheimer β-Amyloid Precursor-like Proteins †
Suzuki T, Ando K, Isohara T, Oishi M, Lim G, Satoh Y, Wasco W, Tanzi R, Nairn A, Greengard P, Gandy S, Kirino Y. Phosphorylation of Alzheimer β-Amyloid Precursor-like Proteins †. Biochemistry 1997, 36: 4643-4649. PMID: 9109675, DOI: 10.1021/bi962618k.Peer-Reviewed Original ResearchConceptsAlzheimer's beta-amyloid precursor proteinCytoplasmic domain peptidePrecursor-like proteinsProtein kinase CCytoplasmic domainCultured cellsCell cycle-dependent mannerKinase CDomain peptideCycle-dependent mannerAmino acid sequenceHomologous amino acid sequencesGene familyKinase siteAcid sequenceExtracellular domainIntact cellsAPLP2Proteolytic processingAPLP1PhosphorylationPrecursor proteinProteinBeta-amyloid precursor proteinCdc2
1995
CaMKI CaM-dependent protein kinase I (vertebrates)
Edelman A, Nairn A. CaMKI CaM-dependent protein kinase I (vertebrates). 1995, 128-130. DOI: 10.1016/b978-012324719-3/50029-7.Peer-Reviewed Original ResearchCystic fibrosis transmembrane conductance regulatorKinase IProtein kinase ICaM kinase ICAMP response element-binding proteinCaM-dependent protein kinase ICalmodulin-dependent protein kinase IPartial amino acid sequence dataShort N-terminal extensionLong C-terminal extensionAmino acid sequence dataFibrosis transmembrane conductance regulatorN-terminal extensionC-terminal extensionCaM-binding domainSynaptic vesicle functionAmino acid sequenceBrain cDNA libraryRat brain cDNA libraryTransmembrane conductance regulatorWidespread tissue distributionResponse element-binding proteinElement-binding proteinIon channel activityKinase domain
1991
Identification and localization of a dogfish homolog of human cystic fibrosis transmembrane conductance regulator.
Marshall J, Martin K, Picciotto M, Hockfield S, Nairn A, Kaczmarek L. Identification and localization of a dogfish homolog of human cystic fibrosis transmembrane conductance regulator. Journal Of Biological Chemistry 1991, 266: 22749-22754. PMID: 1718999, DOI: 10.1016/s0021-9258(18)54631-7.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCell MembraneCloning, MolecularCystic FibrosisCystic Fibrosis Transmembrane Conductance RegulatorDNADogfishHumansImmunoenzyme TechniquesMembrane ProteinsMolecular Sequence DataMolecular WeightProtein KinasesRectumSebaceous GlandsSequence Homology, Nucleic AcidSubstrate SpecificityConceptsCystic fibrosis transmembrane conductance regulatorHuman cystic fibrosis transmembrane conductance regulatorFibrosis transmembrane conductance regulatorTransmembrane conductance regulatorDogfish proteinRectal glandConductance regulatorPutative substrate sitesCyclic AMP-dependent protein kinaseAMP-dependent protein kinaseMajor phosphorylation siteCyclic AMP-dependent protein phosphorylationApical plasma membraneAmino acid sequenceStudy of regulationPhosphorylation sitesProtein phosphorylationCDNA clonesProtein kinaseSimilar molecular massCFTR sequencePlasma membraneAcid sequenceImmunolocalization studiesMolecular mass