2019
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLOS Computational Biology 2019, 15: e1006706. PMID: 30653502, PMCID: PMC6353226, DOI: 10.1371/journal.pcbi.1006706.Peer-Reviewed Original ResearchConceptsReceptor tyrosine kinasesSrc homology 2Autophosphorylation sitesInsulin-like growth factor 1 receptorGrowth factor 1 receptorFactor 1 receptorPTB domain-containing proteinsCopy numberDomain-containing proteinsPhosphotyrosine-binding (PTB) domainProtein copy numbersMultiple autophosphorylation sitesProtein abundance profilesMultiple signaling proteinsShort linear motifsOutcome of competitionCell line-specific modelsHomology 2Cytoplasmic domainSignaling proteinsLinear motifsTyrosine kinaseEffects of competitionRule-based modeling approachRelative abundance
2015
Use of Mechanistic Models to Integrate and Analyze Multiple Proteomic Datasets
Stites E, Aziz M, Creamer M, Von Hoff D, Posner R, Hlavacek W. Use of Mechanistic Models to Integrate and Analyze Multiple Proteomic Datasets. Biophysical Journal 2015, 108: 1819-1829. PMID: 25863072, PMCID: PMC4390817, DOI: 10.1016/j.bpj.2015.02.030.Peer-Reviewed Original ResearchConceptsEpidermal growth factor receptorExperimentally detected interactionsPhosphotyrosine-binding domainSrc homology 2Recruitment of proteinsCell line-specific modelsProtein copy numbersProtein-protein interactionsCell signaling networksEpidermal growth factor receptor signalingCell linesWell-characterized roleCell line-specific differencesLow-affinity interactionsLine-specific differencesActivation of EGFR signalingMultiple cell linesLigand-stimulated activationAutophosphorylation sitesSignaling networksProteomic datasetsCopy numberHomolog 2EGFR signalingMap interactions
2014
Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers
Opatowsky Y, Lax I, Tomé F, Bleichert F, Unger VM, Schlessinger J. Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 1772-1777. PMID: 24449920, PMCID: PMC3918759, DOI: 10.1073/pnas.1323254111.Peer-Reviewed Original ResearchConceptsExtracellular regionConformational statesIg-like domainsReceptor tyrosine kinasesDifferent conformational statesTrans autophosphorylationTyrosine kinase domainMembrane-proximal Ig-like domainsTrans phosphorylationAutophosphorylation sitesDomain organizationKinase domainCytoplasmic regionHomotypic interactionsKinase activityReceptor dimersDimeric receptorTyrosine kinaseAsymmetric arrangementMolecular interactionsPrevalent conformationsCrystal structureAutophosphorylationDimersKinase
2007
Structural and Functional Characterization of the Human Protein Kinase ASK1
Bunkoczi G, Salah E, Filippakopoulos P, Fedorov O, Müller S, Sobott F, Parker SA, Zhang H, Min W, Turk BE, Knapp S. Structural and Functional Characterization of the Human Protein Kinase ASK1. Structure 2007, 15: 1215-1226. PMID: 17937911, PMCID: PMC2100151, DOI: 10.1016/j.str.2007.08.011.Peer-Reviewed Original ResearchConceptsApoptosis signal-regulating kinase 1Autophosphorylation sitesSignal-regulated kinases 1ASK1 kinase activityVitro autophosphorylation sitesAnalytical ultracentrifugationHigh-resolution structuresATP-mimetic inhibitorSite-directed mutantsReporter gene assayPhosphorylation motifsPhosphorylation sitesCatalytic domainFunctional characterizationKinase activityRegulatory mechanismsKinase 1Tight dimerMimetic inhibitorsGene assayEssential roleSelective inhibitorTail fashionCrystallographic analysisMass spectrometry
2005
Activation of Dopamine D4 Receptors Induces Synaptic Translocation of Ca2+/Calmodulin-Dependent Protein Kinase II in Cultured Prefrontal Cortical Neurons
Gu Z, Jiang Q, Yuen E, Yan Z. Activation of Dopamine D4 Receptors Induces Synaptic Translocation of Ca2+/Calmodulin-Dependent Protein Kinase II in Cultured Prefrontal Cortical Neurons. Molecular Pharmacology 2005, 69: 813-822. PMID: 16365279, DOI: 10.1124/mol.105.018853.Peer-Reviewed Original ResearchConceptsD4 receptor activationDependent protein kinase IIProtein kinase IIAlpha-CaMKIID4 receptorsDopamine D4 receptorCaMKII translocationKinase IIReceptor activationF-actinSynaptic translocationPostsynaptic sitesBinding of CaMKIITrisphosphate receptor/Ca2Receptor-mediated excitatory postsynaptic currentsAMPA receptor-mediated excitatory postsynaptic currentsPhospholipase C/inositolPrefrontal cortexCalmodulin binding siteExcitatory postsynaptic currentsGlutamate receptor 1 (GluR1) subunitPrefrontal cortical neuronsD4 receptor stimulationAutophosphorylation sitesSubcellular localization
2004
cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model
Kluger HM, Kluger Y, Gilmore-Hebert M, DiVito K, Chang JT, Rodov S, Mironenko O, Kacinski BM, Perkins AS, Sapi E. cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Laboratory Investigation 2004, 84: 320-331. PMID: 14767486, DOI: 10.1038/labinvest.3700044.Peer-Reviewed Original ResearchConceptsAutophosphorylation sitesHC11 mammary epithelial cellsMAP kinase phosphatase-1SNARE protein Ykt6Macrophage colony-stimulating factor receptorK cDNA microarrayColony-stimulating factor receptorCDNA microarray analysisKinase phosphatase-1Effects of mutationsMammary epithelial cellsTransmembrane tyrosine kinase receptorTyrosine kinase receptorsPhosphatase 1HC11 cellsCDNA microarrayTumorigenic phenotypeChaperonin 10Gene expressionFms oncogeneMicroarray analysisInvasive phenotypeMetastatic competenceKinase receptorsVivo tumorigenesis
1998
The IRS-Signaling System: A Network of Docking Proteins That Mediate Insulin and Cytokine Action
White M, Yenush L. The IRS-Signaling System: A Network of Docking Proteins That Mediate Insulin and Cytokine Action. Current Topics In Microbiology And Immunology 1998, 228: 179-208. PMID: 9401207, DOI: 10.1007/978-3-642-80481-6_8.Peer-Reviewed Original ResearchConceptsTyrosine phosphorylationSrc homology 2 domainTyrosine autophosphorylation sitesProtein-lipid interactionsAssembly of multicomponentSH2 proteinAutophosphorylation sitesPH domainSpecific membrane receptorsCytosolic substratesReceptor kinaseTyrosine autophosphorylationTransmembrane signalsCellular substratesCytokine receptorsActivity of receptorsMembrane receptorsEarly stepsPhosphorylationProteinKinaseGrowth factorCytokine actionReceptorsCascade
1996
The IRS-signalling system in insulin and cytokine action
White M, Marshall C. The IRS-signalling system in insulin and cytokine action. Philosophical Transactions Of The Royal Society B Biological Sciences 1996, 351: 181-189. PMID: 8650265, DOI: 10.1098/rstb.1996.0015.Peer-Reviewed Original ResearchConceptsIRS proteinsSrc homology 2 domainSH2 proteinAutophosphorylation sitesEndocytic pathwayTyrosine residuesIRS-2Cytokine receptorsRecent identificationStoichiometric constraintsMost receptorsIFN-alpha/betaAlpha/betaMultiple receptorsProteinNew insightsCytokine actionIL-13IL-4IGF-1IL-9ReceptorsIFN-gammaGrowth hormoneModular structure
1993
Calcium/calmodulin-dependent protein kinase I. cDNA cloning and identification of autophosphorylation site.
Picciotto MR, Czernik AJ, Nairn AC. Calcium/calmodulin-dependent protein kinase I. cDNA cloning and identification of autophosphorylation site. Journal Of Biological Chemistry 1993, 268: 26512-26521. PMID: 8253780, DOI: 10.1016/s0021-9258(19)74343-9.Peer-Reviewed Original ResearchMeSH KeywordsAdrenal GlandsAmino Acid SequenceAnimalsBase SequenceBinding SitesBrainCalcium-Calmodulin-Dependent Protein Kinase Type 1Calcium-Calmodulin-Dependent Protein KinasesCattleCloning, MolecularDNA, ComplementaryEscherichia coliLiverLungMolecular Sequence DataPhosphorylationRatsRNA, MessengerSequence Homology, Amino AcidConceptsCaM kinase IKinase IProtein kinaseCatalytic domainThreonyl residuesFusion proteinGlutathione S-transferase fusion proteinS-transferase fusion proteinCAMP-dependent protein kinaseDependent protein kinase IComplete amino acid sequenceBovine brain cDNA libraryInvariant amino acidsAmino acidsSynapsin IAmino acid sequenceBrain cDNA libraryClass of enzymesSynaptic vesicle proteinsProtein kinase ICaM kinase IIAutophosphorylation sitesRNase protection assaysSingle geneCDNA library
1988
Ca2+/calmodulin-dependent protein kinase II: identification of threonine-286 as the autophosphorylation site in the alpha subunit associated with the generation of Ca2+-independent activity.
Thiel G, Czernik AJ, Gorelick F, Nairn AC, Greengard P. Ca2+/calmodulin-dependent protein kinase II: identification of threonine-286 as the autophosphorylation site in the alpha subunit associated with the generation of Ca2+-independent activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 1988, 85: 6337-6341. PMID: 2842767, PMCID: PMC281965, DOI: 10.1073/pnas.85.17.6337.Peer-Reviewed Original ResearchConceptsBeta/beta' subunitsAlpha subunitThr-286Beta subunitDependent protein kinase IIProtein kinase IIAutophosphorylation sitesThreonine residuesMajor phosphopeptideNaDodSO4/PAGEPhosphorylated residuesCyanogen bromide peptidesConsensus sequenceKinase IIIndependent activityThermolytic phosphopeptidesPrimary structureGas-phase Edman degradationGeneration of Ca2Edman degradationAutophosphorylationSubunitsThreonine-286Amino acidsAsp-Xaa
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