2022
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling
Mathew B, Bathla S, Williams KR, Nairn AC. Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling. Molecular & Cellular Proteomics 2022, 21: 100422. PMID: 36198386, PMCID: PMC9650050, DOI: 10.1016/j.mcpro.2022.100422.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProximity labelingBiological functionsComplex protein-protein interactionsProximity labeling methodProtein-DNA interactionsCell-cell communicationMost biological functionsDistinct cell typesProtein-RNANerve cell functionCell typesBiomolecular complexesCellular levelPhysical interactionProteomeCell functionSpecific subsetProteinSynaptic plasticityComplete catalogLabeling methodRecent advancesPowerful toolAxonal projections
2021
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells
Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBreast NeoplasmsCell ProliferationCytoskeletal ProteinsDrug Resistance, NeoplasmEndocytosisFemaleHumansMembrane MicrodomainsMyelin and Lymphocyte-Associated Proteolipid ProteinsPhosphoproteinsPlasma Membrane Calcium-Transporting ATPasesReceptor, ErbB-2Sodium-Hydrogen ExchangersTrastuzumabTumor Cells, CulturedConceptsLipid raft formationBreast cancer cellsLipid raftsLipid raft resident proteinsCancer cellsRaft formationRaft-resident proteinsProximity ligation assayProtein complexesMembrane protrusionsProtein interactionsPlasma membraneLigation assayMAL2Membrane stabilityStructural organizationPotential therapeutic targetPhysical interactionMembrane retentionProteinRaftsTherapeutic targetCellsIntracellular calcium concentrationLow intracellular calcium concentration
2018
GAPVD1 and ANKFY1 Mutations Implicate RAB5 Regulation in Nephrotic Syndrome
Hermle T, Schneider R, Schapiro D, Braun DA, van der Ven AT, Warejko JK, Daga A, Widmeier E, Nakayama M, Jobst-Schwan T, Majmundar AJ, Ashraf S, Rao J, Finn LS, Tasic V, Hernandez JD, Bagga A, Jalalah SM, El Desoky S, Kari JA, Laricchia KM, Lek M, Rehm HL, MacArthur DG, Mane S, Lifton RP, Shril S, Hildebrandt F. GAPVD1 and ANKFY1 Mutations Implicate RAB5 Regulation in Nephrotic Syndrome. Journal Of The American Society Of Nephrology 2018, 29: 2123-2138. PMID: 29959197, PMCID: PMC6065084, DOI: 10.1681/asn.2017121312.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell MovementCells, CulturedCohort StudiesDisease ProgressionDrosophila melanogasterExome SequencingFemaleGene Expression RegulationGenetic Predisposition to DiseaseHumansMaleMass ScreeningMembrane ProteinsMutation, MissenseNephrotic SyndromePedigreePhosphate-Binding ProteinsPodocytesrab5 GTP-Binding ProteinsReal-Time Polymerase Chain ReactionRenal Insufficiency, ChronicRNA, Small InterferingConceptsSteroid-resistant nephrotic syndromeNovel monogenic causesCoimmunoprecipitation assaysHomozygous missense mutationPatient-derived mutationsMissense mutationsMonogenic causesHEK293T cellsActive Rab5GAPVD1Nephrotic syndromePodocyte migration rateEctopic expressionCases of SRNSPartial colocalizationSpecific pathogenetic pathwaysWhole-exome sequencingEarly-onset NSHuman NFunctional significancePodocyte migrationProteinMutationsPhysical interactionRab5
2016
IL-13Rα2 uses TMEM219 in chitinase 3-like-1-induced signalling and effector responses
Lee CM, He CH, Nour AM, Zhou Y, Ma B, Park JW, Kim KH, Cruz CD, Sharma L, Nasr ML, Modis Y, Lee CG, Elias JA. IL-13Rα2 uses TMEM219 in chitinase 3-like-1-induced signalling and effector responses. Nature Communications 2016, 7: 12752. PMID: 27629921, PMCID: PMC5027616, DOI: 10.1038/ncomms12752.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisCell Line, TumorChitinase-3-Like Protein 1Heparin-binding EGF-like Growth FactorHumansInterleukin-13 Receptor alpha2 SubunitLung InjuryLung NeoplasmsMAP Kinase Signaling SystemMelanoma, ExperimentalMembrane ProteinsMice, Inbred C57BLNeoplasm MetastasisProto-Oncogene Proteins c-aktTransforming Growth Factor beta1Two-Hybrid System TechniquesWnt Signaling PathwayConceptsNull mutationPKB/Akt activationBimolecular fluorescence complementationDirect physical interactionMAPK/ERKHB-EGF productionFluorescence complementationTwo-hybridMembrane proteinsAkt activationDecoy functionPhysical interactionIL-13Rα2Effect of CHI3L1Chitinase 3Critical roleSignalingMutationsRecent studiesCHI3L1ComplementationTGF-β1YeastMelanoma metastasesERKComputational cell analysis for label-free detection of cell properties in a microfluidic laminar flow
Zhang A, Gu Y, Han Y, Mei Z, Chiu Y, Geng L, Cho S, Lo Y. Computational cell analysis for label-free detection of cell properties in a microfluidic laminar flow. Analyst 2016, 141: 4142-4150. PMID: 27163941, PMCID: PMC4914432, DOI: 10.1039/c6an00295a.Peer-Reviewed Original ResearchConceptsCell typesCell analysis techniquesPhysical properties of cellsDrug-treated cellsFlow cytometerLaminar flowCell stiffnessMachine learning techniquesMolecular markersProperties of cellsHuman cellsSpatial coding techniqueTreated cellsLabel-free methodCancer cellsConventional flow cytometersUntreated cellsMicrofluidic laminar flowLearning techniquesPhysical interactionCell membraneCell mixturesCell sizeCell analysisCellsWAC Regulates mTOR Activity by Acting as an Adaptor for the TTT and Pontin/Reptin Complexes
David-Morrison G, Xu Z, Rui Y, Charng W, Jaiswal M, Yamamoto S, Xiong B, Zhang K, Sandoval H, Duraine L, Zuo Z, Zhang S, Bellen H. WAC Regulates mTOR Activity by Acting as an Adaptor for the TTT and Pontin/Reptin Complexes. Developmental Cell 2016, 36: 139-151. PMID: 26812014, PMCID: PMC4730548, DOI: 10.1016/j.devcel.2015.12.019.Peer-Reviewed Original ResearchConceptsPontin/Reptin complexMTOR activityRapamycin complex 1Energy statusRegulation of metabolismEnergy-dependent activationDrosophila screenEnergy-dependent mannerTTT complexRAG interactionsMTORC1 activityMechanistic targetReptinPhysical interactionRegulatorDimerizationNeuronal dysfunctionComplexesPontinHomologActivationComplexes 1AdaptorAutophagyMTOR
2014
Monte Carlo Simulations of the GE Discovery Alcyone CZT SPECT System
Ljungberg M, Liu C, Fan P, Pretorius P. Monte Carlo Simulations of the GE Discovery Alcyone CZT SPECT System. 2014, 1-3. DOI: 10.1109/nssmic.2014.7430823.Peer-Reviewed Original ResearchTension-Sensitive Actin Assembly Supports Contractility at the Epithelial Zonula Adherens
Leerberg JM, Gomez GA, Verma S, Moussa EJ, Wu SK, Priya R, Hoffman BD, Grashoff C, Schwartz MA, Yap AS. Tension-Sensitive Actin Assembly Supports Contractility at the Epithelial Zonula Adherens. Current Biology 2014, 24: 1689-1699. PMID: 25065757, PMCID: PMC5103636, DOI: 10.1016/j.cub.2014.06.028.Peer-Reviewed Original ResearchConceptsMena/VASPActin assemblyEpithelial zonula adherensZonula adherensMyosin II activationActin filament turnoverCadherin junctionsActomyosin apparatusVASP proteinsActin scaffoldFilament turnoverActin filamentsJunctional integrityVinculinPhysical interactionTissue integrityActomyosin systemEpithelial cellsAdherensAssemblyContractile apparatusRegulationVASPEffective contractilityUnderlying mechanismBudding Yeast Kinetochore Proteins, Chl4 and Ctf19, Are Required to Maintain SPB-Centromere Proximity during G1 and Late Anaphase
Sau S, Sutradhar S, Paul R, Sinha P. Budding Yeast Kinetochore Proteins, Chl4 and Ctf19, Are Required to Maintain SPB-Centromere Proximity during G1 and Late Anaphase. PLOS ONE 2014, 9: e101294. PMID: 25003500, PMCID: PMC4086815, DOI: 10.1371/journal.pone.0101294.Peer-Reviewed Original ResearchConceptsSpindle pole bodyKinetochore proteinsKinetochore componentsLate anaphaseYeast kinetochore proteinsCentromere/kinetochoreMicrotubule-dependent forcesKinetochore microtubule dynamicsProtein-protein interactionsKinetochore-microtubule interactionsWild-type cellsPolar ejection forcesCtf19 complexFunctional kinetochoreProtein complexesPole bodyMutant cellsKinetochoresCentromeresComplex membersMicrotubule dynamicsCell cycleCtf19pRescue frequencyPhysical interaction
2011
Functional and physical interaction between the mismatch repair and FA-BRCA pathways
Williams SA, Wilson JB, Clark AP, Mitson-Salazar A, Tomashevski A, Ananth S, Glazer PM, Semmes OJ, Bale AE, Jones NJ, Kupfer GM. Functional and physical interaction between the mismatch repair and FA-BRCA pathways. Human Molecular Genetics 2011, 20: 4395-4410. PMID: 21865299, PMCID: PMC3196888, DOI: 10.1093/hmg/ddr366.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsCell LineDNA Mismatch RepairDrosophilaFanconi AnemiaFanconi Anemia Complementation Group ProteinsHCT116 CellsHeLa CellsHumansMiceMutL Protein Homolog 1MutS Homolog 2 ProteinNuclear ProteinsProtein BindingSignal TransductionUbiquitin-Protein LigasesConceptsFA cell linesFA-BRCA pathwayInterstrand crosslinksCell linesFanconi anemiaRepair of ICLsDNA interstrand crosslinksMsh2-deficient cellsFANCD2 monoubiquitylationMMR protein MSH2Chromatin localizationChromatin loadingICL repairDrosophila mutantsHuman cell linesEpistatic relationshipFA pathwayMouse cellsFANCD2Foci formationMismatch repairBone marrow failureRadial formationMonoubiquitylationPhysical interactionTranscription factor IRF8 directs a silencing programme for TH17 cell differentiation
Ouyang X, Zhang R, Yang J, Li Q, Qin L, Zhu C, Liu J, Ning H, Shin MS, Gupta M, Qi CF, He JC, Lira SA, Morse HC, Ozato K, Mayer L, Xiong H. Transcription factor IRF8 directs a silencing programme for TH17 cell differentiation. Nature Communications 2011, 2: 314. PMID: 21587231, PMCID: PMC3112536, DOI: 10.1038/ncomms1311.Peer-Reviewed Original ResearchConceptsTh17 cell differentiationRegulatory factor familyTranscription factor IRF8T cell-specific deletionCritical roleFunctional diversityLineage commitmentTranscription factorsCell-specific deletionFactor familyTranscriptional inhibitorIRF8 geneMolecular mechanismsCell differentiationConventional knockoutIRF8IRF8 deficiencyPhysical interactionDifferentiationTh17 cellsPathogenesis of autoimmunityCellsGenesUnique subsetDiversityHuman eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex
Alexandrov A, Colognori D, Steitz JA. Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex. Genes & Development 2011, 25: 1078-1090. PMID: 21576267, PMCID: PMC3093123, DOI: 10.1101/gad.2045411.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsDEAD-box RNA HelicasesEukaryotic Initiation Factor-4AEukaryotic Initiation Factor-4GEvolution, MolecularExonsGene DeletionGenetic Complementation TestHumansModels, MolecularMolecular Sequence DataMutationNuclear ProteinsPhenotypeProtein Structure, TertiaryRNA-Binding ProteinsRNA, Ribosomal, 18SSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentConceptsExon junction complexEIF4GJunction complexDEAD-box helicasePre-rRNA processingDirect physical interactionEIF4G complexExtragenic suppressorsBiogenesis defectsLethal phenotypeGrowth defectTranslation initiationHuman orthologEIF4AIIISaccharomyces cerevisiaeHuman cellsNOM1Physical interactionComplex actsG complexX-ray structureMutationsResiduesComplexesOrthologsBone morphogenetic protein 6-induced interleukin-1β expression in macrophages requires PU.1/Smad1 interaction
Lee G, Jung Y, Lee J, Kim W, Kim I. Bone morphogenetic protein 6-induced interleukin-1β expression in macrophages requires PU.1/Smad1 interaction. Molecular Immunology 2011, 48: 1540-1547. PMID: 21571370, DOI: 10.1016/j.molimm.2011.04.019.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBone Morphogenetic Protein 6Bone Morphogenetic Protein Receptors, Type IBone Morphogenetic Protein Receptors, Type IICells, CulturedExtracellular Signal-Regulated MAP KinasesFluorescent Antibody TechniqueImmunoblottingImmunoprecipitationInterleukin-1betaJNK Mitogen-Activated Protein KinasesMacrophagesMiceNitric Oxide Synthase Type IIProto-Oncogene ProteinsReverse Transcriptase Polymerase Chain ReactionSignal TransductionSmad1 ProteinTrans-ActivatorsConceptsBone morphogenetic protein 6Non-Smad pathwaysProtein 6Transcription factor PUSmads 1Physical interactionSmad1Expression
2010
Regulation of Actin Polymerization and Adhesion-Dependent Cell Edge Protrusion by the Abl-Related Gene (Arg) Tyrosine Kinase and N-WASp
Miller MM, Lapetina S, MacGrath SM, Sfakianos MK, Pollard TD, Koleske AJ. Regulation of Actin Polymerization and Adhesion-Dependent Cell Edge Protrusion by the Abl-Related Gene (Arg) Tyrosine Kinase and N-WASp. Biochemistry 2010, 49: 2227-2234. PMID: 20146487, PMCID: PMC2836179, DOI: 10.1021/bi901721u.Peer-Reviewed Original ResearchConceptsCell edge protrusionN-WASPActin polymerizationEdge protrusionN-WASP-dependent actin polymerizationGene Tyrosine KinaseFluorescent protein fusionsNovel binding partnerExtracellular cuesProtein fusionsSH2 domainExtracellular stimuliActin cytoskeletonSH3 domainBinding partnerCellular protrusionsPoint mutantsAffinity purificationTyrosine kinasePhysical interactionSH3PhosphorylationArgABLPotential link
2008
A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development
Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T. A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development. Journal Of Experimental Medicine 2008, 205: 2813-2825. PMID: 18955569, PMCID: PMC2585832, DOI: 10.1084/jem.20080938.Peer-Reviewed Original ResearchConceptsPoint mutantsUnexpected roleImportant gene functionsThymocyte developmentNovel genetic strategyPoint mutationsEarly thymocyte developmentMammalian geneticsChromatin templatesSWI-SNFBAF complexGene functionATPase subunitsDeletion mutantsFactor complexCD4 locusTarget genesGenetic strategiesCD4 activationMutantsNovel activityPhysical interactionDeletionBRGMutations
2007
Definition of a direct extracellular interaction between Met and E‐cadherin
Reshetnikova G, Troyanovsky S, Rimm DL. Definition of a direct extracellular interaction between Met and E‐cadherin. Cell Biology International 2007, 31: 366-373. PMID: 17336101, DOI: 10.1016/j.cellbi.2007.01.022.Peer-Reviewed Original ResearchConceptsBT-549 cellsE-cadherinCadherin-dependent cell-cell contactsHT-29 cellsE-cadherin interactsHepatocyte growth factorCell-cell adhesionCell-cell contactCross-linking studiesDirect extracellular interactionTyrosine kinase receptor expressionExtracellular interactionsMolecular mechanismsExtracellular domainIntracellular compartmentsPhysical interactionCellular presentationFirst evidenceGrowth factorCellsBT-549HT-29ExpressionReceptor expressionMetS
2006
The polarity-establishment component Bem1p interacts with the exocyst complex through the Sec15p subunit
France Y, Boyd C, Coleman J, Novick P. The polarity-establishment component Bem1p interacts with the exocyst complex through the Sec15p subunit. Journal Of Cell Science 2006, 119: 876-888. PMID: 16478783, DOI: 10.1242/jcs.02849.Peer-Reviewed Original ResearchConceptsBud growthSrc homology 3 domainTwo-hybrid studiesFirst Src homology 3 domainDirect physical interactionGreen fluorescent proteinExocyst complexGolgi traffickingSec15pSecretory pathwaySpatial regulationBem1pSecretory machineryMaster regulatorFluorescent proteinNew budsMachineryExocystSec4pPhysical interactionSubunitsCase of cellsProteinPathwayCrucial role
2005
The Adaptor Protein 3BP2 Binds Human CD244 and Links this Receptor to Vav Signaling, ERK Activation, and NK Cell Killing
Saborit-Villarroya I, Del Valle J, Romero X, Esplugues E, Lauzurica P, Engel P, Martín M. The Adaptor Protein 3BP2 Binds Human CD244 and Links this Receptor to Vav Signaling, ERK Activation, and NK Cell Killing. The Journal Of Immunology 2005, 175: 4226-4235. PMID: 16177062, DOI: 10.4049/jimmunol.175.7.4226.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAnimalsAntigens, CDCell Line, TumorCoculture TechniquesCytotoxicity, ImmunologicExtracellular Signal-Regulated MAP KinasesHumansInterferon-gammaKiller Cells, NaturalLigandsMembrane GlycoproteinsMicePhosphorylationReceptors, ImmunologicSignal TransductionSignaling Lymphocytic Activation Molecule FamilyYeastsConceptsERK activationSrc homology 2 domainThree-hybrid analysisDisease gene productCell surface proteinsLymphocytic activation molecule-associated proteinSAP recruitmentAdaptor proteinConsensus motifGene productsAdaptor 3BP2CD150 familySurface proteinsSAP associationPhysical interactionProteinCellular activationPhosphorylationCell killingMyeloid cellsMotifCellsActivationBindingPresent evidenceThe Notch Regulator Numb Links the Notch and TCR Signaling Pathways
Anderson AC, Kitchens EA, Chan SW, St. Hill C, Jan YN, Zhong W, Robey EA. The Notch Regulator Numb Links the Notch and TCR Signaling Pathways. The Journal Of Immunology 2005, 174: 890-897. PMID: 15634911, DOI: 10.4049/jimmunol.174.2.890.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigen-Presenting CellsCell DifferentiationCells, CulturedGene DeletionIntracellular Signaling Peptides and ProteinsMembrane ProteinsMiceMice, TransgenicNerve Tissue ProteinsReceptor, Notch1Receptors, Antigen, T-CellReceptors, Cell SurfaceSignal TransductionT-LymphocytesThymus GlandTranscription FactorsConceptsT cell developmentTCR signaling pathwaysCell developmentSignaling pathwaysAbsence of NumbT cell-APC interactionsInhibitor of NotchProtein NumbImportant adapterRelated proteinsNumbAPC contactMature T cellsTCR signalsCell membraneT cell activationPhysical interactionPathwayCell activationNotchImportant roleNumblikeProteinMutationsCoclusters
2001
Distinction between signaling mechanisms in lipid rafts vs. caveolae
Sowa G, Pypaert M, Sessa W. Distinction between signaling mechanisms in lipid rafts vs. caveolae. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 14072-14077. PMID: 11707586, PMCID: PMC61169, DOI: 10.1073/pnas.241409998.Peer-Reviewed Original ResearchConceptsCav-1Raft domainsLipid raftsCholesterol-rich lipid raft domainsLipid raft domainsCaveolae assemblyEndothelial nitric oxide synthaseCaveolae biogenesisAcylated proteinsSignal transductionSpatial regulationPlasma membraneNegative regulationCaveolin-1CaveolaeFirst clear exampleRaftsPhysical interactionProteinCellsRegulationENOS functionBiogenesisDomainClear example
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