2023
RIG-I recognizes metabolite-capped RNAs as signaling ligands
Schweibenz B, Solotchi M, Hanpude P, Devarkar S, Patel S. RIG-I recognizes metabolite-capped RNAs as signaling ligands. Nucleic Acids Research 2023, 51: 8102-8114. PMID: 37326006, PMCID: PMC10450190, DOI: 10.1093/nar/gkad518.Peer-Reviewed Original ResearchConceptsRIG-IRNA endsRIG-I signaling pathwayIn vitro transcriptionRIG-I signalingDouble-stranded RNAInnate antiviral immune responseInterferon responseReceptor RIG-ICellular signaling assaysCapped RNACellular rolesPathogenic RNAsViral genomeEndogenous mRNAReplication intermediatesM7GSignaling ligandsImmune responseInnate immune receptor RIG-ISignaling pathwayRNASignaling assaysATPase activityAntiviral immune response
2022
Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Ha B, Yigit S, Natarajan N, Morse E, Calderwood D, Boggon T. Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4). Communications Biology 2022, 5: 1257. PMID: 36385162, PMCID: PMC9669019, DOI: 10.1038/s42003-022-04157-3.Peer-Reviewed Original ResearchConceptsP21-activated kinase 4Integrin adhesion receptorsMolecular basisAdhesion receptorsIntegrin β5Potential cellular rolesIntegrin β tailsKinase 4Membrane-proximal halfSubstrate-binding grooveSubstrate-binding siteSite-directed mutagenesisCellular rolesPhosphoacceptor sitesΒ tailExtracellular ligandsCytoplasmic signalingCytoplasmic tailKinase domainMultiple kinasesIntegrin complexΒ5 integrinsΒ5TailMutagenesisNascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor
Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nature Chemical Biology 2022, 18: 643-651. PMID: 35393574, PMCID: PMC9423127, DOI: 10.1038/s41589-022-01003-9.Peer-Reviewed Original ResearchConceptsRibosomal subunitDNA damage stressImportant cellular rolesGlobal protein synthesisN-terminal extensionCellular rolesCanonical proteinsHuman cellsProtein synthesisAlternative proteinsCell proliferationChemoproteomicsDamage stressSubunitsProteinAssemblyInhibitorsHypothesis generationMicroproteinsCytoplasmProliferationCellsExportDepletion
2021
MRTFA: A critical protein in normal and malignant hematopoiesis and beyond
Reed F, Larsuel ST, Mayday MY, Scanlon V, Krause DS. MRTFA: A critical protein in normal and malignant hematopoiesis and beyond. Journal Of Biological Chemistry 2021, 296: 100543. PMID: 33722605, PMCID: PMC8079280, DOI: 10.1016/j.jbc.2021.100543.Peer-Reviewed Original ResearchConceptsMalignant hematopoiesisActin cytoskeleton dynamicsCritical cellular functionsResponse factorSerum response factorTranscription factor ACellular rolesImmediate early genesProtein partnersTranscriptional regulationCytoskeleton dynamicsCellular functionsTranscriptional targetsTranscription factorsCytoskeletal proteinsCritical proteinsMRTFAEarly genesCell typesChromosomal translocationsHematopoietic cellsCell growthFactor AHematopoiesisMuscle cells
2020
The pseudoGTPase group of pseudoenzymes
Stiegler AL, Boggon TJ. The pseudoGTPase group of pseudoenzymes. The FEBS Journal 2020, 287: 4232-4245. PMID: 32893973, PMCID: PMC7544640, DOI: 10.1111/febs.15554.Peer-Reviewed Original ResearchConceptsSignal transductionAmino acid divergenceEnzymatic activityLeucine-rich repeat kinase 2Amino acid differencesP190RhoGAP proteinsRepeat kinase 2Membrane traffickingCellular rolesEnzyme foldImportant mechanistic componentSmall GTPasesTranscriptional controlCellular functionsGTPasesKinase 2PseudoenzymesAcid differencesEC numbersCell migrationFunctional roleMitochondrial activityProteinCargo transportMechanistic components
2013
Sphingolipid Homeostasis in the Endoplasmic Reticulum and Beyond
Breslow DK. Sphingolipid Homeostasis in the Endoplasmic Reticulum and Beyond. Cold Spring Harbor Perspectives In Biology 2013, 5: a013326. PMID: 23545423, PMCID: PMC3683901, DOI: 10.1101/cshperspect.a013326.BooksConceptsSphingolipid homeostasisEndoplasmic reticulumEssential cellular rolesSphingolipid metabolismCritical regulatory sitePotent signaling moleculesCellular rolesFamily proteinsSphingolipid productionSignaling moleculesRegulatory sitesPhysiologic cuesBasic biochemistryComplex glycosphingolipidsMembrane functionHomeostasisDiverse groupSphingolipidsNew insightsReticulumMetabolic demandsDetailed understandingMetabolismStructural componentsInitial synthesis
2012
Caveolae, Fenestrae and Transendothelial Channels Retain PV1 on the Surface of Endothelial Cells
Tkachenko E, Tse D, Sideleva O, Deharvengt SJ, Luciano MR, Xu Y, McGarry CL, Chidlow J, Pilch PF, Sessa WC, Toomre DK, Stan RV. Caveolae, Fenestrae and Transendothelial Channels Retain PV1 on the Surface of Endothelial Cells. PLOS ONE 2012, 7: e32655. PMID: 22403691, PMCID: PMC3293851, DOI: 10.1371/journal.pone.0032655.Peer-Reviewed Original ResearchConceptsFormation of diaphragmsRemoval of caveolaeDynamin-independent pathwayAbsence of caveolaeEndothelial cellsProtein levelsCellular rolesCavin-1Knockout phenotypesPlasma membraneCaveolin-1CaveolaeLung endothelial cellsCell surfaceRapid internalizationInternalization rateAbundance of structuresMice resultsTransendothelial channelsEssential componentOnly roleFenestral diaphragmsCellsClathrinTranscription
2010
Membranes in Balance: Mechanisms of Sphingolipid Homeostasis
Breslow DK, Weissman JS. Membranes in Balance: Mechanisms of Sphingolipid Homeostasis. Molecular Cell 2010, 40: 267-279. PMID: 20965421, PMCID: PMC2987644, DOI: 10.1016/j.molcel.2010.10.005.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSphingolipid homeostasisCell biologyEukaryotic cell biologyKey cellular rolesComplex membrane compositionCellular rolesSecretory pathwaySphingolipid biosynthesisEnzymatic machineryPhysiologic cuesSphingolipid metabolismMembrane compositionSphingolipidsBiologyNew insightsHomeostasisStructural componentsMembraneCellsBiosynthesisDefining featureMachineryGlycerolipidsEnzymeImproved understanding
2009
Nogo-B Receptor Stabilizes Niemann-Pick Type C2 Protein and Regulates Intracellular Cholesterol Trafficking
Harrison KD, Miao RQ, Fernandez-Hernándo C, Suárez Y, Dávalos A, Sessa WC. Nogo-B Receptor Stabilizes Niemann-Pick Type C2 Protein and Regulates Intracellular Cholesterol Trafficking. Cell Metabolism 2009, 10: 208-218. PMID: 19723497, PMCID: PMC2739452, DOI: 10.1016/j.cmet.2009.07.003.Peer-Reviewed Original ResearchConceptsNiemann-Pick type C2 (NPC2) proteinIntracellular cholesterol traffickingC2 proteinCholesterol traffickingEndoplasmic reticulumTwo-hybrid screenC-terminal domainCellular rolesIntracellular cholesterol accumulationSterol sensingProtein stabilityN-terminusNgBRProteinProtein levelsNPC2 mutationsCholesterol accumulationGenetic deficiencyTraffickingRNAiNPC2TerminusBiologyBaitReticulumLysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M. Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions. Science 2009, 325: 834-840. PMID: 19608861, DOI: 10.1126/science.1175371.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationAmino Acid MotifsBenzamidesCell Line, TumorCell NucleusCell Physiological PhenomenaCytoplasmEnzyme InhibitorsHistone Deacetylase InhibitorsHistone DeacetylasesHumansHydroxamic AcidsLysineMass SpectrometryMetabolic Networks and PathwaysMitochondriaMultiprotein ComplexesProtein Processing, Post-TranslationalProtein Structure, TertiaryProteinsProteomeProteomicsPyridinesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsVorinostatConceptsLysine acetylationCellular rolesPosttranslational modificationsCyclin-dependent kinase Cdc28Phosphorylation-dependent interactionReversible posttranslational modificationDiverse cellular processesMajor cellular functionsTarget protein complexesMajor posttranslational modificationLarge macromolecular complexesLysine acetylation sitesChromatin remodelingActin nucleationNuclear transportProtein complexesCellular functionsCellular processesAcetylation sitesMacromolecular complexesAcetylation changesGene expressionCell cycleDeacetylase inhibitorsAcetylation
2006
Global Analysis of Protein Phosphorylation in Yeast
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney R, Schmidt M, Rachidi N, Lee S, Mah A, Meng L, Stark M, Stern D, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki P, Snyder M. Global Analysis of Protein Phosphorylation in Yeast. The FASEB Journal 2006, 20: a1308-a1308. DOI: 10.1096/fasebj.20.5.a1308.Peer-Reviewed Original ResearchProtein phosphorylationProtein kinaseNovel regulatory moduleDifferent biochemical functionsNumber of kinasesMajor regulatory mechanismSame cellular compartmentSame functional categoryYeast kinasesCellular rolesCyclin subunitPhosphorylation eventsRegulatory modulesYeast proteinsVivo substratePhosphorylation resultsBiochemical functionsRelated kinasesTranscription factorsCellular compartmentsFunctional categoriesBiochemical understandingRegulatory mechanismsDifferent proteinsKinase
2004
Major Molecular Differences between Mammalian Sexes Are Involved in Drug Metabolism and Renal Function
Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. Major Molecular Differences between Mammalian Sexes Are Involved in Drug Metabolism and Renal Function. Developmental Cell 2004, 6: 791-800. PMID: 15177028, DOI: 10.1016/j.devcel.2004.05.005.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDNAFemaleGene Expression ProfilingGene Expression RegulationGenitaliaHumansHypothalamusKidneyLiverMaleMetabolic Clearance RateMiceOligonucleotide Array Sequence AnalysisOrgan SpecificityOvaryPharmaceutical PreparationsReceptors, Cell SurfaceSerpinsSex CharacteristicsTestisTranscortinConceptsMolecular differencesGene expressionExtensive differential gene expressionReproductive tissuesDifferential gene expressionGene expression differencesCellular rolesMammalian sexMouse geneMajor molecular differencesExpression differencesAdult tissuesOsmotic regulationExpression patternsFemale hypothalamusMolecular levelPhysiological differencesGenesDifferent hormonal environmentsRenal functionHormonal environmentExpressionSteroid metabolismMetabolismDrug metabolism
2002
Regulation of Gli1 Transcriptional Activity in the Nucleus by Dyrk1*
Mao J, Maye P, Kogerman P, Tejedor F, Toftgard R, Xie W, Wu G, Wu D. Regulation of Gli1 Transcriptional Activity in the Nucleus by Dyrk1*. Journal Of Biological Chemistry 2002, 277: 35156-35161. PMID: 12138125, DOI: 10.1074/jbc.m206743200.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsCell DifferentiationCell NucleusCOS CellsGene Expression RegulationHedgehog ProteinsMiceOncogene ProteinsPhosphorylationPrecipitin TestsProtein Serine-Threonine KinasesProtein TransportProtein-Tyrosine KinasesSignal TransductionTrans-ActivatorsTranscription FactorsTranscription, GeneticZinc Finger Protein GLI1ConceptsTranscriptional activityGene transcriptionDual-specificity protein kinaseNuclear export mutantGLI1 transcriptional activityMouse C3H10T1/2 cellsReporter gene assayCellular rolesExport mutantsTranscriptional regulationProtein kinaseKinase activityC3H10T1/2 cellsLEF-1Kinase 1DYRK1Sonic hedgehogC-JunGene assayCell nucleiShhTranscriptionRegulationGli1Pathway
2001
Regulation of Ins(1,4,5)P3 receptor isoforms by endogenous modulators
Thrower E, Hagar R, Ehrlich B. Regulation of Ins(1,4,5)P3 receptor isoforms by endogenous modulators. Trends In Pharmacological Sciences 2001, 22: 580-586. PMID: 11698102, DOI: 10.1016/s0165-6147(00)01809-5.Peer-Reviewed Original Research
1999
Antagonism between Goα and Gqα in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for Goα signaling and regulates Gqα activity
Hajdu-Cronin Y, Chen W, Patikoglou G, Koelle M, Sternberg P. Antagonism between Goα and Gqα in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for Goα signaling and regulates Gqα activity. Genes & Development 1999, 13: 1780-1793. PMID: 10421631, PMCID: PMC316886, DOI: 10.1101/gad.13.14.1780.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCaenorhabditis elegansCaenorhabditis elegans ProteinsCOS CellsDNA PrimersGene Expression RegulationGenes, SuppressorGTP-Binding Protein RegulatorsGTP-Binding ProteinsHelminth ProteinsMolecular Sequence DataMutationSequence Homology, Amino AcidSignal TransductionConceptsEGL-30Cellular rolesEAT-16Double mutant analysisMajor cellular roleHeterotrimeric G proteinsG protein signalingMolecular genetic approachesCOS-7 cellsGOA-1Function mutantsCaenorhabditis elegansC. elegansDouble mutantProtein signalingGenetic approachesG proteinsSAG-1ElegansMutantsGenesGoαHyperactive phenotypeProteinMutations
1995
Functional properties of intracellular calcium-release channels
Ehrlich B. Functional properties of intracellular calcium-release channels. Current Opinion In Neurobiology 1995, 5: 304-309. PMID: 7580152, DOI: 10.1016/0959-4388(95)80042-5.Peer-Reviewed Original ResearchConceptsIntracellular calcium release channelsCalcium release channelLarge ion channelsCellular rolesCytoplasmic proteinsMolecular mechanismsRegulatory sitesTrisphosphate receptorFunctional interactionIon channelsRegulatory processesMajor classesRyanodine receptorProteinRecent studiesFunctional propertiesReceptorsCytoplasmInositol
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