2023
Linear motif specificity in signaling through p38α and ERK2 mitogen–activated protein kinases
Robles J, Lou H, Shi G, Pan P, Turk B. Linear motif specificity in signaling through p38α and ERK2 mitogen–activated protein kinases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2316599120. PMID: 37988460, PMCID: PMC10691213, DOI: 10.1073/pnas.2316599120.Peer-Reviewed Original ResearchConceptsExtracellular signal-regulated kinase 2Docking motifERK2 mitogen-activated protein kinaseSignal-regulated kinase 2Protein kinase cascadeMitogen-activated protein kinaseFull-length proteinMAPK substratesEukaryotic cellsKinase cascadeMAPK networkLinear motifsProtein kinaseMotif specificityProteomic librariesDocking siteAcidic residuesKinase 2Diverse stimuliCellular responsesP38αDocking interfaceHigh net chargeMotifSelective interactionDnajb11-Kidney Disease Develops from Reduced Polycystin-1 Dosage but not Unfolded Protein Response in Mice
Roy S, Li Z, Guo Z, Long K, Rehrl S, Tian X, Dong K, Besse W. Dnajb11-Kidney Disease Develops from Reduced Polycystin-1 Dosage but not Unfolded Protein Response in Mice. Journal Of The American Society Of Nephrology 2023, 34: 1521-1534. PMID: 37332102, PMCID: PMC10482070, DOI: 10.1681/asn.0000000000000164.Peer-Reviewed Original ResearchConceptsUnfolded protein responseAutosomal dominant tubulointerstitial kidney diseaseAutosomal dominant polycystic kidney diseasePolycystin-1Autosomal-dominant polycystic kidney diseaseProtein responseTubulointerstitial kidney diseaseKidney diseaseRenal failureRenal failure in adulthoodPolycystic kidney diseaseUnfolded protein response activationFull-length proteinProteins polycystin-1C-terminal fragmentCystic kidneysSite of maturationCystic kidney dysplasiaKidney disease pathogenesisHeterozygous inactivating mutationsHsp40 cochaperonesEndoplasmic reticulumMouse model studiesConditional allelesDNAJB11
2019
The Functionally Important N‑Terminal Half of Fission Yeast Mid1p Anillin Is Intrinsically Disordered and Undergoes Phase Separation
Chatterjee M, Pollard TD. The Functionally Important N‑Terminal Half of Fission Yeast Mid1p Anillin Is Intrinsically Disordered and Undergoes Phase Separation. Biochemistry 2019, 58: 3031-3041. PMID: 31243991, PMCID: PMC7336169, DOI: 10.1021/acs.biochem.9b00217.Peer-Reviewed Original ResearchConceptsN-terminal halfFission yeast Schizosaccharomyces pombeYeast Schizosaccharomyces pombeC-terminal halfFull-length proteinSchizosaccharomyces pombeStructure prediction toolsPH domainScaffold proteinInsect cellsAnimal cellsContractile ringMyosin IIOrganizing centerAnillinMid1pProteinHydrodynamic measurementsPombeCytokinesisUndergoes phase separationCellsFungalPrediction tools
2017
The N‐terminus of SECIS Binding Protein 2 is Required for Processive Selenocystine Incorporation in Selenoprotein P
Pinkerton M, Vetick M, Shetty S, Copeland P. The N‐terminus of SECIS Binding Protein 2 is Required for Processive Selenocystine Incorporation in Selenoprotein P. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.600.9.Peer-Reviewed Original ResearchSelenocysteine insertion sequenceN-terminusSec codonAmino acid selenocysteineTranslation elongation factorProtein 2UGA stop codonFull-length proteinIncorporation of SecFrame UGA codonBinding protein 2Sec residueTrans factorsElongation factorMammalian systemsSec incorporationUGA codonC-terminusLength proteinSelenocysteine tRNAUntranslated regionSpecialized functionsStop codonC-terminalCodon
2016
When Good Ribosomes Go Bad
Baserga S, McCann K, Teramoto T, Zhang J, Tanaka Hall T. When Good Ribosomes Go Bad. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.387.1.Peer-Reviewed Original ResearchProtein-protein interactionsRNA recognition motifANE syndromeRibosome biogenesisRRNA processingProtein functionMolecular basisPre-rRNA processing defectThird RNA recognition motifDefective protein foldingHuman genetic diseasesFull-length proteinSingle amino acid substitutionNumerous human disordersAmino acid substitutionsYeast orthologMature ribosomesEukaryotic cellsGood ribosomeRibosome synthesisHub proteinsNucleolar proteinsNucleolar functionDomain foldingNucleolar dysfunctionDual Genetic Encoding of Acetyl‐lysine and Non‐deacetylatable Thioacetyl‐lysine Mediated by Flexizyme
Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Dual Genetic Encoding of Acetyl‐lysine and Non‐deacetylatable Thioacetyl‐lysine Mediated by Flexizyme. Angewandte Chemie International Edition 2016, 55: 4083-4086. PMID: 26914285, PMCID: PMC4789153, DOI: 10.1002/anie.201511750.Peer-Reviewed Original ResearchConceptsPost-translational modificationsHistone H3Post-translational protein modificationImportant post-translational protein modificationHuman histone H3Non-histone proteinsFull-length proteinTranscriptional regulationLysine acetylationDNA replicationProtein acetylationDNA repairProtein modificationGenetic encodingLysine residuesAcetyl lysineAcetylationHistonesLysine positionsH3ProteinFlexizymesCrosstalkPowerful toolResidues
2015
A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting
Herbert KM, Sarkar SK, Mills M, De la Herran H, Neuman KC, Steitz JA. A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting. RNA 2015, 22: 175-183. PMID: 26683315, PMCID: PMC4712668, DOI: 10.1261/rna.054684.115.Peer-Reviewed Original ResearchConceptsPri-miRNA substratesMicroprocessor complexHeterotrimeric complexDeletion constructsSingle-molecule subunit countingRNA-binding proteinFull-length proteinAbsence of RNAStem-loop structureSingle-molecule photobleachingSize exclusion chromatographyPresence of RNARNaseIII enzymesPhotobleaching assaysMicroRNA biogenesisSubunit countingMammalian cellsDroshaDGCR8Fluorescent proteinHuman cellsMultiple copiesRNAProteinExact stoichiometryA flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation
Pirman NL, Barber KW, Aerni HR, Ma NJ, Haimovich AD, Rogulina S, Isaacs FJ, Rinehart J. A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation. Nature Communications 2015, 6: 8130. PMID: 26350500, PMCID: PMC4566969, DOI: 10.1038/ncomms9130.Peer-Reviewed Original ResearchConceptsProtein phosphorylationProtein phosphorylation eventsFull-length proteinNon-phosphorylated formPhosphoserine-containing proteinsPhosphorylation eventsMEK1 kinaseUAG codonKinase activityRecombinant DNADNA templateEscherichia coliE. coliCodonPhosphorylationFunctional informationSerineProteinColiBiochemical investigationsPhosphoproteomeInefficient productionKinasePhosphoserineDNA
2014
Follicle-stimulating hormone receptor (FSHR) alternative skipping of exon 2 or 3 affects ovarian response to FSH
Karakaya C, Guzeloglu-Kayisli O, Hobbs RJ, Gerasimova T, Uyar A, Erdem M, Oktem M, Erdem A, Gumuslu S, Ercan D, Sakkas D, Comizzoli P, Seli E, Lalioti MD. Follicle-stimulating hormone receptor (FSHR) alternative skipping of exon 2 or 3 affects ovarian response to FSH. Molecular Human Reproduction 2014, 20: 630-643. PMID: 24670307, PMCID: PMC4072182, DOI: 10.1093/molehr/gau024.Peer-Reviewed Original ResearchConceptsAlternative splicingAlternative skippingExon 2Species-specific regulationDNA sequence variationPost-transcriptional modificationsFull-length proteinNorth American originMammalian ovarian functionAmino acid substitutionsDifferent genetic backgroundsHormone receptor geneGood comparative modelResult of evolutionSequence variationFollicle-stimulating hormoneSplicing variantsSplicingSpecies-specific formsAcid substitutionsHEK293 cellsFollicle-stimulating hormone receptor (FSHR) geneGenetic backgroundHuman FSHRAmerican origin
2007
COP1D, an alternatively spliced constitutive photomorphogenic-1 (COP1) product, stabilizes UV stress-induced c-Jun through inhibition of full-length COP1
Savio M, Rotondo G, Maglie S, Rossetti G, Bender J, Pardi R. COP1D, an alternatively spliced constitutive photomorphogenic-1 (COP1) product, stabilizes UV stress-induced c-Jun through inhibition of full-length COP1. Oncogene 2007, 27: 2401-2411. PMID: 17968316, DOI: 10.1038/sj.onc.1210892.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBreast NeoplasmsCell LineDown-RegulationEnzyme StabilityHealthHeLa CellsHumansIsoenzymesJNK Mitogen-Activated Protein KinasesKineticsMolecular Sequence DataProteasome Endopeptidase ComplexRNA, MessengerTranscription, GeneticTumor Suppressor Protein p53Ubiquitin-Protein LigasesConceptsFull-length proteinC-JunCullin-RING ligase complexRING finger ubiquitin ligaseProteasome-dependent degradationDominant-negative functionCoiled-coil regionFunction of COP1Post-translational changesP53 protein levelsLigase complexCRL complexesE3 ligasesE3 ligaseUbiquitin ligaseCOP1Ectopic expressionRNA interferenceUV stressElevated c-JunPolyubiquitinationSplice variantsMembrane Topography of the Hydrophobic Anchor Sequence of Poliovirus 3A and 3AB Proteins and the Functional Effect of 3A/3AB Membrane Association upon RNA Replication †
Fujita K, Krishnakumar SS, Franco D, Paul AV, London E, Wimmer E. Membrane Topography of the Hydrophobic Anchor Sequence of Poliovirus 3A and 3AB Proteins and the Functional Effect of 3A/3AB Membrane Association upon RNA Replication †. Biochemistry 2007, 46: 5185-5199. PMID: 17417822, PMCID: PMC2519882, DOI: 10.1021/bi6024758.Peer-Reviewed Original ResearchConceptsModel membrane vesiclesAnchor sequenceHydrophobic anchor sequenceMembrane vesiclesViral protein 3ABFull-length proteinN-terminal boundaryTransmembrane topographyMembrane associationSuppressor mutationsTransmembrane segmentsProtein 3ABRNA polymeraseMembranous vesiclesC-terminusMembrane topographyCytoplasmic surfaceHost cellsRNA replicationPoliovirus RNAHeLa cellsSingle tryptophanProteinUridylylation reactionLipid bilayers
2006
Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein †
Bunick CG, Miller MR, Fuller BE, Fanning E, Chazin WJ. Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein †. Biochemistry 2006, 45: 14965-14979. PMID: 17154534, PMCID: PMC2579963, DOI: 10.1021/bi061370o.Peer-Reviewed Original ResearchConceptsXPC functionXeroderma pigmentosum complementation group C proteinFirst functional roleComplementation group C proteinFunctional roleProtease protection assaysStructural domain analysesFull-length proteinXeroderma pigmentosum (XP) diseaseLimited proteolysis experimentsN-terminal portionMultidomain proteinsGlobal genomeMutational defectsProtein interactionsAberrant DNAC-terminal fragmentMolecular basisExcision repairProteolysis experimentsBiochemical characterizationC proteinSequence analysisStructural domainsProtection assaysHuman Sec31B: a family of new mammalian orthologues of yeast Sec31p that associate with the COPII coat
Stankewich MC, Stabach PR, Morrow JS. Human Sec31B: a family of new mammalian orthologues of yeast Sec31p that associate with the COPII coat. Journal Of Cell Science 2006, 119: 958-969. PMID: 16495487, DOI: 10.1242/jcs.02751.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAmino Acid SequenceAnimalsCarrier ProteinsCell LineCells, CulturedChlorocebus aethiopsCloning, MolecularCOP-Coated VesiclesCOS CellsExonsGene Expression RegulationHumansMolecular Sequence DataPhosphoproteinsRNA, MessengerSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentVesicular Transport ProteinsConceptsCOPII coatProline-rich C-terminal regionEndoplasmic reticulumTerminal proline-rich regionCOPII vesicle coatVesicular tubular clustersProline-rich regionWD repeat domainFull-length proteinAlternative mRNA splicingN-terminal domainC-terminal regionVesicle coatWD repeatsMammalian orthologuesVesicular trafficSecretory pathwayMRNA splicingExon utilizationExon 13Sec31pChromosome 10q24Gene productsSec31BSpecialized functions
1998
A Mutation in α-Catenin Disrupts Adhesion in Clone A Cells Without Perturbing its Actin and β-Catenin Binding Activity
Roe S, Koslov E, Rimm D. A Mutation in α-Catenin Disrupts Adhesion in Clone A Cells Without Perturbing its Actin and β-Catenin Binding Activity. Cell Communication & Adhesion 1998, 5: 283-296. PMID: 9762469, DOI: 10.3109/15419069809040298.Peer-Reviewed Original ResearchMeSH KeywordsActinsalpha Cateninbeta CateninCadherinsCell AdhesionCloning, MolecularColonic NeoplasmsCytoskeletal ProteinsCytoskeletonDesmoplakinsExonsgamma CateninHeLa CellsHumansIntercellular JunctionsMutationOctoxynolPrecipitin TestsProtein BindingRecombinant Fusion ProteinsReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSequence Analysis, DNASolubilityTrans-ActivatorsTransfectionTumor Cells, CulturedConceptsN-terminusE-cadherin-catenin complexBundles F-actinCo-sedimentation assaysCell-cell adhesionFull-length proteinClone A cellsCo-precipitation experimentsInternal deletion mutationsWhole cell lysatesAdhesive complexesMutant proteinsA mutantsMutant bindsHuman colon carcinoma cell lineColon carcinoma cell lineMutant formsLength proteinWild typeCytoplasmic connectionsF-actinAdhesive phenotypeDeletion mutationsCell lysatesCarcinoma cell lines
1997
Examination of the function of two kelch proteins generated by stop codon suppression
Robinson D, Cooley L. Examination of the function of two kelch proteins generated by stop codon suppression. Development 1997, 124: 1405-1417. PMID: 9118811, DOI: 10.1242/dev.124.7.1405.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAnimalsAnimals, Genetically ModifiedCarrier ProteinsCodon, TerminatorDrosophilaDrosophila ProteinsFemaleGene Expression Regulation, DevelopmentalImmunohistochemistryInfertility, FemaleInsect ProteinsMaleMicrofilament ProteinsMutationOogenesisOpen Reading FramesOvaryRNA, MessengerSuppression, GeneticTissue DistributionConceptsRing canalsKelch proteinStop codon suppressionStop codonCodon suppressionDrosophila kelch geneOvarian ring canalsUGA stop codonFull-length proteinOpen reading frameTissue-specific mannerUAA stop codonFemale sterilitySense codonsReading frameSingle transcriptKelch geneORF1 proteinCodonKelchDifferent tissuesProteinMutantsORF1Transcripts
1995
Alpha 1(E)-catenin is an actin-binding and -bundling protein mediating the attachment of F-actin to the membrane adhesion complex.
Rimm DL, Koslov ER, Kebriaei P, Cianci CD, Morrow JS. Alpha 1(E)-catenin is an actin-binding and -bundling protein mediating the attachment of F-actin to the membrane adhesion complex. Proceedings Of The National Academy Of Sciences Of The United States Of America 1995, 92: 8813-8817. PMID: 7568023, PMCID: PMC41057, DOI: 10.1073/pnas.92.19.8813.Peer-Reviewed Original ResearchConceptsF-actinBundling proteinE-cadherin-mediated cell-cell contactsHomotypic cell-cell adhesionBundles F-actinEpithelial cell polarityCortical actin cytoskeletonCell-cell adhesionActin-binding proteinsFull-length proteinE-cadherinCell-cell contactMembrane adhesion complexesBundles actinCell polarityHierarchy of interactionsActin cytoskeletonAdhesion complexesCytoplasmic domainCosedimentation assaysSedimentation assaysAdditional proteinsMolecular basisActin filamentsActin complexStructural Model of the Phospholamban Ion Channel Complex in Phospholipid Membranes
Arkin I, Rothman M, Ludlam C, Aimoto S, Engelman D, Rothschild K, Smith S. Structural Model of the Phospholamban Ion Channel Complex in Phospholipid Membranes. Journal Of Molecular Biology 1995, 248: 824-834. PMID: 7752243, DOI: 10.1006/jmbi.1995.0263.Peer-Reviewed Original ResearchConceptsSelective ion conductanceTransmembrane domainAmino acid residuesN-terminal 30 amino acid residuesAcid residuesCircular dichroismPentameric protein complexFull-length proteinC-terminal 22 amino acid residuesPhospholipid membranesIon channel complexTransmembrane helicesProtein complexesPhosphorylation sitesMembrane proteinsIon conductanceCarboxy terminusHelix bundleIon poreReticulum membraneInhibitory complexLong helixPentameric complexSecondary structureProtein
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