2025
Weak, specific chemical interactions dictate barnase stability in diverse cellular environments
Tahir U, Davis C. Weak, specific chemical interactions dictate barnase stability in diverse cellular environments. Protein Science 2025, 34: e70128. PMID: 40248880, PMCID: PMC12006822, DOI: 10.1002/pro.70128.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCell NucleusCytoplasmEnzyme StabilityHumansProtein FoldingRibonucleasesConceptsCellular environmentMacromolecular crowdingFast Relaxation ImagingUnfolded stateDiverse cellular environmentsProteins in situProtein folding modelBacterial ribonucleaseU2-OS cellsProtein interactionsProtein stabilityNuclear lysatesHost organismBacterial cellsSmall proteinsIn vitroIntracellular compartmentsLarger proteinsBarnaseProteinNative environmentBiologically relevant environmentsCytoplasmSpecific interactionsIn-cell
2023
Transposable elements cause the loss of self‐incompatibility in citrus
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin R, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong V, Chai L. Transposable elements cause the loss of self‐incompatibility in citrus. Plant Biotechnology Journal 2023, 22: 1113-1131. PMID: 38038155, PMCID: PMC11022811, DOI: 10.1111/pbi.14250.Peer-Reviewed Original ResearchConceptsMiniature inverted-repeat transposable elementsMiniature inverted-repeat transposable element insertionSelf-incompatibilityTransposable elementsS-locusS-RNaseS-RNase-based SI systemPromoter regionLoss of self-incompatibilityPromote genetic diversityS-RNase allelesPrezygotic mechanismsGenetic diversityInbreeding depressionSelf-compatibleNucleotide mutationsFlowering plantsLoss of SiTransgenic experimentsBreeding strategiesCitrus genusAllelesSI phenotypePromoterCitrus
2011
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP. Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid. Biophysical Journal 2011, 101: 411-420. PMID: 21767494, PMCID: PMC3136797, DOI: 10.1016/j.bpj.2011.05.039.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsAmino acidsMeiboom-Gill (CPMG) relaxation dispersion experimentsWild-type ribonuclease AProtein energy landscapesNonnatural amino acidsRelaxation dispersion experimentsSingle residueProtein motionsMillisecond motionsConformational motionsEnzyme motionsHistidine-48Ribonuclease ACatalytic turnoverSimilar pH rangeRate limitingMolecular dynamics simulationsEnergy landscapeCorrelated motionAcidCatalytic cycleDispersion experimentsResiduesDynamics simulationsOnconase mediated NFKβ downregulation in malignant pleural mesothelioma
Goparaju CM, Blasberg JD, Volinia S, Palatini J, Ivanov S, Donington JS, Croce C, Carbone M, Yang H, Pass HI. Onconase mediated NFKβ downregulation in malignant pleural mesothelioma. Oncogene 2011, 30: 2767-2777. PMID: 21317924, PMCID: PMC3118086, DOI: 10.1038/onc.2010.643.Peer-Reviewed Original ResearchConceptsDownstream targetsMiRNA mimicsCell linesCell proliferationSoft agar colony formationMPM cell linesMiRNA expression patternsAgar colony formationProtein translationABC transportersExpression patternsGene expressionReverse transcription-PCRSpecific microRNAsBcl-xLCertain miRNAsMiRNA expressionOnconaseFunctional assaysClosure assayFunctional implicationsMatrigel invasionColony formationCell apoptosisNuclear factor kappa B
2006
An RNA Sensor for Intracellular Mg2+
Cromie MJ, Shi Y, Latifi T, Groisman EA. An RNA Sensor for Intracellular Mg2+. Cell 2006, 125: 71-84. PMID: 16615891, DOI: 10.1016/j.cell.2006.01.043.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAdenosine TriphosphatasesBacterial ProteinsBiosensing TechniquesConserved SequenceCytoplasmGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsModels, GeneticMutationNucleic Acid ConformationOpen Reading FramesPhylogenyPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidRibonucleasesRNA, BacterialRNA, MessengerTerminator Regions, GeneticTranscription, GeneticConceptsMost RNA moleculesDifferent cellular compartmentsStem-loop structureOnly protein componentSalmonella enterica serovar TyphimuriumDifferent stem-loop structuresTransporter MgtAMgtA geneEnterica serovar TyphimuriumMgtA transcriptionRNA polymeraseCellular compartmentsGene transcriptionRNA moleculesTranscription systemUntranslated regionProtein componentsTranscriptionRNA sensorsEnzymatic propertiesSerovar TyphimuriumMgtACytoplasmicDisparate stepsSingular example
2004
Premature termination codons do not affect the rate of splicing of neighboring introns
Lytle JR, Steitz JA. Premature termination codons do not affect the rate of splicing of neighboring introns. RNA 2004, 10: 657-668. PMID: 15037775, PMCID: PMC1370556, DOI: 10.1261/rna.5241404.Peer-Reviewed Original Research
2003
Architecture of the Flaviviral Replication Complex PROTEASE, NUCLEASE, AND DETERGENTS REVEAL ENCASEMENT WITHIN DOUBLE-LAYERED MEMBRANE COMPARTMENTS*
Uchil P, Satchidanandam V. Architecture of the Flaviviral Replication Complex PROTEASE, NUCLEASE, AND DETERGENTS REVEAL ENCASEMENT WITHIN DOUBLE-LAYERED MEMBRANE COMPARTMENTS*. Journal Of Biological Chemistry 2003, 278: 24388-24398. PMID: 12700232, DOI: 10.1074/jbc.m301717200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineDetergentsEndopeptidasesFlavivirusRibonucleasesRNA, ViralVirus ReplicationConceptsViral genomic RNAVesicle packetsMembrane compartmentsGenomic RNADouble-membrane compartmentsInner membrane vesiclesViral RNA speciesHost cell membraneHeavy membrane fractionNonionic detergent extractsRNA speciesReplicative intermediate RNAViral NS3Replication complexPrior trypsin treatmentMicrococcal nucleaseComplex proteaseMembranous sitesReplicative form RNASpecialized structuresActive proteinIntermediate RNAMembrane vesiclesMembrane fractionForm RNAVgRBP71 Stimulates Cleavage at a Polyadenylation Signal in Vg1 mRNA, Resulting in the Removal of a cis-Acting Element that Represses Translation
Kolev NG, Huber PW. VgRBP71 Stimulates Cleavage at a Polyadenylation Signal in Vg1 mRNA, Resulting in the Removal of a cis-Acting Element that Represses Translation. Molecular Cell 2003, 11: 745-755. PMID: 12667456, DOI: 10.1016/s1097-2765(03)00071-6.Peer-Reviewed Original Research3' Untranslated RegionsAnimalsBase SequenceBinding SitesBinding, CompetitiveBlotting, WesternGlutathione TransferaseGlycoproteinsMolecular Sequence DataNucleic Acid ConformationOocytesPlasmidsPolymerase Chain ReactionProtein BindingProtein BiosynthesisProtein Structure, SecondaryReverse Transcriptase Polymerase Chain ReactionRibonucleasesRNARNA HelicasesRNA-Binding ProteinsRNA, MessengerTranscription, GeneticTransforming Growth Factor betaXenopusXenopus Proteins
1998
Substitution of the Human β-Spectrin Promoter for the Human Aγ-Globin Promoter Prevents Silencing of a Linked Human β-Globin Gene in Transgenic Mice
Sabatino D, Cline A, Gallagher P, Garrett L, Stamatoyannopoulos G, Forget B, Bodine D. Substitution of the Human β-Spectrin Promoter for the Human Aγ-Globin Promoter Prevents Silencing of a Linked Human β-Globin Gene in Transgenic Mice. Molecular And Cellular Biology 1998, 18: 6634-6640. PMID: 9774678, PMCID: PMC109248, DOI: 10.1128/mcb.18.11.6634.Peer-Reviewed Original Research
1997
Expression of 11 beta-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2) in the human fetal adrenal.
Freije W, Pezzi V, Arici A, Carr B, Rainey W. Expression of 11 beta-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2) in the human fetal adrenal. Reproductive Sciences 1997, 4: 305-9. PMID: 9408886, DOI: 10.1016/s1071-5576(97)00066-x.Peer-Reviewed Original ResearchAU-rich elements target small nuclear RNAs as well as mRNAs for rapid degradation
Fan X, Myer V, Steitz J. AU-rich elements target small nuclear RNAs as well as mRNAs for rapid degradation. Genes & Development 1997, 11: 2557-2568. PMID: 9334320, PMCID: PMC316563, DOI: 10.1101/gad.11.19.2557.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, SurfaceBase SequenceELAV ProteinsELAV-Like Protein 1Gene Expression RegulationGenes, ReporterGlobinsHerpesvirus 2, SaimiriineMolecular Sequence DataMutationRepetitive Sequences, Nucleic AcidRibonucleasesRNA-Binding ProteinsRNA, MessengerRNA, Small NuclearRNA, ViralTranscription, GeneticTransfectionConceptsAU-rich elementsMRNA degradation machinerySmall nuclear RNAHSUR 1Host RNA moleculesDegradation machineryMammalian mRNAsNuclear RNARNA moleculesMutational analysisSequence requirementsTarget RNAHuR proteinOngoing translationRNA 1MRNARapid degradationRNASimilar mechanismDegradation activityDeadenylationSnRNAMachineryProteinDegradation
1995
Frequent alterations in E-cadherin and alpha- and beta-catenin expression in human breast cancer cell lines.
Pierceall W, Woodard A, Morrow J, Rimm D, Fearon E. Frequent alterations in E-cadherin and alpha- and beta-catenin expression in human breast cancer cell lines. Oncogene 1995, 11: 1319-26. PMID: 7478552.Peer-Reviewed Original ResearchMeSH Keywordsalpha CateninBase Sequencebeta CateninBlotting, SouthernBlotting, WesternBreast NeoplasmsCadherinsCytoskeletal ProteinsFemaleGene DeletionGene ExpressionHumansMolecular Sequence DataMutationOligodeoxyribonucleotidesPolymerase Chain ReactionPolymorphism, Single-Stranded ConformationalReceptor, ErbB-2RibonucleasesTrans-ActivatorsTumor Cells, CulturedConceptsAlpha-catenin proteinE-cadherin transcriptE-cadherinE-cadherin expressionBeta-catenin expressionCell linesBreast cancer cell linesEpithelial cell-cell interactionsCancer cell linesBeta-catenin proteinCancer-derived cell linesMembrane cytoskeletal proteinsCell-cell interactionsBreast cancer-derived cell linesE-cadherin geneHuman breast cancer-derived cell linesLoss of functionTransmembrane proteinAdherens junctionsCytoskeletal matrixCadherin proteinCytoskeletal proteinsTranscript levelsFrequent alterationsSequence alterationsRelative expression of the human epithelial Na+ channel subunits in normal and cystic fibrosis airways
Burch L, Talbot C, Knowles M, Canessa C, Rossier B, Boucher R. Relative expression of the human epithelial Na+ channel subunits in normal and cystic fibrosis airways. American Journal Of Physiology 1995, 269: c511-c518. PMID: 7653534, DOI: 10.1152/ajpcell.1995.269.2.c511.Peer-Reviewed Original ResearchConceptsAirway epitheliumSuperficial epitheliumCF airwaysGamma-ENaC mRNACF airway diseaseENaC subunit mRNAsCystic fibrosis airway epitheliaCF airway epitheliaAirway diseaseSitu hybridization studiesDuctal epitheliumCF transmembrane conductance regulator (CFTR) proteinRibonuclease protection assaysAcinar epitheliumMolecular pathogenesisCystic fibrosisChannel mRNAInhibitory regulationSubunit mRNAsEpitheliumChannel subunitsRatio of alphaAirwayRelative expressionPathogenesis
1993
Human granulosa-luteal cells secrete parathyroid hormone-related protein in vivo and in vitro.
Gutmann JN, Burtis WJ, Dreyer BE, Andrade-Gordon P, Penzias AS, Polan ML, Insogna KL. Human granulosa-luteal cells secrete parathyroid hormone-related protein in vivo and in vitro. The Journal Of Clinical Endocrinology & Metabolism 1993, 76: 1314-1318. PMID: 8496323, DOI: 10.1210/jcem.76.5.8496323.Peer-Reviewed Original ResearchConceptsGranulosa-luteal cellsOvarian follicular fluidImmunoradiometric assayHuman granulosa-luteal cellsHuman ovarian follicular fluidCultured granulosa-luteal cellsParathyroid hormone-related proteinSubsequent prospective analysisAdenylate cyclase-stimulating activityHormone-related proteinCyclase-stimulating activityPresence of mRNAPossible paracrineShort-term culturePTHrP levelsNormal mammalian tissuesBasal secretionImmunohistochemical studyFollicular fluidAutocrine rolePTHrP immunoreactivityProspective analysisPTHrPPTHImmunoreactivity
1992
The Significance of Platelets with Increased RNA Content (Reticulated Platelets) A Measure of the Rate of Thrombopoiesis
Ault K, Rinder H, Mitchell J, Carmody M, Vary C, Hillman R. The Significance of Platelets with Increased RNA Content (Reticulated Platelets) A Measure of the Rate of Thrombopoiesis. American Journal Of Clinical Pathology 1992, 98: 637-646. PMID: 1281383, DOI: 10.1093/ajcp/98.6.637.Peer-Reviewed Original ResearchConceptsPlatelet-associated immunoglobulinsRate of thrombopoiesisThrombocytopenic patientsAbsolute numberSignificance of plateletsSubset of patientsNucleic acid contentAnti-platelet antiserumStudies of micePeripheral destructionPlatelet countReticulocyte responseSubnormal levelsNormal rangePatientsAverage absolute numberFlow cytometric measurementsThrombopoietic responseNormal levelsPlatelet increaseElevated levelsFluorescent dye thiazole orangeImmunoglobulinPlateletsCytometric measurements
1991
Trans splicing in trypanosomes requires methylation of the 5' end of the spliced leader RNA.
Ullu E, Tschudi C. Trans splicing in trypanosomes requires methylation of the 5' end of the spliced leader RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1991, 88: 10074-10078. PMID: 1719544, PMCID: PMC52870, DOI: 10.1073/pnas.88.22.10074.Peer-Reviewed Original Research
1990
Transition-State Analogues in Protein Crystallography: Probes of the Structural Source of Enzyme Catalysis
Lolis E, Petsko G. Transition-State Analogues in Protein Crystallography: Probes of the Structural Source of Enzyme Catalysis. Annual Review Of Biochemistry 1990, 59: 597-630. PMID: 2197984, DOI: 10.1146/annurev.bi.59.070190.003121.Peer-Reviewed Original Research
1989
[31] Determination of RNA-protein and RNA-ribonucleoprotein interactions by nuclease probing
Parker K, Steitz J. [31] Determination of RNA-protein and RNA-ribonucleoprotein interactions by nuclease probing. Methods In Enzymology 1989, 180: 454-468. PMID: 2482428, DOI: 10.1016/0076-6879(89)80117-x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodiesCarrier ProteinsElectrophoresis, Polyacrylamide GelEndoribonucleasesHumansIndicators and ReagentsKineticsMiceMicrococcal NucleaseNucleotide MappingRibonuclease HRibonuclease T1RibonucleasesRibonucleoproteinsRNARNA PrecursorsRNA SplicingRNA-Binding ProteinsRNA, Ribosomal, 28STranscription, Genetic
1988
Evidence that developmentally regulated control of gene expression by a parvoviral allotropic determinant is particle mediated
Gardiner E, Tattersall P. Evidence that developmentally regulated control of gene expression by a parvoviral allotropic determinant is particle mediated. Journal Of Virology 1988, 62: 1713-1722. PMID: 3357208, PMCID: PMC253210, DOI: 10.1128/jvi.62.5.1713-1722.1988.Peer-Reviewed Original ResearchConceptsProgeny virusIncoming viral capsidInfectious molecular cloneViral transcriptionInfectious centersAllotropic determinantHost cell susceptibilityImmunosuppressive strainAutonomous parvovirus minute virusMolecular cloneCell susceptibilityViral RNASame low levelVirusParvovirus minute virusCell linesRescue of virusPhenotype characteristicViral DNAIntracellular factorsDifferent infectivitySimilar numberFibroblastsMinute virusMouse cell lines
1985
Effects of monovalent cations on Semliki Forest virus entry into BHK-21 cells.
Helenius A, Kielian M, Wellsteed J, Mellman I, Rudnick G. Effects of monovalent cations on Semliki Forest virus entry into BHK-21 cells. Journal Of Biological Chemistry 1985, 260: 5691-5697. PMID: 3988769, DOI: 10.1016/s0021-9258(18)89078-0.Peer-Reviewed Original ResearchConceptsSemliki Forest virusEndosome membraneViral envelopeBaby hamster kidney cellsMammalian cellsEndosomal membranesLow endosomalBHK-21 cellsHamster kidney cellsVirus endocytosisIntact cellsConformational changesEndosomesPrelysosomal endosomesViral spike glycoproteinVirus fusionKidney cellsAcidic endosomal pHViral RNAVoltage-sensitive probeEndocytosisVirus entryEndosomal pHCellsSpike glycoprotein
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