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 ResearchConceptsCellular 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
Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids
Jiang H, Weng J, Wang Y, Tsou J, Chen P, Ko A, Söll D, Tsai M, Wang Y. Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Frontiers In Genetics 2023, 14: 1277489. PMID: 37904728, PMCID: PMC10613524, DOI: 10.3389/fgene.2023.1277489.Peer-Reviewed Original ResearchUnique biophysical propertiesTree of lifeAmino acidsSuperfolder green fluorescent proteinGreen fluorescent proteinSubstrate polyspecificityTranslational machinerySynthetic biologistsSmall proteinsFluorescent proteinPhysiological roleRibosomal synthesisProteinBiophysical propertiesKinetic assaysHuman heavy chain ferritinHeavy-chain ferritinPylRSTRNAMutantsAminoacylationPeptidesBiologistsPhysiochemical propertiesMachineryChemical interactions modulate λ6‐85 stability in cells
Knab E, Davis C. Chemical interactions modulate λ6‐85 stability in cells. Protein Science 2023, 32: e4698. PMID: 37313657, PMCID: PMC10288553, DOI: 10.1002/pro.4698.Peer-Reviewed Original Research
2020
Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter
Yeom J, Shao Y, Groisman EA. Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 20235-20243. PMID: 32753384, PMCID: PMC7443967, DOI: 10.1073/pnas.2006116117.Peer-Reviewed Original ResearchConceptsSmall proteinsAmino acid identityFacultative intracellular pathogenTransporter MgtAProtease FtsHMagnesium transportersAcid identityMacrophage proteinRelated transportersSame transcriptPathogen survivalMgtBIntracellular pathogensSerovar TyphimuriumProteinLimitation conditionsHost tissuesMgtROxidative stressTransportersSalmonella survivalSingular exampleFtsHMacrophagesMgtA
2019
Proteomic Detection and Validation of Translated Small Open Reading Frames
Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Current Protocols In Chemical Biology 2019, 11: e77. PMID: 31750990, PMCID: PMC6878975, DOI: 10.1002/cpch.77.Peer-Reviewed Original ResearchConceptsSiRNA-based silencingSmall open reading framesNon-AUG start codonsOpen reading frameStandard proteomic methodsSpecific transcript isoformsCultured human cellsUnique tryptic peptidesGenomic lociShorter proteinTranscript isoformsProtein databaseProteomic methodsNovel regulatorReading frameProteomic detectionStart codonFunctional characterizationMass spectrometry-based detectionComplete annotationSmall proteinsHuman cellsTryptic peptidesProtein extractionSmORFs
2017
Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein
Yuan P, D’Lima N, Slavoff SA. Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein. Biochemistry 2017, 57: 56-60. PMID: 29039649, PMCID: PMC5761644, DOI: 10.1021/acs.biochem.7b00864.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, High Pressure LiquidEscherichia coliEscherichia coli K12Escherichia coli ProteinsGene Expression Regulation, BacterialGreen Fluorescent ProteinsHeat-Shock ProteinsHeat-Shock Proteins, SmallHeat-Shock ResponseMembrane ProteinsModels, MolecularMolecular Sequence AnnotationOpen Reading FramesPhosphogluconate DehydrogenaseProtein Conformation, alpha-HelicalProtein Interaction Domains and MotifsProtein TransportProteogenomicsProteomicsRecombinant Fusion ProteinsTandem Mass SpectrometryConceptsHeat shock proteinsShock proteinsMembrane proteomicsE. coli heat shock proteinsComparative membrane proteomicsSmall open reading framesMembrane protein enrichmentQuantitative membrane proteomicsQuantitative proteomics protocolBacterial stress responseQuantitative mass spectrometryOpen reading frameDiscovery of thousandsEscherichia coli K12Transmembrane helicesProteomics protocolMembrane proteinsEvolutionary spaceReading frameSmall proteinsStress responseProteomicsColi K12Amino acidsProtein enrichment
2015
Flagella-independent surface motility in Salmonella enterica serovar Typhimurium
Park SY, Pontes MH, Groisman EA. Flagella-independent surface motility in Salmonella enterica serovar Typhimurium. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 1850-1855. PMID: 25624475, PMCID: PMC4330729, DOI: 10.1073/pnas.1422938112.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAmino Acid SequenceBacterial ProteinsBase SequenceCation Transport ProteinsComputational BiologyFlagellaGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsMitochondrial Proton-Translocating ATPasesMolecular Sequence DataMovementMutagenesisSalmonella typhimuriumSequence AlignmentSequence Analysis, DNAConceptsSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumPhoP/PhoQ regulatory systemMgtC mutantFlagellum-independent mannerFlagella-mediated motilitySerovar TyphimuriumForm of motilityWild-type SalmonellaNull mutantsMultiprotein complexesMgtC proteinF1Fo-ATPaseHeterologous promoterSmall proteinsUnknown functionProteinase K treatmentSurface motilityMgtAMutantsGroup motilityAllelic formsRegulatory systemBacterial replicationGenes
2014
Small transmembrane protein inhibitors of the platelet‐derived growth factor β receptor (LB215)
Petti L, Talbert‐Slagle K, Chacon K, Hochstrasser M, DiMaio D. Small transmembrane protein inhibitors of the platelet‐derived growth factor β receptor (LB215). The FASEB Journal 2014, 28 DOI: 10.1096/fasebj.28.1_supplement.lb215.Peer-Reviewed Original ResearchTransmembrane domainTransmembrane proteinPlatelet-derived growth factor β receptorProtein inhibitorGrowth factor receptor signalingSingle conservative amino acid substitutionSmall transmembrane proteinConservative amino acid substitutionsGrowth factor β receptorParticular tyrosine residueReceptor tyrosine kinasesAmino acid substitutionsSequence similarityGrowth factor receptorTraptamersReceptor dimerizationEffects of PDGFSmall proteinsTyrosine residuesExtracellular domainTyrosine kinaseAcid substitutionsReceptor signalingRetroviral libraryPDGFβR
2013
Glutaredoxin 1 is a major player in copper metabolism in neuroblastoma cells
De Benedetto ML, Capo CR, Ferri A, Valle C, Polimanti R, Carrì MT, Rossi L. Glutaredoxin 1 is a major player in copper metabolism in neuroblastoma cells. Biochimica Et Biophysica Acta 2013, 1840: 255-261. PMID: 24041990, DOI: 10.1016/j.bbagen.2013.09.008.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisBlotting, WesternCation Transport ProteinsCell ProliferationChromatography, AffinityCopperCopper Transporter 1GlutaredoxinsGlutathioneHumansMitochondriaNeuroblastomaOxidation-ReductionReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSuperoxide DismutaseSuperoxide Dismutase-1Tumor Cells, CulturedConceptsIntracellular copper levelsCopper transporter 1Copper-induced toxicityHomeostasis of copperCopper metabolismCopper-binding propertiesGRX1 overexpressionProtein chaperonesHuman neuroblastoma SH-SY5Y cellsCopper overloadCopper chaperoneMajor playersNeuroblastoma SH-SY5Y cellsThioredoxin familyProtein disulfidesGrx1Glutaredoxin-1SH-SY5Y cellsSmall proteinsCuSO4 treatmentNeuronal cellsMixed disulfidesChaperonesControl cellsEnzyme activity
2011
A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans
Engelmann I, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ. A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans. PLOS ONE 2011, 6: e19055. PMID: 21602919, PMCID: PMC3094335, DOI: 10.1371/journal.pone.0019055.Peer-Reviewed Original ResearchConceptsC. elegansGenome-wide transcriptional changesFuture functional dissectionGene expression changesInnate immune signalingFunctional dissectionTranscriptional responseAnnotation analysisTranscriptional changesD. coniosporaRNA sequencingFungal pathogensCertain genesExpression changesImmune signalingSmall proteinsStress responseElegansGenesDistinct pathogensBacterial pathogensPathogensPhysiological imbalanceFungal infectionsHost response
2010
Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering
Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, DiMaio D. Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Engineering Design And Selection 2010, 24: 311-320. PMID: 21149273, PMCID: PMC3038463, DOI: 10.1093/protein/gzq112.Peer-Reviewed Original ResearchConceptsSignificant genetic bottleneckRetroviral expression libraryDeep DNA sequencingAmino acid segmentNovel biological activitiesGenetic bottleneckTransmembrane domainMammalian cellsLibrary sequencesRandom mutagenesisProtein engineeringExpression libraryDeep sequencingDifferent proteinsSmall proteinsGenetic selectionAcid segmentRetroviral libraryDNA sequencingSequencing resultsRandomized libraryProteinPowerful approachSequencingDiversity
2009
CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron Microscopy
Meng X, Wang G, Viero C, Wang Q, Mi W, Su XD, Wagenknecht T, Williams AJ, Liu Z, Yin CC. CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron Microscopy. Journal Of Molecular Biology 2009, 387: 320-334. PMID: 19356589, PMCID: PMC2667806, DOI: 10.1016/j.jmb.2009.01.059.Peer-Reviewed Original ResearchConceptsCryo-electron microscopyChannel activitySkeletal ryanodine receptorsAffinity of ryanodineSkeletal sarcoplasmic reticulum vesiclesSmall proteinsClamp regionConformational changesPhysiological functionsDomain 5Closed stateSingle-channel recordingsStructural familyRyR1 channelsRyanodine receptorSkeletal muscleRyR1VesiclesOpen probabilityRyR channelsChannel 2Channel recordingsEfflux rateSarcoplasmic reticulum vesiclesReticulum vesicles
2008
The bovine papillomavirus E5 protein and the PDGF β receptor: It takes two to tango
Talbert-Slagle K, DiMaio D. The bovine papillomavirus E5 protein and the PDGF β receptor: It takes two to tango. Virology 2008, 384: 345-351. PMID: 18990418, PMCID: PMC2661243, DOI: 10.1016/j.virol.2008.09.033.Peer-Reviewed Original ResearchConceptsBovine papillomavirus E5 proteinE5 proteinTransmembrane domainTransmembrane proteinTarget proteinsPlatelet-derived growth factor beta receptorArtificial transmembrane proteinsMembrane-spanning segmentsHuman erythropoietin receptorBPV E5 proteinGrowth factor beta receptorCellular receptor tyrosine kinasesLigand-independent activationReceptor tyrosine kinasesGenetic screenPDGF β-receptorNovel proteinTransmembrane sequenceCellular proteinsMitogenic signalingHydrophobic proteinsReceptor dimerizationLarger target proteinsErythropoietin receptorSmall proteins
2007
A connector of two-component regulatory systems promotes signal amplification and persistence of expression
Kato A, Mitrophanov AY, Groisman EA. A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 12063-12068. PMID: 17615238, PMCID: PMC1924540, DOI: 10.1073/pnas.0704462104.Peer-Reviewed Original ResearchConceptsTwo-component regulatory systemBacterial signal transductionRegulatory systemPersistence of expressionSignal transductionGene transcriptionRegulatory architectureSmall proteinsSalmonella entericaPathwayFunctional characteristicsPmrDExpressionFunctional propertiesPhoP.AmplificationTranscriptionSignal amplificationTransductionGenesDominant formOrganismsProteinPersistenceEnterica
2000
A small protein that mediates the activation of a two‐component system by another two‐component system
Kox L, Wösten M, Groisman E. A small protein that mediates the activation of a two‐component system by another two‐component system. The EMBO Journal 2000, 19: 1861-1872. PMID: 10775270, PMCID: PMC302009, DOI: 10.1093/emboj/19.8.1861.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBacterial ProteinsBase SequenceDrug Resistance, MicrobialIronMagnesiumModels, BiologicalMolecular Sequence DataMutagenesisMutationPhosphorylationPlasmidsPolymyxinsProtein BindingRecombinant ProteinsRNA Processing, Post-TranscriptionalSalmonella entericaSignal TransductionSingle-Strand Specific DNA and RNA EndonucleasesTranscription FactorsTranscription, GeneticConceptsTwo-component systemTranscription of PmrAPost-transcriptional levelExpression of pmrAPeptide antibiotic polymyxin BPmrD proteinPhoP-PhoQTranscriptional activationGenetic basisHeterologous promoterPmrA-PmrBSmall proteinsGenesPhoP-PhoQ.PmrB proteinAntimicrobial proteinsPhoQ genesProteinPmrAPhoPTranscriptionSalmonella entericaAntibiotic polymyxin BPmrDHigh ironElectron Capture Dissociation Produces Many More Protein Backbone Cleavages Than Collisional and IR Excitation
Zubarev R, Fridriksson E, Horn D, Kelleher N, Kruger N, Lewis M, Carpenter B, Mclafferty F. Electron Capture Dissociation Produces Many More Protein Backbone Cleavages Than Collisional and IR Excitation. 2000, 111-120. DOI: 10.1007/978-1-59259-719-2_7.Peer-Reviewed Original ResearchElectron capture dissociationCapture dissociationProtein backbone cleavageProtein cationsLabile HBackbone cleavageMolecular ionsReduction stepY ionsECD spectraIR excitationCleavage mechanismActivation methodRecombination energyLow-energy electronsInfrared irradiationElectron captureIonsSubsequent cleavageY cleavageConventional activation methodDissociationCleavageSmall proteinsCleavage products
1993
High-resolution gold labeling
Hainfeld J, Furuya F, Carbone K, Simon M, Lin B, Braig K, Horwich A, Safer D, Blechschmidt B, Sprinzl M, Ofengand J, Boublik M. High-resolution gold labeling. Microscopy And Microanalysis 1993, 51: 330-331. DOI: 10.1017/s0424820100147491.Peer-Reviewed Original ResearchGroEL complexDihydrofolate reductaseNascent polypeptide chainsChaperonin GroELMacromolecular complexesOligomeric complexesSmall proteinsActive proteinPolypeptide chainGroELChaperoninGold clustersCentral cavityGold labelingSpecific sitesGold compoundsModel substrateProteinMacromolecular sitesComplexesExternal surfaceRibosomesReductaseSitesChainMolecular cloning and immunological characterization of the gamma polypeptide, a small protein associated with the Na,K-ATPase.
Mercer R, Biemesderfer D, Bliss D, Collins J, Forbush B. Molecular cloning and immunological characterization of the gamma polypeptide, a small protein associated with the Na,K-ATPase. Journal Of Cell Biology 1993, 121: 579-586. PMID: 8387529, PMCID: PMC2119561, DOI: 10.1083/jcb.121.3.579.Peer-Reviewed Original ResearchConceptsNa,K-ATPaseGamma subunitK-ATPaseSmall membrane proteinsN-linked glycosylationTissue-specific fashionCardiac glycoside bindingGamma subunit mRNAGamma-specific antibodiesNorthern blot analysisHydropathy analysisSequenced proteinsNAB-ouabainMembrane proteinsGamma polypeptidesMolecular cloningGlycoside bindingSmall proteinsNephron segmentsBeta subunitSubunit mRNAAlpha subunitSubunitAmino acidsHydrophobic domains
1986
Proton NMR Studies of RNA’S and Related Enzymes Using Isotope Labels
Redfield A, Choi B, Griffey R, Jarema M, Rosevear P, Hoben P, Swanson R, Soll D. Proton NMR Studies of RNA’S and Related Enzymes Using Isotope Labels. NATO Science Series A: 1986, 99-112. DOI: 10.1007/978-1-4684-5173-3_9.Peer-Reviewed Original ResearchTransfer RNATRNA synthetasesProton NMRAminoacyl-tRNA synthetasesSmall RNA fragmentsDetails of recognitionProton NMR studiesNitrogen-15 labellingSmall proteinsTRNARNA fragmentsSmall enzymeNMR methodologyRelated enzymesNMR studiesRNANMRSmall moleculesLarge moleculesIsotope labelsSynthetasesImportant moleculesEnzymeNucleic acidsMolecules
1981
Nucleotide sequences of the mRNA's encoding the vesicular stomatitis virus N and NS proteins
Gallione C, Greene J, Iverson L, Rose J. Nucleotide sequences of the mRNA's encoding the vesicular stomatitis virus N and NS proteins. Journal Of Virology 1981, 39: 529-535. PMID: 6268841, PMCID: PMC171363, DOI: 10.1128/jvi.39.2.529-535.1981.Peer-Reviewed Original ResearchConceptsNS proteinsAUG codonReading frameNucleotide sequenceThird AUG codonAmino acidsComplete nucleotide sequenceVesicular stomatitis virus mRNAOpen reading frameSodium dodecyl sulfate-polyacrylamide gelsAnomalous electrophoretic mobilityDodecyl sulfate-polyacrylamide gelsSecond reading frameSulfate-polyacrylamide gelsCDNA clonesTranslational initiationSmall proteinsMRNA sequencesN proteinVirus NPolyadenylic acidVirus mRNACodonProteinMRNA
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