2015
Development of a Targeted Urine Proteome Assay for kidney diseases
Cantley LG, Colangelo CM, Stone KL, Chung L, Belcher J, Abbott T, Cantley JL, Williams KR, Parikh CR. Development of a Targeted Urine Proteome Assay for kidney diseases. Proteomics Clinical Applications 2015, 10: 58-74. PMID: 26220717, PMCID: PMC5003777, DOI: 10.1002/prca.201500020.Peer-Reviewed Original ResearchConceptsKidney diseaseUrinary proteinGraft functionImmediate graft functionDelayed graft functionKidney transplant patientsMultiple kidney diseasesTransplant patientsKidney transplantClinical relevancePotential biomarkersUrine proteomeDiseaseAvailable biofluidBiomarkersPatientsProtein biomarkersAssaysSingle assayProteome changesHuman urineQuantifiable proteinsTransplantProteinPeptides
2013
Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies
Bruce C, Stone K, Gulcicek E, Williams K. Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies. Current Protocols In Bioinformatics 2013, 41: 13.21.1-13.21.17. PMID: 23504934, PMCID: PMC3688054, DOI: 10.1002/0471250953.bi1321s41.Peer-Reviewed Original ResearchConceptsMore post-translational modificationsStudy of proteomesPost-translational modificationsFragment ionsChemical structureProtein profiling technologiesMass spectrometryProteolytic peptidesCharge ratioProteomic dataProtein sequencesSpectral dataPrecursor proteinProteomeProteomicsProteinQuantitationSpectrometryIons
2012
A molecular characterization of the choroid plexus and stress-induced gene regulation
Sathyanesan M, Girgenti MJ, Banasr M, Stone K, Bruce C, Guilchicek E, Wilczak-Havill K, Nairn A, Williams K, Sass S, Duman JG, Newton SS. A molecular characterization of the choroid plexus and stress-induced gene regulation. Translational Psychiatry 2012, 2: e139-e139. PMID: 22781172, PMCID: PMC3410626, DOI: 10.1038/tp.2012.64.Peer-Reviewed Original ResearchConceptsStress-induced gene regulationGene expression changesGene expression analysisCP gene expressionGlial fibrillary acidic proteinChoroid plexusMolecular functionsGene regulationSitu hybridization analysisTranscriptomic characterizationHigh-resolution tandem mass spectrometryTarget genesExpression analysisGene expressionExpression changesTarget proteinsCP proteinsMolecular characterizationAdult choroid plexusHybridization analysisCP functionGene profilesProteinBlood-cerebrospinal fluid barrierResolution tandem mass spectrometry
2008
The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis
SIERAKOWSKA H, WILLIAMS K, SZER I, SZER W. The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis. Clinical & Experimental Immunology 2008, 94: 435-439. PMID: 8252804, PMCID: PMC1534440, DOI: 10.1111/j.1365-2249.1993.tb08214.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsArthritis, JuvenileAutoantigensCells, CulturedChild, PreschoolChromatography, High Pressure LiquidChromatography, Ion ExchangeChromosomal Proteins, Non-HistoneElectrophoresis, Polyacrylamide GelHeLa CellsHumansLeukemia, MyeloidMolecular Sequence DataMolecular WeightOncogene ProteinsPeptide MappingPoly-ADP-Ribose Binding ProteinsRatsConceptsJuvenile rheumatoid arthritisAcute myeloid leukemiaRheumatoid arthritisMyeloid leukemiaRare subtypeLeukaemic cellsBone marrowImmunoblot assayRat tissuesDEK proteinArthritisFive-step chromatographic procedureAutoantigensLeukemiaOncogene DEKAntigenSerumPartial amino acid sequencingDEKAmino acid sequencingOncoprotein DEKPatientsSpleenProteinMarrow
2005
Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies
Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B. Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies. Current Protocols In Bioinformatics 2005, 10: 13.1.1-13.1.31. PMID: 18428746, PMCID: PMC3863626, DOI: 10.1002/0471250953.bi1301s10.Peer-Reviewed Original ResearchConceptsProtein/peptide chemistryHundreds of proteinsProtein profiling technologiesPeptide chemistryBioanalytical chemistryProteomic methodologiesChromatographic separationProteomic dataMass spectrometryCellular biologyBiological fluidsCell typesChemistryRelative levelsDiverse scientific disciplinesProteomicsSpectrometryBiologyBioinformaticsProteinSeparationExpression
1999
Identification of the RNA Binding Domain of T4 RegA Protein by Structure-based Mutagenesis*
Gordon J, Sengupta T, Phillips C, O'Malley S, Williams K, Spicer E. Identification of the RNA Binding Domain of T4 RegA Protein by Structure-based Mutagenesis*. Journal Of Biological Chemistry 1999, 274: 32265-32273. PMID: 10542265, DOI: 10.1074/jbc.274.45.32265.Peer-Reviewed Original ResearchConceptsRegA proteinBeta-sheet residuesGel mobility shift assaysRNA gel mobility shift assaysProtein-RNA interactionsMutagenesis of residuesRNA Binding DomainRNA binding siteMobility shift assaysRNA recognition propertiesBeta-sheet regionUnique structural motifMutant proteinsRNA bindingProtein foldsShift assaysBinding domainsMutagenesis studiesStructural domainsDomain IIMutagenesisEquilibrium binding assaysProteinRNABinding sites
1995
Digestion of Proteins in Gels for Sequence Analysis
Stone K, Williams K. Digestion of Proteins in Gels for Sequence Analysis. Current Protocols In Protein Science 1995, 00: 11.3.1-11.3.13. DOI: 10.1002/0471140864.ps1103s00.Peer-Reviewed Original ResearchProtein samplesSDS-PAGEDigestion of proteinsSDS-polyacrylamide gelsAbsence of detergentCDNA cloningAmino terminusPartial sequencesSequencing studiesSequence analysisInternal sequencingInhibits trypsinAmino acid analysisAmount of proteinProteinAlternate protocolGel slicesAcid analysisEnzymatic cleavageReversed-phase HPLCSubsequent washing stepsResidual SDSPmol amountsCloningTerminusIdentifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping
Williams K, Stone K. Identifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping. Methods In Molecular Biology 1995, 40: 157-175. PMID: 7633521, DOI: 10.1385/0-89603-301-5:157.Peer-Reviewed Original ResearchConceptsHPLC peptide mappingMass spectrometryPosttranslational modificationsIntact proteinPeptide mappingAtomic mass unitsAccurate massNet chargeDifferent posttranslational modificationsSulfoxide formationMass unitsCovalent changesOxidationSpectrometryProtein stabilityDeamidationProteinIsoelectric focusingPhosphorylationModificationMultiple RNA binding domains (RBDs) just don't add up
Shamoo Y, Abdul-Manan N, Williams K. Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Research 1995, 23: 725-728. PMID: 7535921, PMCID: PMC306750, DOI: 10.1093/nar/23.5.725.Peer-Reviewed Original ResearchMutagenesis of the COOH-terminal Region of Bacteriophage T4 regA Protein (∗)
O'Malley S, Sattar A, Williams K, Spicer E. Mutagenesis of the COOH-terminal Region of Bacteriophage T4 regA Protein (∗). Journal Of Biological Chemistry 1995, 270: 5107-5114. PMID: 7890619, DOI: 10.1074/jbc.270.10.5107.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial ProteinsBacteriophage T4Base SequenceBinding SitesChymotrypsinCircular DichroismCloning, MolecularDNA PrimersGenes, ViralKineticsMolecular Sequence DataMutagenesis, Site-DirectedPeptide FragmentsPoly UProtein ConformationRecombinant ProteinsSequence DeletionTranscription FactorsConceptsBacteriophage T4 regA proteinRegA proteinPhe-106Deletion mutantsWild-type regA proteinAmino acid substitutionsCOOH-terminal regionSpecific RNA ligandsT4 proteinsTranslational repressorRNA ligandsPartial proteolysisAcid substitutionsMutantsAmino acidsProteinRNAMajor siteNucleic acidsProteolysisOverall free energyChymotryptic cleavageSpecific targetsDomain structureAffinity
1994
Purification and nucleic acid binding properties of a fragment of type C1/C2 heterogeneous nuclear ribonucleoprotein from thymic nuclear extracts.
Amrute S, Abdul-Manan Z, Pandey V, Williams K, Modak M. Purification and nucleic acid binding properties of a fragment of type C1/C2 heterogeneous nuclear ribonucleoprotein from thymic nuclear extracts. Biochemistry 1994, 33: 8282-91. PMID: 7518245, DOI: 10.1021/bi00193a015.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCattleCell NucleusChromatographyChromatography, High Pressure LiquidCross-Linking ReagentsCyanogen BromideDNA, Single-StrandedHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear Ribonucleoprotein Group CHeterogeneous-Nuclear RibonucleoproteinsMolecular Sequence DataOligodeoxyribonucleotidesPeptide FragmentsRibonucleoproteinsRNASpectrometry, FluorescenceThymus GlandUltraviolet RaysConceptsHnRNP proteinsOccluded site sizeHeterogeneous nuclear ribonucleoproteinsNucleic acidsSingle-strand nucleic acidNH2-terminal sequencingEukaryotic RNATight tetramerSDS-polyacrylamide gel electrophoresisApparent molecular weightNuclear ribonucleoproteinNuclear extractsLimited proteolysisMass spectrometric analysisRNAProteinPhenylalanine 19Calf thymusGel electrophoresisAdditional ionic interactionsTerminal deoxynucleotidyl transferaseSite sizeAB formMajor siteCell disruptionDetermination of the secondary structure and folding topology of an RNA binding domain of mammalian hnRNP A1 protein using three-dimensional heteronuclear magnetic resonance spectroscopy.
Garrett D, Lodi P, Shamoo Y, Williams K, Clore G, Gronenborn A. Determination of the secondary structure and folding topology of an RNA binding domain of mammalian hnRNP A1 protein using three-dimensional heteronuclear magnetic resonance spectroscopy. Biochemistry 1994, 33: 2852-8. PMID: 8130198, DOI: 10.1021/bi00176a015.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesConserved SequenceEscherichia coliHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsMagnetic Resonance SpectroscopyMammalsMolecular Sequence DataProtein FoldingProtein Structure, SecondaryRecombinant ProteinsRibonucleoproteinsRNA, Heterogeneous NuclearSequence Homology, Amino AcidConceptsHnRNP A1 proteinA1 proteinMultidimensional heteronuclear NMR spectroscopySecondary structureHeteronuclear magnetic resonance spectroscopyHeteronuclear NMR spectroscopySecondary structure elementsFirst RNARNAFolding patternProteinStructure elementsDomainLong domainNMR spectroscopyMarked variationFamilyMagnetic resonance spectroscopyMembersAntiparallelResonance spectroscopy
1991
A retrovirus-like zinc domain is essential for translational repression of bacteriophage T4 gene 32
Shamoo Y, Webster K, Williams K, Konigsberg W. A retrovirus-like zinc domain is essential for translational repression of bacteriophage T4 gene 32. Journal Of Biological Chemistry 1991, 266: 7967-7970. PMID: 2022625, DOI: 10.1016/s0021-9258(18)92923-6.Peer-Reviewed Original ResearchConceptsZinc-binding subdomainsGene 32 mRNALevel of translationCooperative bindingBacteriophage T4 gene 32Zinc-binding motifDNA-binding proteinsGene 32 proteinRibosome binding siteT4 gene 32Stem-loop structureTranslational repressionVariety of retrovirusesGene 32Pseudoknot sequencesPlant virusesZinc domainUnstructured regionsBacteriophage T4Sequence homologyAutoregulatory regionGp32RNA pseudoknotsEssential roleProteinSingle‐stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids
Ruvolo P, Keating K, Williams K, Chase J. Single‐stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids. Proteins Structure Function And Bioinformatics 1991, 9: 120-134. PMID: 2008432, DOI: 10.1002/prot.340090206.Peer-Reviewed Original ResearchConceptsAmino acid residuesSSB proteinDNA bindingE. coli SSB proteinAcid residuesHelix-destabilizing proteinsEscherichia coli SSBAmino acid sequenceNH2-terminal regionCOOH-terminal regionProteins divergeSequence comparisonProtein sequencesSequence homologyAcid sequenceF plasmidPhe-60Trp-40Trp-54NH2-terminalTerminal thirdDNA binding studiesElongation rateTyr-70ProteinAmino Acid Analysis and Sequencing — What is State-of-the-Art?
Niece R, Ericsson L, Fowler A, Smith A, Speicher D, Crabb J, Williams K. Amino Acid Analysis and Sequencing — What is State-of-the-Art? Advances In Life Sciences 1991, 133-141. DOI: 10.1007/978-3-0348-5678-2_12.Peer-Reviewed Original Research
1990
Mammalian heterogeneous nuclear ribonucleoprotein A1. Nucleic acid binding properties of the COOH-terminal domain.
Kumar A, Casas-Finet J, Luneau C, Karpel R, Merrill B, Williams K, Wilson S. Mammalian heterogeneous nuclear ribonucleoprotein A1. Nucleic acid binding properties of the COOH-terminal domain. Journal Of Biological Chemistry 1990, 265: 17094-17100. PMID: 2145269, DOI: 10.1016/s0021-9258(17)44873-3.Peer-Reviewed Original ResearchConceptsCOOH-terminal domainNH2-terminal domainTerminal domainCOOH-terminal fragmentNucleic acid-binding proteinsCOOH-terminalHeterogeneous nuclear ribonucleoproteinsTwo-domain proteinVertebrate homologuesNucleic acidsAcid-binding proteinIntact A1Nuclear ribonucleoproteinAmino acids bindFluorescent reportersPrimary structureIntact proteinPolynucleotide latticeCore proteinProteinProteolytic fragmentsAcid bindsDNAFragmentsDomainStudies of the domain structure of mammalian DNA polymerase beta. Identification of a discrete template binding domain.
Kumar A, Widen S, Williams K, Kedar P, Karpel R, Wilson S. Studies of the domain structure of mammalian DNA polymerase beta. Identification of a discrete template binding domain. Journal Of Biological Chemistry 1990, 265: 2124-2131. PMID: 2404980, DOI: 10.1016/s0021-9258(19)39949-1.Peer-Reviewed Original ResearchConceptsNH2-terminal domainDNA polymerase betaLarge-scale overproductionPolymerase betaMammalian DNA polymerase betaCOOH-terminal domainProtease-sensitive regionNucleic acidsProteolysis experimentsRat proteinRecombinant proteinsPolypeptide chainDNA polymerase activityIntact proteinEscherichia coliAmino acidsTryptic peptidesDNA polymeraseDomain structureProteinPolymerase activityDomainPolymeraseAcidDNA
1989
Primary structure differences between proteins C1 and C2 of HeLa 40S nuclear ribonucleoprotein particles
Merrill B, Barnett S, LeStourgeon W, Williams K. Primary structure differences between proteins C1 and C2 of HeLa 40S nuclear ribonucleoprotein particles. Nucleic Acids Research 1989, 17: 8441-8449. PMID: 2587210, PMCID: PMC335017, DOI: 10.1093/nar/17.21.8441.Peer-Reviewed Original ResearchConceptsInsert sequenceHeterogeneous nuclear ribonucleoprotein particleSingle transcription unitAlternative splicing mechanismNuclear ribonucleoprotein particleAmino acid sequencingResidue insertHnRNP proteinsTranscription unitTryptic peptide mappingSplicing mechanismPrimary structure differencesC2 proteinSDS-polyacrylamide gel electrophoresisNuclear ribonucleoproteinProtein C1Ribonucleoprotein particleUntranslated regionPrimary structurePolyacrylamide gel electrophoresisAmino acidsPeptide mappingGel electrophoresisMolecular weight differencesProteinThe 44P Subunit of the T4 DNA Polymerase Accessory Protein Complex Catalyzes ATP Hydrolysis
Rush J, Lin T, Quinones M, Spicer E, Douglas I, Williams K, Konigsberg W. The 44P Subunit of the T4 DNA Polymerase Accessory Protein Complex Catalyzes ATP Hydrolysis. Journal Of Biological Chemistry 1989, 264: 10943-10953. PMID: 2786875, DOI: 10.1016/s0021-9258(18)60410-7.Peer-Reviewed Original ResearchConceptsAccessory proteinsATP hydrolysisDNA-dependent ATP hydrolysisT4 DNA polymerase accessory proteinsDNA polymerase accessory proteinPolymerase accessory proteinsTotal cellular proteinAccessory protein complexProtein complexesCellular proteinsPlasmid resultsSubunitsProteinATPase activityOverexpression plasmidProductive interactionInduction of cellsPlasmidSpecific activityComplexesSubcomplexInductionGenesOverexpressionATPase
1988
Phenylalanines that are conserved among several RNA-binding proteins form part of a nucleic acid-binding pocket in the A1 heterogeneous nuclear ribonucleoprotein.
Merrill B, Stone K, Cobianchi F, Wilson S, Williams K. Phenylalanines that are conserved among several RNA-binding proteins form part of a nucleic acid-binding pocket in the A1 heterogeneous nuclear ribonucleoprotein. Journal Of Biological Chemistry 1988, 263: 3307-3313. PMID: 2830282, DOI: 10.1016/s0021-9258(18)69073-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesCarrier ProteinsCattleChromatography, AffinityChromatography, High Pressure LiquidDNA HelicasesDNA, Single-StrandedElectrophoresis, Polyacrylamide GelHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsMolecular Sequence DataNucleic AcidsPeptide FragmentsPhenylalaninePhenylthiohydantoinPhotochemistryPoly TRatsRibonucleoproteinsRNA-Binding ProteinsSerine EndopeptidasesThymus HormonesTrypsinConceptsRNA-binding proteinHeterogeneous nuclear ribonucleoproteinsA1 heterogeneous nuclear ribonucleoproteinNuclear ribonucleoproteinRepeat sequencesPhenylalanine residuesRNA-binding pocketDNA-cellulose chromatographyInternal repeat sequencesStaphylococcus aureus VSequence homologyCovalent adduct formationA1 proteinPrimary structurePartial proteolysisAnalogous positionsAmino acidsTryptic peptidesProteinPolypeptideProteolytic fragmentsRibonucleoproteinFirst experimental evidenceResiduesCellulose chromatography