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
2004
A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies
Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. Journal Of The American Medical Informatics Association 2004, 12: 90-98. PMID: 15492032, PMCID: PMC543832, DOI: 10.1197/jamia.m1571.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceComputational BiologyComputing MethodologiesMass SpectrometryMicroarray AnalysisPhenotypeSequence AnalysisConceptsHigh performance computationLow-maintenance approachBioinformatics applicationsRepresentative bioinformatics applicationsIntensive bioinformatics applicationsBioinformatics case studyGenome-wide sequence comparisonHPC expertsHPC platformsComplex genetic analysisBioinformatics researchersSignificant speedupMass spectrometry data setsHigh-throughput biotechnologiesSequence comparisonVast amountProteomic dataOrdinal phenotypesSpectrum of techniquesDNA microarraysGenetic analysisGene expressionCase studyIterative refinementMaintenance approach
1998
Identification of Protein-ArginineN-Methyltransferase as 10-Formyltetrahydrofolate Dehydrogenase*
Kim S, Park G, Joo W, Paik W, Cook R, Williams K. Identification of Protein-ArginineN-Methyltransferase as 10-Formyltetrahydrofolate Dehydrogenase*. Journal Of Biological Chemistry 1998, 273: 27374-27382. PMID: 9765265, DOI: 10.1074/jbc.273.42.27374.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBlotting, WesternChromatography, AffinityChromatography, High Pressure LiquidGas Chromatography-Mass SpectrometryLeucovorinLiverMolecular Sequence DataOxidoreductases Acting on CH-NH Group DonorsPeptide MappingProtein-Arginine N-MethyltransferasesRatsRecombinant ProteinsSepharoseSequence Analysis
1997
Identification of N G-Methylarginine Residues in Human Heterogeneous RNP Protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe Is a Preferred Recognition Motif †
Kim S, Merrill B, Rajpurohit R, Kumar A, Stone K, Papov V, Schneiders J, Szer W, Wilson S, Paik W, Williams K. Identification of N G-Methylarginine Residues in Human Heterogeneous RNP Protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe Is a Preferred Recognition Motif †. Biochemistry 1997, 36: 5185-5192. PMID: 9136880, DOI: 10.1021/bi9625509.Peer-Reviewed Original ResearchAmino Acid SequenceArginineChromatography, High Pressure LiquidEnzyme InhibitorsHeLa CellsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHumansMethylationMolecular Sequence DataPeptide MappingRibonucleoproteinsRNA, Heterogeneous NuclearRNA-Binding ProteinsSpectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
1996
Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry
McAtee C, Zhang Y, Yarbough P, Fuerst T, Stone K, Samander S, Williams K. Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry. Journal Of Chromatography B 1996, 685: 91-104. PMID: 8930757, DOI: 10.1016/0378-4347(96)00143-0.Peer-Reviewed Original ResearchConceptsMass spectrometryCarboxyl terminusReversed phase liquid chromatographyAmino terminusLaser desorption mass spectrometryDesorption mass spectrometryMolecular massLiquid chromatography-mass spectrometryCarboxyl-terminal sequencingChromatography-mass spectrometryBaculovirus expression vectorSodium dodecyl sulfate-polyacrylamide gel electrophoresisDodecyl sulfate-polyacrylamide gel electrophoresisSulfate-polyacrylamide gel electrophoresisLC-MSLiquid chromatographyExpression vectorTerminal sequencingSequence analysisPolyacrylamide gel electrophoresisSpectrometryIntact proteinInternal sequencesDoublet proteinsTerminusOrigins of Binding Specificity of the A1 Heterogeneous Nuclear Ribonucleoprotein †
Abdul-Manan N, O'Malley S, Williams K. Origins of Binding Specificity of the A1 Heterogeneous Nuclear Ribonucleoprotein †. Biochemistry 1996, 35: 3545-3554. PMID: 8639505, DOI: 10.1021/bi952298p.Peer-Reviewed Original ResearchAmino Acid SequenceBase SequenceDNAGlobinsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsIonsMolecular Sequence DataNucleic Acid ConformationOligoribonucleotidesProtein BindingRecombinant ProteinsRepetitive Sequences, Nucleic AcidRibonucleoproteinsRNA, MessengerRNA-Binding ProteinsStructure-Activity Relationship
1995
Structural specificity of substrate for S-adenosylmethionine protein arginine N-methyltransferases
Rawal N, Rajpurohit R, Lischwe M, Williams K, Paik W, Kim S. Structural specificity of substrate for S-adenosylmethionine protein arginine N-methyltransferases. Biochimica Et Biophysica Acta 1995, 1248: 11-18. PMID: 7536038, DOI: 10.1016/0167-4838(94)00213-z.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsMethylationMolecular Sequence DataMyelin Basic ProteinOligopeptidesPeptide FragmentsProtein-Arginine N-MethyltransferasesRatsRibonucleoproteinsS-AdenosylmethionineSubstrate SpecificityTrypsinConceptsProtein methylase IArginine residuesProtein A1Protein arginine N-methyltransferasesEnzymatic methylationPreferred amino acid sequencesArginine-methylated proteinsProtein arginine N-methyltransferaseHnRNP protein A1Arginine-rich motifAmino acid sequenceArginine N-methyltransferaseN-methyltransferasesRich motifN-terminal fragmentHPLC amino acid analysisC-terminusMethyl acceptorAmino acid analysisDisulfide bridgesS-adenosylmethionineProtein moleculesTrypsin digestionNG-monomethylarginineGood substrateMultiple 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 ResearchMeSH KeywordsAmino Acid SequenceBinding SitesMolecular Sequence DataRNARNA-Binding ProteinsSequence AlignmentMutagenesis 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
Both RNA-binding domains in heterogenous nuclear ribonucleoprotein A1 contribute toward single-stranded-RNA binding.
Shamoo Y, Abdul-Manan N, Patten A, Crawford J, Pellegrini M, Williams K. Both RNA-binding domains in heterogenous nuclear ribonucleoprotein A1 contribute toward single-stranded-RNA binding. Biochemistry 1994, 33: 8272-81. PMID: 7518244, DOI: 10.1021/bi00193a014.Peer-Reviewed Original ResearchAmino Acid SequenceBinding SitesCircular DichroismCloning, MolecularDNAElectrochemistryHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHydrogen-Ion ConcentrationMolecular Sequence DataOligonucleotidesPeptide FragmentsPoly UProtein Structure, SecondaryRibonucleoproteinsRNASodium ChlorideThermodynamicsPurification 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
1993
Synthesis and Use of an Internal Amino Acid Sequencing Standard Peptide
Elliott J, Stone K, Williams K. Synthesis and Use of an Internal Amino Acid Sequencing Standard Peptide. Analytical Biochemistry 1993, 211: 94-101. PMID: 8323041, DOI: 10.1006/abio.1993.1238.Peer-Reviewed Original Research
1992
Identification of amino acid residues at the interface of a bacteriophage T4 regA protein-nucleic acid complex.
Webster K, Keill S, Konigsberg W, Williams K, Spicer E. Identification of amino acid residues at the interface of a bacteriophage T4 regA protein-nucleic acid complex. Journal Of Biological Chemistry 1992, 267: 26097-26103. PMID: 1464621, DOI: 10.1016/s0021-9258(18)35722-3.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial ProteinsBacteriophage T4Base SequenceBinding SitesChromatography, High Pressure LiquidCross-Linking ReagentsMolecular Sequence DataOligoribonucleotidesPeptide FragmentsPlasmidsPromoter Regions, GeneticRNA, MessengerRNA, ViralSequence Homology, Amino AcidTrypsinUltraviolet RaysConceptsCross-linked peptidesProtein-nucleic acid complexesAnion-exchange high-performance liquid chromatographyNucleic acidsIntact proteinHigh-performance liquid chromatographyCross-linked complexGas-phase sequencingPerformance liquid chromatographyAcid complexesExchange high performance liquid chromatographyLiquid chromatographyChemical cleavageBacteriophage T4 regA proteinNucleic acid bindingTryptic peptidesComplexesUltraviolet lightCNBr peptidesPeptidesCN6Amino acid residuesMeasurable affinityAcid bindingAcidPurification and characterization of an endo-exonuclease from adult flies of Drosophila melanogaster
Shuai K, Gupta C, Hawley R, Chase J, Stone K, Williams K. Purification and characterization of an endo-exonuclease from adult flies of Drosophila melanogaster. Nucleic Acids Research 1992, 20: 1379-1385. PMID: 1313969, PMCID: PMC312186, DOI: 10.1093/nar/20.6.1379.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino AcidsAnimalsChromatography, DEAE-CelluloseChromatography, High Pressure LiquidDNA, Single-StrandedDrosophila melanogasterElectrophoresis, Polyacrylamide GelEndonucleasesExonucleasesHot TemperatureHydrogen-Ion ConcentrationKineticsMolecular Sequence DataMolecular WeightSodium ChlorideSubstrate SpecificityUltracentrifugationShuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif.
Nadler S, Kapouch J, Elliott J, Williams K. Shuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif. Journal Of Biological Chemistry 1992, 267: 3750-3757. PMID: 1740426, DOI: 10.1016/s0021-9258(19)50589-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesCarrier ProteinsCircular DichroismFungal ProteinsGenes, FungalHot TemperatureMolecular Sequence DataNucleic Acid DenaturationNucleic AcidsPeptide FragmentsPoly APoly A-UPoly(A)-Binding ProteinsRNA, FungalRNA-Binding ProteinsSaccharomyces cerevisiaeSpectrometry, FluorescenceSubstrate SpecificityConceptsNucleic acidsPeptide studiesResidue peptideSynthetic peptide studiesSynthetic peptidesSynthetic peptide analoguesFree energyProperties of fragmentsPeptide analoguesNucleic acid-binding domainParent proteinLatter peptideNucleic acid bindingAmino acidsStructure/function studiesAmino acid sequenceSignificant affinityAcidEukaryotic RNAPeptidesRNA specificityAmino acid compositionSimilar RNACarboxyl halfMolecular basis
1991
State‐of‐the‐art biomolecular core facilities: a comprehensive survey1
Niece R, Beach C, Cook R, Hathaway G, Williams K. State‐of‐the‐art biomolecular core facilities: a comprehensive survey1. The FASEB Journal 1991, 5: 2756-2760. PMID: 1916100, DOI: 10.1096/fasebj.5.13.1916100.Peer-Reviewed Original ResearchA 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 roleProteinInteractions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions.
Nadler S, Merrill B, Roberts W, Keating K, Lisbin M, Barnett S, Wilson S, Williams K. Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions. Biochemistry 1991, 30: 2968-76. PMID: 1848781, DOI: 10.1021/bi00225a034.Peer-Reviewed Original ResearchAmino Acid SequenceCircular DichroismDNA HelicasesDNA-Binding ProteinsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsKineticsMolecular Sequence DataNucleic Acid DenaturationPoly A-UPoly dA-dTPolydeoxyribonucleotidesPolyribonucleotidesRibonucleoproteinsSpectrometry, FluorescenceThermodynamicsThymus HormonesSingle‐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-70Protein