1994
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.
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
Single‐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[25] Identification of amino acid residues at interface of protein—Nucleic acid complexes by photochemical cross-linking
Williams K, Konigsberg W. [25] Identification of amino acid residues at interface of protein—Nucleic acid complexes by photochemical cross-linking. Methods In Enzymology 1991, 208: 516-539. PMID: 1779846, DOI: 10.1016/0076-6879(91)08027-f.Peer-Reviewed Original ResearchAdenosine TriphosphateAnimalsBinding SitesChromatography, High Pressure LiquidChromatography, Ion ExchangeColiphagesCross-Linking ReagentsDNADNA-Binding ProteinsElectrophoresis, Polyacrylamide GelEscherichia coliHumansKineticsOligodeoxyribonucleotidesPeptide FragmentsPhosphorus RadioisotopesPhotochemistryPolydeoxyribonucleotidesProtein BindingRadioisotope Dilution Technique
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 bindsDNAFragmentsDomainA novel function for zinc(II) in a nucleic acid-binding protein. Contribution of zinc(II) toward the cooperativity of bacteriophage T4 gene 32 protein binding.
Nadler S, Roberts W, Shamoo Y, Williams K. A novel function for zinc(II) in a nucleic acid-binding protein. Contribution of zinc(II) toward the cooperativity of bacteriophage T4 gene 32 protein binding. Journal Of Biological Chemistry 1990, 265: 10389-10394. PMID: 2113053, DOI: 10.1016/s0021-9258(18)86958-7.Peer-Reviewed Original ResearchStudies 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
Site-specific mutagenesis of T4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions.
Shamoo Y, Ghosaini L, Keating K, Williams K, Sturtevant J, Konigsberg W. Site-specific mutagenesis of T4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions. Biochemistry 1989, 28: 7409-17. PMID: 2684276, DOI: 10.1021/bi00444a039.Peer-Reviewed Original ResearchMeSH KeywordsCalorimetry, Differential ScanningCircular DichroismDNA-Binding ProteinsDNA, Single-StrandedDNA, ViralElectrophoresis, Polyacrylamide GelEscherichia coliGene Expression RegulationGenes, ViralMutationNucleic Acid DenaturationPoly dA-dTPoly TProtein DenaturationT-PhagesTemperatureThermodynamicsTrypsinTyrosineViral ProteinsZinc
1988
Mammalian heterogeneous nuclear ribonucleoprotein complex protein A1. Large-scale overproduction in Escherichia coli and cooperative binding to single-stranded nucleic acids.
Cobianchi F, Karpel R, Williams K, Notario V, Wilson S. Mammalian heterogeneous nuclear ribonucleoprotein complex protein A1. Large-scale overproduction in Escherichia coli and cooperative binding to single-stranded nucleic acids. Journal Of Biological Chemistry 1988, 263: 1063-1071. PMID: 2447078, DOI: 10.1016/s0021-9258(19)35461-4.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsBase SequenceCelluloseDNADNA, Single-StrandedEscherichia coliFluorescent DyesHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsMolecular Sequence DataPoly ARecombinant ProteinsRibonucleoproteinsRNAConceptsLarge-scale overproductionNH2-terminal domainTerminal domainDomain peptideCooperative protein-protein interactionsEscherichia coliProtein-induced fluorescence enhancementAmino acidsProtein-protein interactionsNucleic acidsAlpha-helix structureProtein A1Cooperative bindingAssociation constantsSynthetic polypeptide analogueProteinDirect interactionNatural proteinsRecombinant A1Low association constantsBindingIntact A1ColiFluorescence enhancementOverproduction
1987
Photoaffinity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking.
Pandey V, Williams K, Stone K, Modak M. Photoaffinity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking. Biochemistry 1987, 26: 7744-8. PMID: 3322406, DOI: 10.1021/bi00398a031.Peer-Reviewed Original ResearchConceptsCross-linking reactionReversed-phase high-performance liquid chromatographyHigh-performance liquid chromatographyCross-linking sitesEscherichia coli DNA polymerase IPeptide lossKlenow fragmentChelate formLiquid chromatographyAmino acid analysisE. coli DNA Pol ISmall peptidesTryptic digestionSubstrate deoxynucleoside triphosphateHistidine residuesTryptic peptidesAmino acidsSingle peptideOptimal conditionsPeptide mappingDNA Pol IStaphylococcus aureus V8 protease digestionDNA polymerase IAcceptor sitesPeptidesThe function of zinc in gene 32 protein from T4.
Giedroc D, Keating K, Williams K, Coleman J. The function of zinc in gene 32 protein from T4. Biochemistry 1987, 26: 5251-9. PMID: 3314985, DOI: 10.1021/bi00391a007.Peer-Reviewed Original ResearchFerrate oxidation of Escherichia coli DNA polymerase-I. Identification of a methionine residue that is essential for DNA binding.
Basu A, Williams K, Modak M. Ferrate oxidation of Escherichia coli DNA polymerase-I. Identification of a methionine residue that is essential for DNA binding. Journal Of Biological Chemistry 1987, 262: 9601-9607. PMID: 3298259, DOI: 10.1016/s0021-9258(18)47976-8.Peer-Reviewed Original Research
1986
Cloning of T4 gene 32 and expression of the wild-type protein under lambda promoter PL regulation in Escherichia coli.
Shamoo Y, Adari H, Konigsberg W, Williams K, Chase J. Cloning of T4 gene 32 and expression of the wild-type protein under lambda promoter PL regulation in Escherichia coli. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 8844-8848. PMID: 2947239, PMCID: PMC387029, DOI: 10.1073/pnas.83.23.8844.Peer-Reviewed Original ResearchConceptsGene 32T4 gene 32Bacteriophage T4 gene 32T4 DNA replicationWild-type proteinWild-type geneHost cell viabilityTranslational regulationCodon TAGDNA replicationNative promoterPromoter PLAutoregulatory regionRich sequencesRestriction fragmentsEscherichia coliTranscriptsCell viabilityProteinRegulationSynthetic oligodeoxynucleotidesDeleterious effectsCloningMutagenesisG32PEscherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA).
Chase J, Rabin B, Murphy J, Stone K, Williams K. Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA). Journal Of Biological Chemistry 1986, 261: 14929-14935. PMID: 3021756, DOI: 10.1016/s0021-9258(18)66806-1.Peer-Reviewed Original ResearchConceptsExonuclease VII activityLarge subunitStandard E. coli genetic mapE. coli genetic mapEscherichia coli exonuclease VIIDeletion mutant strainAmino acid sequenceGenetic mapGene productsAcid sequenceMutant strainActive enzymeCell extractsBase pairsGenesExonuclease VIIAmino acidsSubunitsProteinSequenceGuaBXseACloningPromoterMolecular weightZinc metalloproteins involved in replication and transcription
Giedroc D, Keating K, Martin C, Williams K, Coleman J. Zinc metalloproteins involved in replication and transcription. Journal Of Inorganic Biochemistry 1986, 28: 155-169. PMID: 3543219, DOI: 10.1016/0162-0134(86)80079-4.Peer-Reviewed Original ResearchConceptsRNA polymeraseP-hydroxymercuriphenylsulfonateMultisubunit RNA polymerasesGene 32 proteinTranscription initiationDNA binding propertiesTranslational controlProtein essentialDNA replicationAccessory proteinsBacteriophage T7Allosteric roleRPaseBacteriophage T4Apo-g32PZinc metalloproteinsDNA polymeraseElongation ratePolymeraseE. coliProteinBiosynthesisLife cycleBinding propertiesMetalloproteinsSingle-Stranded DNA Binding Proteins Required for DNA Replication
Chase J, Williams K. Single-Stranded DNA Binding Proteins Required for DNA Replication. Annual Review Of Biochemistry 1986, 55: 103-136. PMID: 3527040, DOI: 10.1146/annurev.bi.55.070186.000535.Peer-Reviewed Original Research1H NMR (500 MHz) identification of aromatic residues of gene 32 protein involved in DNA binding by use of protein containing perdeuterated aromatic residues and by site-directed mutagenesis.
Prigodich R, Shamoo Y, Williams K, Chase J, Konigsberg W, Coleman J. 1H NMR (500 MHz) identification of aromatic residues of gene 32 protein involved in DNA binding by use of protein containing perdeuterated aromatic residues and by site-directed mutagenesis. Biochemistry 1986, 25: 3666-72. PMID: 3013293, DOI: 10.1021/bi00360a029.Peer-Reviewed Original ResearchConceptsGene 32 proteinTyr-115Aromatic residuesPhe residueDNA binding surfaceAmino acid sequenceSite-directed mutationsSite-directed mutagenesisComplex formationAcid sequenceBinding surfaceUse of proteinsTyr residuesNMR difference spectraTyr-73ProteinResiduesPhenylalanyl residuesDNANMR identificationTyrMutagenesisMutationsTyrosylDifference spectra
1984
Bacteriophage T4 gene 44 DNA polymerase accessory protein. Sequences of gene 44 and its protein product.
Spicer E, Nossal N, Williams K. Bacteriophage T4 gene 44 DNA polymerase accessory protein. Sequences of gene 44 and its protein product. Journal Of Biological Chemistry 1984, 259: 15425-15432. PMID: 6096371, DOI: 10.1016/s0021-9258(17)42566-x.Peer-Reviewed Original ResearchConceptsGene 44DNA polymerase accessory proteinEscherichia coli RNA polymeraseT4 middle genesT4 DNA replicationAmino acidsPolymerase accessory proteinsPotential regulatory regionsColi RNA polymeraseDirect protein sequencingT4-infected cellsTranslation initiation regionRegA proteinMiddle genesSequence similarityAmino acid compositionDNA replicationRNA polymeraseRegulatory regionsProtein sequencingAccessory proteinsDNA sequencesNucleotide sequenceProtein sequencesNucleotides 5Characterization of the structural and functional defect in the Escherichia coli single-stranded DNA binding protein encoded by the ssb-1 mutant gene. Expression of the ssb-1 gene under lambda pL regulation.
Williams K, Murphy J, Chase J. Characterization of the structural and functional defect in the Escherichia coli single-stranded DNA binding protein encoded by the ssb-1 mutant gene. Expression of the ssb-1 gene under lambda pL regulation. Journal Of Biological Chemistry 1984, 259: 11804-11811. PMID: 6384214, DOI: 10.1016/s0021-9258(20)71283-4.Peer-Reviewed Original ResearchConceptsWild-type SSBMutant proteinsSSB-1Solid-phase protein sequencingSsb-1 mutationSSB-1 proteinHelix-destabilizing proteinNormal cellular concentrationTryptic peptide analysisSubstitution of tyrosineSingle-strand DNAProtein sequencingDNA sequencesMutant geneResidues 55Thermal melting transitionCellular concentrationTemperature inductionTetrameric structureEscherichia coliProteinGenesProtein concentrationPeptide analysisT transitionStructure and Expression of a Complementary DNA for the Nuclear Coded Precursor of Human Mitochondrial Ornithine Transcarbamylase
Horwich A, Fenton W, Williams K, Kalousek F, Kraus J, Doolittle R, Konigsberg W, Rosenberg L. Structure and Expression of a Complementary DNA for the Nuclear Coded Precursor of Human Mitochondrial Ornithine Transcarbamylase. Science 1984, 224: 1068-1074. PMID: 6372096, DOI: 10.1126/science.6372096.Peer-Reviewed Original ResearchConceptsComplementary DNALeader peptideOrnithine transcarbamylaseAmino-terminal leader peptideMost mitochondrial proteinsComplete primary structureHuman ornithine transcarbamylaseFree cytoplasmic ribosomesMitochondrial matrix enzymeCultured HeLa cellsMitochondrial proteinsCytoplasmic ribosomesRegulatory elementsNucleotide sequenceStable transformantsMatrix enzymeAsparagine residuesAcidic residuesLarger precursorMature formPrimary structureProtein occursHeLa cellsEscherichia coliAmino acids1H NMR (500 MHz) of gene 32 protein--oligonucleotide complexes.
Prigodich R, Casas-Finet J, Williams K, Konigsberg W, Coleman J. 1H NMR (500 MHz) of gene 32 protein--oligonucleotide complexes. Biochemistry 1984, 23: 522-9. PMID: 6367821, DOI: 10.1021/bi00298a019.Peer-Reviewed Original ResearchConceptsN-terminal B-domainGene 32 proteinC-terminal domainCore proteinComplex formationGene 32Bacteriophage T4Bacteriophage fdC-terminalOligonucleotide bindingChemical shift changesTyr residuesB domainAromatic residuesNucleotide basesProteinResiduesLong rotational correlation timeOligonucleotide complexesHigh affinityComplexesShift changesDomainProton resonancesRotational correlation time