2015
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research. Genomics Proteomics & Bioinformatics 2015, 13: 25-35. PMID: 25712262, PMCID: PMC4411476, DOI: 10.1016/j.gpb.2014.11.002.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, LiquidComputational BiologyDatabases, ProteinHumansPeptide FragmentsProteomeProteomicsTandem Mass SpectrometryConceptsMultiple reaction monitoringPeptides/proteinsYale Protein Expression DatabaseReaction monitoringProteomics researchMass spectrometry-based proteomics researchMS/MSMass spectrometryDatabase search resultsPeptide identificationSpectral librarySite localizationProteomics communityGroup of laboratoriesSpectrometryProtein Expression DatabaseMS
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 substrateIdentifying 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 ResearchMeSH KeywordsAmino AcidsChromatography, High Pressure LiquidPeptide FragmentsPeptide MappingProtein Processing, Post-TranslationalConceptsHPLC peptide mappingMass spectrometryPosttranslational modificationsIntact proteinPeptide mappingAtomic mass unitsAccurate massNet chargeDifferent posttranslational modificationsSulfoxide formationMass unitsCovalent changesOxidationSpectrometryProtein stabilityDeamidationProteinIsoelectric focusingPhosphorylationModificationMutagenesis 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 disruption
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 bindingAcidShuffling 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
[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 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[21] Reversed-phase high-performance liquid chromatography for fractionation of enzymatic digests and chemical cleavage products of proteins
Stone K, Elliott J, Peterson G, McMurray W, Williams K. [21] Reversed-phase high-performance liquid chromatography for fractionation of enzymatic digests and chemical cleavage products of proteins. Methods In Enzymology 1990, 193: 389-412. PMID: 2074828, DOI: 10.1016/0076-6879(90)93429-o.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceChromatography, High Pressure LiquidMolecular Sequence DataPeptide FragmentsPeptide MappingProteinsTransferrinTrypsinConceptsHigh-performance liquid chromatographyReversed-phase high-performance liquid chromatographyReversed phase high performance liquid chromatographyLiquid chromatographyEnzymatic digestsHigh peak capacityMass spectrometric approachProtein chemistsSpectrometric approachMass spectrometryPeak capacityComplex mixturesMolecular weightChemical cleavageGradient timeCleavage productsChromatographyTryptic peptidesPeptidesDigestsChemistsSpectrometryFractionationProductsPrimary structure
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
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 sitesPeptidesFerrate 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 ResearchAmino acid sequence of UP1, an hnRNP‐derived single‐stranded nucleic acid binding protein from calf thymus
MERRILL B, LOPRESTI M, STONE K, WILLIAMS K. Amino acid sequence of UP1, an hnRNP‐derived single‐stranded nucleic acid binding protein from calf thymus. Chemical Biology & Drug Design 1987, 29: 21-39. PMID: 3032834, DOI: 10.1111/j.1399-3011.1987.tb02226.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCattleChromatography, High Pressure LiquidCyanogen BromideDNA HelicasesHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsPeptide FragmentsPeptide HydrolasesRibonucleoproteinsThymus GlandThymus HormonesConceptsHeterogeneous nuclear ribonucleoproteinsAmino acid sequenceHnRNP proteinsAcid sequenceSolid-phase sequencingComplete amino acid sequenceNucleic acidsSingle-strand nucleic acidA1 hnRNP proteinCalf thymusInternal sequence homologyGlutamic acid residuesStaphylococcus aureus proteaseA1 heterogeneous nuclear ribonucleoproteinNuclear ribonucleoproteinSequence homologySequencing of peptides
1986
High pressure liquid chromatography purification of UP1 and UP2, two related single-stranded nucleic acid-binding proteins from calf thymus.
Merrill B, LoPresti M, Stone K, Williams K. High pressure liquid chromatography purification of UP1 and UP2, two related single-stranded nucleic acid-binding proteins from calf thymus. Journal Of Biological Chemistry 1986, 261: 878-883. PMID: 3941105, DOI: 10.1016/s0021-9258(17)36178-1.Peer-Reviewed Original Research
1985
Amino acid sequence of the UP1 calf thymus helix-destabilizing protein and its homology to an analogous protein from mouse myeloma.
Williams K, Stone K, LoPresti M, Merrill B, Planck S. Amino acid sequence of the UP1 calf thymus helix-destabilizing protein and its homology to an analogous protein from mouse myeloma. Proceedings Of The National Academy Of Sciences Of The United States Of America 1985, 82: 5666-5670. PMID: 2994041, PMCID: PMC390612, DOI: 10.1073/pnas.82.17.5666.Peer-Reviewed Original ResearchConceptsAmino acid sequenceAmino acidsAnalogous proteinsAcid sequenceHelix-destabilizing proteinsComplete amino acid sequenceHelix-destabilizing proteinStaphylococcus aureus V8 proteaseSimilar amino acidsAureus V8 proteaseMouse proteinCyanogen bromide cleavageMouse sequencesProtein sequencesSequence homologyCOOH terminusNH2 terminusSolid-phase sequencingGas-phase sequencingV8 proteaseEndoproteinase LysTryptic peptidesProteinUP1Calf thymusIdentification of a nucleic acid helix-destabilizing protein from rat liver as lactate dehydrogenase-5.
Williams K, Reddigari S, Patel G. Identification of a nucleic acid helix-destabilizing protein from rat liver as lactate dehydrogenase-5. Proceedings Of The National Academy Of Sciences Of The United States Of America 1985, 82: 5260-5264. PMID: 2991914, PMCID: PMC390547, DOI: 10.1073/pnas.82.16.5260.Peer-Reviewed Original ResearchConceptsHelix-destabilizing proteinSs-DNAAmino acid compositionHPLC tryptic peptide mapsNucleic acid helix-destabilizing proteinSolid-phase protein sequencingChemical modification studiesCoenzyme binding siteTyrosine-238Molecular weightSimilar amino acid compositionsTryptic peptide mapsAcid compositionLactate dehydrogenase 5Molecular homogeneitySimilar specific activitiesProtein sequencingLDH proteinDNA bindingAmino terminusBiological roleSingle proteinM chainTryptic peptidesVivo role
1984
Characterization of the Escherichia coli SSB-113 mutant single-stranded DNA-binding protein. Cloning of the gene, DNA and protein sequence analysis, high pressure liquid chromatography peptide mapping, and DNA-binding studies.
Chase J, L'Italien J, Murphy J, Spicer E, Williams K. Characterization of the Escherichia coli SSB-113 mutant single-stranded DNA-binding protein. Cloning of the gene, DNA and protein sequence analysis, high pressure liquid chromatography peptide mapping, and DNA-binding studies. Journal Of Biological Chemistry 1984, 259: 805-814. PMID: 6363409, DOI: 10.1016/s0021-9258(17)43529-0.Peer-Reviewed Original Research