2010
Quantitative Characterization of the Interactions among c-myc Transcriptional Regulators FUSE, FBP, and FIR
Hsiao HH, Nath A, Lin CY, Folta-Stogniew EJ, Rhoades E, Braddock DT. Quantitative Characterization of the Interactions among c-myc Transcriptional Regulators FUSE, FBP, and FIR. Biochemistry 2010, 49: 4620-4634. PMID: 20420426, DOI: 10.1021/bi9021445.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceCarrier ProteinsDimerizationDNA HelicasesDNA-Binding ProteinsGuanine Nucleotide Exchange FactorsHumansModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein BindingProto-Oncogene Proteins c-mycRepressor ProteinsRho Guanine Nucleotide Exchange FactorsRNA Splicing FactorsRNA-Binding ProteinsSolutionsTrans-ActivatorsConceptsDNA strand preferencesProtein-DNA interactionsC-myc transcriptionPotent oncogenic factorHuman c-mycFBP bindsTranscriptional regulationActive transcriptionNear-physiological conditionsTripartite interactionCell homeostasisInhibitory complexStrand preferenceC-MycOncogenic factorRegulatory systemUnique modeTranscriptionStrand DNABiological experimentsComplex formationLow micromolar rangeDNADifferent conformationsMicromolar range
2007
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c‐myc inhibition
Crichlow GV, Zhou H, Hsiao HH, Frederick KB, Debrosse M, Yang Y, Folta-Stogniew EJ, Chung HJ, Fan C, De La Cruz EM, Levens D, Lolis E, Braddock D. Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c‐myc inhibition. The EMBO Journal 2007, 27: 277-289. PMID: 18059478, PMCID: PMC2206118, DOI: 10.1038/sj.emboj.7601936.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCrystallography, X-RayDimerizationDNADNA HelicasesDNA-Binding ProteinsDrosophila ProteinsGene Expression RegulationHumansMagnetic Resonance SpectroscopyMolecular Sequence DataPromoter Regions, GeneticProtein BindingProto-Oncogene Proteins c-mycRepressor ProteinsRNA Splicing FactorsRNA-Binding ProteinsTranscription Factor TFIIHConceptsRRM domainDNA bindingFirst RRM domainSecond RRM domainC-myc transcriptional controlSite-directed mutationsDNA upstreamTranscriptional controlInfluences transcriptionC-Myc inhibitionNucleic acid recognitionPromoter sitesP1 promoterAnalogous mutationCell homeostasisC-MycTFIIHProteinLight scattering revealBinding sitesDNATranscriptionSingle strandsMutationsSize exclusion chromatography
2004
NMR-Driven Discovery of Benzoylanthranilic Acid Inhibitors of Far Upstream Element Binding Protein Binding to the Human Oncogene c-myc Promoter
Huth JR, Yu L, Collins I, Mack J, Mendoza R, Isaac B, Braddock DT, Muchmore SW, Comess KM, Fesik SW, Clore GM, Levens D, Hajduk PJ. NMR-Driven Discovery of Benzoylanthranilic Acid Inhibitors of Far Upstream Element Binding Protein Binding to the Human Oncogene c-myc Promoter. Journal Of Medicinal Chemistry 2004, 47: 4851-4857. PMID: 15369388, DOI: 10.1021/jm0497803.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCombinatorial Chemistry TechniquesDNA HelicasesDNA-Binding ProteinsDNA, Single-StrandedDrug DesignGenes, mycHumansInhibitory Concentration 50LigandsMagnetic Resonance SpectroscopyModels, MolecularPromoter Regions, GeneticProtein ConformationProtein Structure, TertiaryProto-Oncogene MasRepetitive Sequences, Amino AcidRNA-Binding ProteinsStructure-Activity RelationshipConceptsUpstream element binding proteinC-myc expressionElement-binding proteinC-Myc pathwayTranscription factorsBinding proteinHost of proteinsRelated transcription factorsAberrant gene expressionC-myc promoterGel shift analysisSlow cell growthC-myc regulationProto-oncogene c-mycFBP bindsKH domainsFBP functionInhibits DNADevelopment of therapeuticsOwn expressionGene expressionHydrophobic pocketC-MycBinding pocketsCell growth
2002
Molecular basis of sequence‐specific single‐stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single‐stranded DNA
Braddock DT, Baber JL, Levens D, Clore GM. Molecular basis of sequence‐specific single‐stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single‐stranded DNA. The EMBO Journal 2002, 21: 3476-3485. PMID: 12093748, PMCID: PMC126100, DOI: 10.1093/emboj/cdf352.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCrystallography, X-RayDNA HelicasesDNA, Single-StrandedDNA-Binding ProteinsHeterogeneous-Nuclear Ribonucleoprotein KHeterogeneous-Nuclear RibonucleoproteinsHumansHydrogen BondingModels, MolecularMolecular Sequence DataNuclear Magnetic Resonance, BiomolecularNucleic Acid ConformationProtein BindingProtein ConformationProtein Structure, TertiaryRibonucleoproteinsRNA-Binding ProteinsSequence AlignmentSequence Homology, Amino AcidSolutionsSubstrate SpecificityConceptsKH domainsDNA recognitionHeterogeneous nuclear ribonucleoprotein KK homology domainSolution structureProtein-ssDNA complexResidues N-terminalHomology domainKH3 domainGXXG motifKH4 domainsMolecular basisN-terminalCytosine basesIsoleucine residueAmino acidsKH3Crucial roleComplexesTetradsDomainDNAMotifMethyl groupResiduesStructure and dynamics of KH domains from FBP bound to single-stranded DNA
Braddock DT, Louis JM, Baber JL, Levens D, Clore GM. Structure and dynamics of KH domains from FBP bound to single-stranded DNA. Nature 2002, 415: 1051-1056. PMID: 11875576, DOI: 10.1038/4151051a.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceDNA HelicasesDNA, Single-StrandedDNA-Binding ProteinsGene Expression RegulationGenes, mycHumansHydrogen BondingMacromolecular SubstancesMagnetic Resonance SpectroscopyModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein BindingProtein ConformationProtein FoldingProtein Structure, TertiaryRNA-Binding Proteins
2001
Rapid Identification of Medium- to Large-Scale Interdomain Motion in Modular Proteins Using Dipolar Couplings
Braddock D, Cai M, Baber J, Huang Y, Clore G. Rapid Identification of Medium- to Large-Scale Interdomain Motion in Modular Proteins Using Dipolar Couplings. Journal Of The American Chemical Society 2001, 123: 8634-8635. PMID: 11525687, DOI: 10.1021/ja016234f.Peer-Reviewed Original ResearchMeSH KeywordsDNADNA-Binding ProteinsMembrane ProteinsNuclear Magnetic Resonance, BiomolecularNuclear ProteinsProtein FoldingProtein Structure, TertiaryConceptsLarge-scale interdomain motions