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
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
2000
Biophysical Characterization of gp41 Aggregates Suggests a Model for the Molecular Mechanism of HIV-associated Neurological Damage and Dementia*
Caffrey M, Braddock D, Louis J, Abu-Asab M, Kingma D, Liotta L, Tsokos M, Tresser N, Pannell L, Watts N, Steven A, Simon M, Stahl S, Wingfield P, Clore G. Biophysical Characterization of gp41 Aggregates Suggests a Model for the Molecular Mechanism of HIV-associated Neurological Damage and Dementia*. Journal Of Biological Chemistry 2000, 275: 19877-19882. PMID: 10747981, DOI: 10.1074/jbc.m001036200.Peer-Reviewed Original ResearchMeSH KeywordsAIDS Dementia ComplexBrainBrain DiseasesChromatography, GelEndopeptidasesExtracellular SpaceHIV Envelope Protein gp41HIV SeropositivityHumansHydrogen-Ion ConcentrationImmunohistochemistryMembrane GlycoproteinsMicroscopy, ElectronProtein BindingProtein Structure, TertiaryRetroviridae ProteinsConceptsNeurological damageBrains of HIVHuman immunodeficiency virusImmunodeficiency virusEnvelope protein gp41HIVBrain tissueDementiaHigh molecular weight formExtracellular aggregatesMolecular weight formsSimian immunodeficiency virus gp41Gp41Molecular mechanismsWeight formsHIV gp41HIV envelope protein gp41Extracellular ectodomainBiochemical methodsDamagePatientsImmunohistochemistryHigh molecular weight aggregatesBrain
1996
Conformationally Specific Enhancement of Receptor-Mediated LDL Binding and Internalization by Peptide Models of a Conserved Anionic N-Terminal Domain of Human Apolipoprotein E †
Braddock D, Mercurius K, Subramanian R, Dominguez S, Davies P, Meredith S. Conformationally Specific Enhancement of Receptor-Mediated LDL Binding and Internalization by Peptide Models of a Conserved Anionic N-Terminal Domain of Human Apolipoprotein E †. Biochemistry 1996, 35: 13975-13984. PMID: 8909295, DOI: 10.1021/bi960006u.Peer-Reviewed Original ResearchAmino Acid SequenceAnimalsApolipoproteins EBinding SitesBinding, CompetitiveCell LineCell MembraneConserved SequenceHeparin LyaseHumansIn Vitro TechniquesLipoproteins, LDLLiverModels, MolecularMolecular Sequence DataPeptide FragmentsPolysaccharide-LyasesProtein BindingProtein ConformationRatsReceptors, LDL