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
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-Binding ProteinsDNA, Single-StrandedHeterogeneous-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-Binding ProteinsDNA, Single-StrandedGene Expression RegulationGenes, mycHumansHydrogen BondingMacromolecular SubstancesMagnetic Resonance SpectroscopyModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein BindingProtein ConformationProtein FoldingProtein Structure, TertiaryRNA-Binding Proteins
1998
Structure−Function Relationships in Side Chain Lactam Cross-Linked Peptide Models of a Conserved N-Terminal Domain of Apolipoprotein E †
Benzinger T, Braddock D, Dominguez S, Burkoth T, Miller-Auer H, Subramanian R, Fless G, Jones D, Lynn D, Meredith S. Structure−Function Relationships in Side Chain Lactam Cross-Linked Peptide Models of a Conserved N-Terminal Domain of Apolipoprotein E †. Biochemistry 1998, 37: 13222-13229. PMID: 9748329, DOI: 10.1021/bi980482f.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsApolipoproteins ECell LineCircular DichroismConserved SequenceEmbryo, MammalianFibroblastsIodine RadioisotopesLactamsMiceModels, MolecularMolecular Sequence DataNuclear Magnetic Resonance, BiomolecularPeptide FragmentsProtein Structure, SecondaryReceptors, LDLStructure-Activity RelationshipConceptsPeptide IVPeptide modelsConformational switchSide chain lactamLipid surfaceSide chainsBioactive peptidesStructural orderMultiple conformationsBiological activityStructure-function relationshipsLactamsAlpha-helixStrategic modificationsSecondary structureHelical segmentsPeptide IIIConformationAlpha-helical segmentsShort alpha helixCOOHHelixAntipodeStructureSolution
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
1994
Structural and thermodynamic characterization of a bioactive peptide model of apolipoprotein E: side-chain lactam bridges to constrain the conformation.
Luo P, Braddock D, Subramanian R, Meredith S, Lynn D. Structural and thermodynamic characterization of a bioactive peptide model of apolipoprotein E: side-chain lactam bridges to constrain the conformation. Biochemistry 1994, 33: 12367-77. PMID: 7918459, DOI: 10.1021/bi00207a003.Peer-Reviewed Original ResearchConceptsSide-chain lactam bridgePeptide modelsAlpha-helical peptidesLoss of entropyModel peptidesBioactive structuresNMR dataAlpha-helical structureLactam constraintsConformational flexibilityLactam bridgeKcal/Thermodynamic characterizationAlpha-helical domainBiological activityPlasma lipoprotein clearanceUnfolded stateCell surface receptorsBiological functionsPeptidesSurface receptorsStructureResiduesCentral bendCritical role