2016
Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection
Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Molecular Cell 2016, 62: 453-461. PMID: 27153540, PMCID: PMC5291166, DOI: 10.1016/j.molcel.2016.03.032.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateBinding SitesBiological TransportCell Cycle ProteinsChromatin Assembly and DisassemblyDNA-Binding ProteinsDNA, FungalHydrolysisMicrofilament ProteinsMutationNuclear ProteinsNucleosomesProtein BindingProtein Interaction Domains and MotifsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTime FactorsTranscription Factors
2009
Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotein Assemblies Having Implications for Biological Regulation
Levene S, Zhang Y. Closing the Loop on Protein-DNA Interactions: Interplay Between Shape and Flexibility in Nucleoprotein Assemblies Having Implications for Biological Regulation. The IMA Volumes In Mathematics And Its Applications 2009, 150: 195-212. DOI: 10.1007/978-1-4419-0670-0_10.Peer-Reviewed Original ResearchDNA loop formationProtein-DNA interactionsProtein-binding sitesArchitectural proteinsGene repressionLoop formationGene regulationProtein domainsDNA replicationDNA loopsNucleoprotein assembliesBiological regulationLac repressorBiological processesBiological importanceConformational flexibilityProteinEssential mechanistic aspectsDNARegulationSingle moleculesRepressorMechanistic aspectsDistant sitesRepression
2006
Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. PLOS ONE 2006, 1: e136. PMID: 17205140, PMCID: PMC1762422, DOI: 10.1371/journal.pone.0000136.Peer-Reviewed Original ResearchConceptsGene regulationNucleoprotein complexesNon-specific DNA-binding proteinE. coli lac repressorWild-type E. coli strainDNA-binding proteinsSmall DNA loopsSame DNA moleculeGene repressionDNA loopingDNA loopsOperator sitesOperator affinityDNA rigidityLac repressorE. coli strainsProtein conformationDNA persistence lengthDNA moleculesRepressor concentrationRepressionColi strainsDNARegulationVivo