2016
Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers
Jiao J, Rebane AA, Ma L, Zhang Y. Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers. Methods In Molecular Biology 2016, 1486: 357-390. PMID: 27844436, PMCID: PMC5508109, DOI: 10.1007/978-1-4939-6421-5_14.Peer-Reviewed Original ResearchConceptsOptical tweezersProtein complexesHigh-resolution optical tweezersSingle-molecule manipulationFolding of proteinsFundamental biological problemOptical trapSingle-molecule measurementsUnprecedented spatiotemporal resolutionThree-dimensional structureTweezersSingle proteinSpontaneous foldingDetailed protocolAmino acidsMolecule proteinProteinBiological problemsPowerful approachMechanical forcesFoldingSpatiotemporal resolutionEnergyTransition kineticsLinear chainsRegulation 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
2010
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
Xi Z, Zhang Y, Hegde RS, Shakked Z, Crothers DM. Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA. Nucleic Acids Research 2010, 38: 3827-3833. PMID: 20185566, PMCID: PMC2887970, DOI: 10.1093/nar/gkq114.Peer-Reviewed Original Research
2005
Statistical-Mechanical Theory of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Statistical-Mechanical Theory of DNA Looping. Biophysical Journal 2005, 90: 1903-1912. PMID: 16361335, PMCID: PMC1386771, DOI: 10.1529/biophysj.105.070490.Peer-Reviewed Original ResearchConceptsMechanical theoryRigorous analytical theoryStatistical mechanical theoryMechanics of DNARigorous theoryAnalytical theoryGeometric propertiesAccount protein flexibilityTopological constraintsTheoryDNA cyclizationTerms of amplitudeLoop topologyStrong couplingProtein geometryMultiple classesTheoretical similaritiesDependenceMechanicsLoop closureGeometryTopologyDNA length dependenceWritheLoop
2004
Predicting indirect readout effects in protein–DNA interactions
Zhang Y, Xi Z, Hegde RS, Shakked Z, Crothers DM. Predicting indirect readout effects in protein–DNA interactions. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 8337-8341. PMID: 15148366, PMCID: PMC420395, DOI: 10.1073/pnas.0402319101.Peer-Reviewed Original Research