2014
Common intermediates and kinetics, but different energetics, in the assembly of SNARE proteins
Zorman S, Rebane AA, Ma L, Yang G, Molski MA, Coleman J, Pincet F, Rothman JE, Zhang Y. Common intermediates and kinetics, but different energetics, in the assembly of SNARE proteins. ELife 2014, 3: e03348. PMID: 25180101, PMCID: PMC4166003, DOI: 10.7554/elife.03348.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsEnergy TransferHumansKineticsModels, MolecularMolecular Sequence DataMultiprotein ComplexesOptical TweezersProtein FoldingProtein Structure, QuaternaryProtein Structure, SecondaryQa-SNARE ProteinsRatsSequence Homology, Amino AcidSNARE ProteinsThermodynamicsVesicle-Associated Membrane Protein 2Vesicular Transport ProteinsConceptsSoluble N-ethylmaleimide-sensitive factor attachment protein receptorsSNARE complexN-ethylmaleimide-sensitive factor attachment protein receptorsMembrane fusionFactor attachment protein receptorsAttachment protein receptorsHigh-resolution optical tweezersNeuronal SNARE complexFolding/assemblyEnergy releaseSNARE proteinsSingle-molecule levelProtein receptorsDomain associationOptical tweezersTerminal partZippering mechanismFusion kineticsZipperingComplexesAssemblyDifferent energeticsEnergyYeastTweezers
2013
High-resolution optical tweezers for single-molecule manipulation.
Zhang X, Ma L, Zhang Y. High-resolution optical tweezers for single-molecule manipulation. The Yale Journal Of Biology And Medicine 2013, 86: 367-83. PMID: 24058311, PMCID: PMC3767221.Peer-Reviewed Original ResearchConceptsHigh-resolution optical tweezersOptical tweezersComplex multi-scale dynamicsATP-dependent chromatinDynamics of biomacromoleculesSingle-molecule manipulationSingle-molecule levelMolecular motorsTweezersChromatin structureSNARE complexProtein foldingCoil proteinsBiomacromoleculesMulti-scale dynamicsConformational fluctuationsTranslocation propertiesTiny forceUnprecedented resolutionDirectional movementMicron distancesComplexesFoldingRevolutionary toolUnique advantages
2012
Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy
Sirinakis G, Ren Y, Gao Y, Xi Z, Zhang Y. Combined versatile high-resolution optical tweezers and single-molecule fluorescence microscopy. Review Of Scientific Instruments 2012, 83: 093708. PMID: 23020384, PMCID: PMC3465359, DOI: 10.1063/1.4752190.Peer-Reviewed Original ResearchConceptsOptical tweezersSingle-molecule fluorescence microscopyDual-trap optical tweezersForce modeHigh-resolution optical tweezersConstant force modeSingle-molecule fluorescence detectionFluorescence microscopySingle-molecule approachOptical trappingDNA hairpin moleculesSingle-molecule fluorescenceSimilar microscopesSingle-molecule levelImaging configurationsΛ-DNA moleculesTweezersMolecular machinesDNA moleculesEasy data interpretationFluorescence signalHairpin moleculesSpatiotemporal resolutionMicroscopyComplementary oligonucleotidesChapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers
Zhang Y, Sirinakis G, Gundersen G, Xi Z, Gao Y. Chapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers. Methods In Enzymology 2012, 513: 3-28. PMID: 22929763, DOI: 10.1016/b978-0-12-391938-0.00001-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateBase SequenceBinding SitesChromatin Assembly and DisassemblyDNADNA HelicasesElectrophoresis, Polyacrylamide GelEscherichia coliMicroscopy, Atomic ForceMolecular Sequence DataNucleic Acid ConformationNucleosomesOptical TweezersPlasmidsTandem Repeat SequencesConceptsChromatin remodelingChromatin structureDNA translocationATP-dependent chromatin remodeling factorsATP-dependent chromatin remodelingATP-dependent chromatinChromatin remodeling factorsDNA moleculesOptical tweezersHigh-resolution optical tweezersSingle-molecule assaysRemodeler ATPasesDNA translocasesRemodeling factorsSingle DNA moleculesDNA substratesSingle-molecule levelATP hydrolysisBiological functionsBare DNASingle-molecule experimentsMolecular mechanismsDetailed protocolTranslocationMolecular motors
2011
Highly Anisotropic Stability and Folding Kinetics of a Single Coiled Coil Protein under Mechanical Tension
Gao Y, Sirinakis G, Zhang Y. Highly Anisotropic Stability and Folding Kinetics of a Single Coiled Coil Protein under Mechanical Tension. Journal Of The American Chemical Society 2011, 133: 12749-12757. PMID: 21707065, PMCID: PMC3670761, DOI: 10.1021/ja204005r.Peer-Reviewed Original ResearchConceptsSingle-molecule levelSingle-molecule methodsStructural motifsProtein transitionsProtein structural motifsCoiled-Coil Protein