2018
Single-Molecule Optical Tweezers Study of Regulated SNARE Assembly
Ma L, Jiao J, Zhang Y. Single-Molecule Optical Tweezers Study of Regulated SNARE Assembly. Methods In Molecular Biology 2018, 1860: 95-114. PMID: 30317500, PMCID: PMC6441361, DOI: 10.1007/978-1-4939-8760-3_6.Peer-Reviewed Original ResearchConceptsSoluble N-ethylmaleimide-sensitive factor attachment protein receptorsSNARE assemblyHigh-resolution optical tweezersN-ethylmaleimide-sensitive factor attachment protein receptorsMembrane fusionFactor attachment protein receptorsOptical tweezers studiesNeuronal SNARE assemblyIntracellular membrane fusionAttachment protein receptorsOptical tweezersΑ-SNAPDetailed experimental protocolCellular compartmentsRegulatory proteinsProtein receptorsDifferent cellsSpatiotemporal resolutionProteinAssemblyFusion processManipulation approachTweezersExperimental approachFusion
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 chainsHidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding
Zhang Y, Jiao J, Rebane AA. Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding. Biophysical Journal 2016, 111: 2110-2124. PMID: 27851936, PMCID: PMC5112951, DOI: 10.1016/j.bpj.2016.09.045.Peer-Reviewed Original ResearchConceptsDetailed balanceThermodynamic equilibriumOptical tweezersIndependent fitting parametersDegenerate statesSingle-molecule trajectoriesSatisfies detailed balanceExtension trajectoriesEnergy landscapeFitting parametersShort trajectoriesProtein foldingExperimental dataTransition stateSNARE zipperingTweezersFree energyStructure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers
Rebane AA, Ma L, Zhang Y. Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers. Biophysical Journal 2016, 110: 441-454. PMID: 26789767, PMCID: PMC4724646, DOI: 10.1016/j.bpj.2015.12.003.Peer-Reviewed Original ResearchConceptsOptical tweezersSingle-molecule manipulation experimentsProtein Folding IntermediatesSingle-molecule trajectoriesAbsence of forceCorresponding experimental measurementsRepresentative protein complexesStructure‐based derivationIntrinsic extensionTransition ratesEnergy of proteinsPrevious data analysisTweezersExperimental measurementsEnergySynaptic SNARE proteinsSingle macromoleculeFolding intermediatesExperimental dataProtein structureFunction of forceTransition stateHigh-resolution structuresDifferent folding statesFolding states
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 oligonucleotides