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
2017
Single-molecule force spectroscopy of protein-membrane interactions
Ma L, Cai Y, Li Y, Jiao J, Wu Z, O'Shaughnessy B, De Camilli P, Karatekin E, Zhang Y. Single-molecule force spectroscopy of protein-membrane interactions. ELife 2017, 6: e30493. PMID: 29083305, PMCID: PMC5690283, DOI: 10.7554/elife.30493.Peer-Reviewed Original ResearchConceptsProtein-membrane interactionsC2 domainPlasma membraneMultiple C2 domainsSingle-molecule force spectroscopy approachSingle-molecule force spectroscopyOptical tweezersE-SytsUnprecedented spatiotemporal resolutionForce spectroscopyMembrane bindingMembrane fusionSingle proteinSynaptotagmin-1Biological processesEndoplasmic reticulumSpectroscopy approachLipid exchangeSynaptic vesiclesSynaptotagmin 2ProteinSilica beadsMechanical forcesHigh-resolution methodsSpatiotemporal resolutionTwo Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly
Rebane AA, Wang B, Ma L, Qu H, Coleman J, Krishnakumar S, Rothman JE, Zhang Y. Two Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly. Journal Of Molecular Biology 2017, 430: 479-490. PMID: 29056461, PMCID: PMC5805579, DOI: 10.1016/j.jmb.2017.10.012.Peer-Reviewed Original ResearchConceptsSoluble N-ethylmaleimide-sensitive factor attachment receptorSNARE assemblySynaptic exocytosisMembrane fusionSingle-molecule optical tweezersT-SNARE complexVesicle-associated SNAREsTarget plasma membraneC-terminal assemblyFour-helix bundleC-terminal regionSNARE complexPlasma membraneMolecular mechanismsZipperingMutationsNumerous diseasesAssembly energyNeurotransmitter releaseExocytosisAttachment receptorAssemblyNeurological disordersOptical tweezersComplexesEnergetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers
Zhang Y. Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers. Protein Science 2017, 26: 1252-1265. PMID: 28097727, PMCID: PMC5477538, DOI: 10.1002/pro.3116.Peer-Reviewed Original ResearchConceptsSoluble N-ethylmaleimide-sensitive factor attachment protein receptorsSynaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptorSNARE assemblyMembrane fusionSNARE complexN-ethylmaleimide-sensitive factor attachment protein receptorsFactor attachment protein receptorsFast calcium-triggered fusionAttachment protein receptorsHigh-resolution optical tweezersCalcium-triggered fusionC-terminal domainFour-helix bundleNeurotransmitter-containing vesiclesLinker domainPlasma membraneDomain associationProtein receptorsMolecular engineDifferent functionsPathwayAssemblyMembraneOptical tweezersSynaptic transmission
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 energyα-SNAP Enhances SNARE Zippering by Stabilizing the SNARE Four-Helix Bundle
Ma L, Kang Y, Jiao J, Rebane AA, Keun HK, Xi Z, Qu H, Zhang Y. α-SNAP Enhances SNARE Zippering by Stabilizing the SNARE Four-Helix Bundle. Cell Reports 2016, 15: 531-539. PMID: 27068468, PMCID: PMC4838522, DOI: 10.1016/j.celrep.2016.03.050.Peer-Reviewed Original ResearchConceptsSoluble N-ethylmaleimide-sensitive factor attachment protein receptorsC-terminal domainN-terminal domainMembrane fusionLinker domainΑ-SNAPSynaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptorN-ethylmaleimide-sensitive factor attachment protein receptorsFactor attachment protein receptorsIntracellular membrane fusionAttachment protein receptorsConformational selection mechanismFour-helix bundleSNARE assemblySNARE complexProtein receptorsDynamic assemblyStepwise assemblyAssemblyDomainFusionZipperingOptical tweezersRecent experimentsReceptorsStructure-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
2015
Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis
Ma L, Rebane AA, Yang G, Xi Z, Kang Y, Gao Y, Zhang Y. Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis. ELife 2015, 4: e09580. PMID: 26701912, PMCID: PMC4744192, DOI: 10.7554/elife.09580.Peer-Reviewed Original ResearchConceptsN-terminal regulatory domainSNARE assemblyMunc18-1Folding/assemblySNARE domainVesicle dockingDifferent assembly stagesRegulatory domainLinker domainSynaptic exocytosisDistinct functionsRapid exocytosisC-terminalN-terminalExocytosisAttachment receptorAssemblyDistinct stagesSyntaxinDomainMutationsFusionOptical tweezersAssembly stageDocking
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 oligonucleotidesSingle Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages
Gao Y, Zorman S, Gundersen G, Xi Z, Ma L, Sirinakis G, Rothman JE, Zhang Y. Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages. Science 2012, 337: 1340-1343. PMID: 22903523, PMCID: PMC3677750, DOI: 10.1126/science.1224492.Peer-Reviewed Original ResearchChapter 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
The RSC chromatin remodelling ATPase translocates DNA with high force and small step size
Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. The EMBO Journal 2011, 30: 2364-2372. PMID: 21552204, PMCID: PMC3116276, DOI: 10.1038/emboj.2011.141.Peer-Reviewed Original ResearchConceptsATP-dependent chromatinHigh-resolution optical tweezersDNA-histone interactionsBp/sDNA translocation processRSC chromatinATPase domainTranslocase systemDiverse functionsATP hydrolysisBare DNATranslocation processBiophysical knowledgeDNAChromatinNucleosomesMechanical forcesBPForce generationRemodellersTranslocaseProcessivityTranslocationATPaseOptical tweezers