2019
Synaptic vesicle fusion: today and beyond
Brose N, Brunger A, Cafiso D, Chapman ER, Diao J, Hughson FM, Jackson MB, Jahn R, Lindau M, Ma C, Rizo J, Shin YK, Söllner TH, Tamm L, Yoon TY, Zhang Y. Synaptic vesicle fusion: today and beyond. Nature Structural & Molecular Biology 2019, 26: 663-668. PMID: 31384060, DOI: 10.1038/s41594-019-0277-z.Peer-Reviewed Original ResearchAnimalsCalciumCryoelectron MicroscopyEndocytosisExocytosisHumansMacromolecular SubstancesMembrane FusionMembrane LipidsMembrane ProteinsNerve Tissue ProteinsNeurophysiologyNeurotransmitter AgentsOptical TweezersProtein Interaction MappingSingle Molecule ImagingSNARE ProteinsSynaptic TransmissionSynaptic Vesicles
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
Two 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 ResearchMeSH KeywordsAnimalsEnergy MetabolismHumansMembrane FusionOptical TweezersProtein DomainsProtein FoldingSNARE ProteinsConceptsSoluble 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
Stability, folding dynamics, and long-range conformational transition of the synaptic t-SNARE complex
Zhang X, Rebane AA, Ma L, Li F, Jiao J, Qu H, Pincet F, Rothman JE, Zhang Y. Stability, folding dynamics, and long-range conformational transition of the synaptic t-SNARE complex. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e8031-e8040. PMID: 27911771, PMCID: PMC5167175, DOI: 10.1073/pnas.1605748113.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsMembrane FusionMiceMicroscopy, Atomic ForceMolecular Dynamics SimulationMunc18 ProteinsOptical TweezersProtein ConformationProtein DomainsProtein FoldingProtein StabilityQa-SNARE ProteinsSNARE ProteinsSynaptic TransmissionSynaptosomal-Associated Protein 25Vesicle-Associated Membrane Protein 2ConceptsSynaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptorT-SNARE complexC-terminal domainN-terminal domainSNARE zipperingPlasma membraneN-ethylmaleimide-sensitive factor attachment protein receptorsSoluble N-ethylmaleimide-sensitive factor attachment protein receptorsFactor attachment protein receptorsTarget plasma membraneAttachment protein receptorsFour-helix bundleThree-helix bundleSynaptic vesicle fusionSingle-molecule force spectroscopyV-SNARESNARE assemblySNARE complexHelical bundleConformational switchC-terminusMembrane fusionVesicle fusionProtein receptorsZipperingSingle-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 chainsStructure-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 ResearchMeSH KeywordsAmino Acid SequenceHIV Envelope Protein gp41Molecular Sequence DataOptical TweezersProtein FoldingSNARE ProteinsThermodynamicsConceptsOptical 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
Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition
Jiao J, Rebane AA, Ma L, Gao Y, Zhang Y. Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e2855-e2864. PMID: 26038562, PMCID: PMC4460471, DOI: 10.1073/pnas.1424995112.Peer-Reviewed Original ResearchMunc18-1-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 ResearchMeSH KeywordsBacteriophage lambdaBase SequenceCarbocyaninesDNA, ViralInverted Repeat SequencesMicroscopy, FluorescenceOptical TweezersConceptsOptical 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
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 Research