2016
Structure-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 Research
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
2012
Single-molecule observation of helix staggering, sliding, and coiled coil misfolding
Xi Z, Gao Y, Sirinakis G, Guo H, Zhang Y. Single-molecule observation of helix staggering, sliding, and coiled coil misfolding. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 5711-5716. PMID: 22451899, PMCID: PMC3326506, DOI: 10.1073/pnas.1116784109.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
2003
Statistical Mechanics of Sequence-Dependent Circular DNA and Its Application For DNA Cyclization
Zhang Y, Crothers DM. Statistical Mechanics of Sequence-Dependent Circular DNA and Its Application For DNA Cyclization. Biophysical Journal 2003, 84: 136-153. PMID: 12524271, PMCID: PMC1302599, DOI: 10.1016/s0006-3495(03)74838-3.Peer-Reviewed Original ResearchConceptsStatistical mechanicsAccurate analytic expressionsInhomogeneous DNAMonte Carlo simulationsAnalytic expressionsPartition functionHarmonic approximationEffect of curvatureCarlo simulationsEquilibrium configurationsLinear formThermal fluctuationsThermodynamic quantitiesSequence-dependent DNA bendingDNA cyclizationMinimum energy configurationIterative searchNew theoryMechanicsJ factorEnergy configurationTheoryCurvatureSimulationsApproximation