2016
Hidden 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
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 Research
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
2006
Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. PLOS ONE 2006, 1: e136. PMID: 17205140, PMCID: PMC1762422, DOI: 10.1371/journal.pone.0000136.Peer-Reviewed Original ResearchConceptsGene regulationNucleoprotein complexesNon-specific DNA-binding proteinE. coli lac repressorWild-type E. coli strainDNA-binding proteinsSmall DNA loopsSame DNA moleculeGene repressionDNA loopingDNA loopsOperator sitesOperator affinityDNA rigidityLac repressorE. coli strainsProtein conformationDNA persistence lengthDNA moleculesRepressor concentrationRepressionColi strainsDNARegulationVivo
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