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