2018
A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy
Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chemical Science 2018, 9: 9002-9011. PMID: 30647892, PMCID: PMC6301204, DOI: 10.1039/c8sc03786h.Peer-Reviewed Original ResearchMixed quantum/classical calculationsClassical calculationsExperimental observablesRelaxation dynamicsSame time scaleTemperature-jump experimentsProbe frequencyIntermediate stateReaction coordinatesVibrational spectroscopyExperimental observationsMolecular dynamics simulationsQuantitative connectionMolecular dynamics trajectoriesDirect structural evidenceObservablesTime dependenceSpectraTime scalesReaction kineticsHigh temperatureLow temperatureAmide IDynamics simulationsSpectral amplitude
2016
The Role of Electrostatic Interactions in Folding of β‑Proteins
Davis CM, Dyer RB. The Role of Electrostatic Interactions in Folding of β‑Proteins. Journal Of The American Chemical Society 2016, 138: 1456-1464. PMID: 26750867, PMCID: PMC4749129, DOI: 10.1021/jacs.5b13201.Peer-Reviewed Original ResearchConceptsElectrostatic interactionsAmide I regionAtomic-level molecular dynamics simulationsProtonation stateExtended β-sheet structureRelaxation dynamicsAspartic acid side chainMolecular dynamics simulationsΒ-sheet formΒ-sheet structureAcid side chainsFTIR spectroscopyPin1 WW domainPeptide backboneWW domainsAspartic acidSide chainsNegative chargeΒ-turnDynamics simulationsGood agreementTurn stabilitySimulation predictionsSpectroscopyΒ-sheet
2014
WW Domain Folding Complexity Revealed by Infrared Spectroscopy
Davis CM, Dyer RB. WW Domain Folding Complexity Revealed by Infrared Spectroscopy. Biochemistry 2014, 53: 5476-5484. PMID: 25121968, PMCID: PMC4151701, DOI: 10.1021/bi500556h.Peer-Reviewed Original ResearchConceptsLaser-induced temperatureWavelength-dependent measurementsDry molten globule statesInfrared SpectroscopyProtein Folding DynamicsFBP28 WW domainCorresponding IR bandsRelaxation dynamicsSubmillisecond time scaleWild-type WW domainComplementary probesDry molten globuleSingle exponential kineticsAmide I regionFolding DynamicsFluorescence spectraFluorescence spectroscopyPeptide backboneMolten globule stateRelaxation kineticsConvenient probeSpectroscopyFluorescence measurementsIR bandsSide chains