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
2015
Fast Helix Formation in the B Domain of Protein A Revealed by Site-Specific Infrared Probes
Davis CM, Cooper AK, Dyer RB. Fast Helix Formation in the B Domain of Protein A Revealed by Site-Specific Infrared Probes. Biochemistry 2015, 54: 1758-1766. PMID: 25706439, PMCID: PMC4356530, DOI: 10.1021/acs.biochem.5b00037.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCircular DichroismInfrared RaysKineticsMethionineMolecular Dynamics SimulationMolecular ProbesMolecular Sequence DataPeptidesProtein FoldingProtein Structure, SecondaryProtein Structure, TertiarySpectrophotometry, InfraredSpectroscopy, Fourier Transform InfraredStaphylococcal Protein AConceptsLaser-induced temperatureWavelength-dependent measurementsSite-specific infrared probeMicrosecond phaseSubmillisecond time scaleIntermediate stateRelaxation kineticsComputational proteinInfrared probeStructural resolutionTime scalesSingle residue levelSpectroscopyTransition statePeptide backboneExperimental evidenceProbeResolutionMeasurementsComputer simulationsDirect measureHelical structureStatePartial formationAmide I region