2022
An in Vitro Cytomimetic of In‐Cell RNA Folding
Yoo H, Davis C. An in Vitro Cytomimetic of In‐Cell RNA Folding. ChemBioChem 2022, 23: e202200406. PMID: 35999178, DOI: 10.1002/cbic.202200406.Peer-Reviewed Original Research
2020
An in vitro mimic of in‐cell solvation for protein folding studies
Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in‐cell solvation for protein folding studies. Protein Science 2020, 29: 1046-1054. PMID: 31994240, PMCID: PMC7096716, DOI: 10.1002/pro.3833.Peer-Reviewed Original ResearchConceptsPhosphoglycerate kinaseLysis bufferCytoplasmic protein interactionsSignificant nonadditive effectsVariety of proteinsProtein folding studiesEukaryotic cellsProtein foldingProtein interactionsCellular crowdingProtein-like sequencesEffect of FicollFolding studiesHydrophobic patchVariable major protein-like sequenceNonadditive effectsCellular effectsProteinCell environmentInert macromoleculesBiomolecular interactionsCellsTest tubeSmall crowdersMimics
2019
Quantifying protein dynamics and stability in a living organism
Feng R, Gruebele M, Davis CM. Quantifying protein dynamics and stability in a living organism. Nature Communications 2019, 10: 1179. PMID: 30862837, PMCID: PMC6414637, DOI: 10.1038/s41467-019-09088-y.Peer-Reviewed Original Research
2018
Non‐Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells
Davis CM, Gruebele M. Non‐Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. ChemPhysChem 2018, 19: 2290-2294. PMID: 29877016, DOI: 10.1002/cphc.201800534.Peer-Reviewed Original ResearchConceptsProtein foldingProtein stabilityNon-steric interactionsSteric interactionsEukaryotic cellsProtein flexibilityIntracellular environmentBiochemical assaysCell lysatesPGKCells resultsSolvation environmentFoldingChemical behaviorLysis bufferGreater stabilizationStability trendCellsCell studiesVlsESystematic seriesIonic bufferEffective newsProteinInteraction
2017
How does solvation in the cell affect protein folding and binding?
Davis CM, Gruebele M, Sukenik S. How does solvation in the cell affect protein folding and binding? Current Opinion In Structural Biology 2017, 48: 23-29. PMID: 29035742, DOI: 10.1016/j.sbi.2017.09.003.Peer-Reviewed Original ResearchConceptsMild environmental changesProtein functionCellular processesProtein foldingCellular environmentProtein surface areaProtein studiesLive cellsEnvironmental changesNon-steric interactionsProtein processesNatural contextCellsInteraction typesSolute environmentFoldingProteinRecent examplesBindingRapid changesSolute compositionParallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation
Zanetti‐Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Letters 2017, 591: 3265-3275. PMID: 28881468, PMCID: PMC5658256, DOI: 10.1002/1873-3468.12836.Peer-Reviewed Original ResearchAmino Acid MotifsKineticsModels, MolecularMolecular Dynamics SimulationNIMA-Interacting Peptidylprolyl IsomeraseProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein DomainsProtein EngineeringProtein FoldingProtein UnfoldingQuantum TheorySpectrophotometry, InfraredThermodynamicsDual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics
Davis CM, Reddish MJ, Dyer RB. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics. Spectrochimica Acta Part A Molecular And Biomolecular Spectroscopy 2017, 178: 185-191. PMID: 28189834, PMCID: PMC5346054, DOI: 10.1016/j.saa.2017.01.069.Peer-Reviewed Original ResearchConceptsQuantum cascade lasersTime-resolved IRYAG laserTunable quantum cascade laserFluorescence spectroscopyProtein dynamicsAbsorbance detection limitCascade lasersSapphire laserComplex folding mechanismsLaserIR frequenciesOverall fluorescence intensityFluorescence spectrometerSpectroscopyIR spectrometerFluorescence measurementsFluorescence sensitivityHigh sensitivityT-jumpSpectrometerFast protein dynamicsFolding mechanismPowerful techniqueFluorescence
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
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
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
2012
Raising the Speed Limit for β‑Hairpin Formation
Davis CM, Xiao S, Raleigh DP, Dyer RB. Raising the Speed Limit for β‑Hairpin Formation. Journal Of The American Chemical Society 2012, 134: 14476-14482. PMID: 22873643, PMCID: PMC3443077, DOI: 10.1021/ja3046734.Peer-Reviewed Original Research