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
2017
Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing
Reid KA, Davis CM, Dyer RB, Kindt JT. Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing. Biochimica Et Biophysica Acta (BBA) - Biomembranes 2017, 1860: 792-800. PMID: 29291379, PMCID: PMC5780206, DOI: 10.1016/j.bbamem.2017.12.019.Peer-Reviewed Original ResearchConceptsΒ-hairpin peptidesSVS-1POPC/POPG bilayersPOPC bilayersAtomistic molecular dynamics simulationsLipid bilayersInfluence of electrostaticsLipid bilayer surfaceMolecular dynamics simulationsCircular dichroism studiesCHARMM C36DPPG lipidsMixture of DPPCPOPG bilayersSpectroscopic studiesTail packingBilayer surfaceHydrophobic interactionsForce fieldHeadgroup packingTransient foldingDPPC bilayersDichroism studiesDynamics simulationsFluorescent peptides
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