2024
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33: e5219. PMID: 39548730, PMCID: PMC11568256, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchMeSH KeywordsFluorescence Resonance Energy TransferMolecular Dynamics SimulationProtein ConformationProteinsConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesProteins in vivoForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesDynamics in vivoStructures in vivoInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAmino
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 peptidesHow 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, InfraredThermodynamics
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