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 PMID: 38800659, PMCID: PMC11118665, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMD simulationsFRET pairsOrganelles
2023
Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions
Sivadas A, McDonald E, Shuster S, Davis C, Plate L. Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions. Advances In Biological Regulation 2023, 90: 100987. PMID: 37806136, PMCID: PMC11108229, DOI: 10.1016/j.jbior.2023.100987.Peer-Reviewed Original ResearchConceptsProtein interactionsProtein-protein interactionsSite-specific crosslinkingSite-specific incorporationMetabolic proteinsRegulated stepProtein assembliesCentral enzymePuncta formationMetabolic fluxHuman cellsInterface 2Amino acidsCytoskeletonLiver isoformCentral roleCompartmentalizationGlycolysisActive siteInteractorsInhibitionInterface 1IsoformsProteinCitrate inhibitionChemical interactions modulate λ6‐85 stability in cells
Knab E, Davis C. Chemical interactions modulate λ6‐85 stability in cells. Protein Science 2023, 32: e4698. PMID: 37313657, PMCID: PMC10288553, DOI: 10.1002/pro.4698.Peer-Reviewed Original Research
2020
Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells
Davis CM, Gruebele M. Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells. Biochemistry 2020, 59: 2650-2659. PMID: 32567840, DOI: 10.1021/acs.biochem.0c00299.Peer-Reviewed Original ResearchConceptsCytoskeletal drugsPhosphoglycerate kinaseActin filamentsDynamic cytoskeletal networksEffects of cytoskeletonProtein energy landscapesOff-target proteinsOpposite responseCytoskeletal networkProtein stabilityCellular milieuProtein-like sequencesVariable major protein-like sequenceOverall cell volumeCytoskeletonCell migrationEnergy landscapeMacromolecular crowdingMacromolecular crowdersProteinNonspecific surface interactionsTarget effectsMicrotubulesCytoplasmCellsAn 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
Cell Volume Controls Protein Stability and Compactness of the Unfolded State
Wang Y, Sukenik S, Davis CM, Gruebele M. Cell Volume Controls Protein Stability and Compactness of the Unfolded State. The Journal Of Physical Chemistry B 2018, 122: 11762-11770. PMID: 30289261, DOI: 10.1021/acs.jpcb.8b08216.Peer-Reviewed Original ResearchSoluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins
Kisley L, Miller K, Davis CM, Guin D, Murphy EA, Gruebele M, Leckband DE. Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins. Biomacromolecules 2018, 19: 3894-3901. PMID: 30064224, DOI: 10.1021/acs.biomac.8b01120.Peer-Reviewed Original ResearchConceptsProtein melting temperatureBiotechnological applicationsSpecific proteinsProtein conformationTryptophan fluorescenceProteinTryptophan residuesThermal denaturation studiesDenaturation studiesCooperativity increasesProtein bindingPSBLocal polarityInteractsResiduesPEG solutionBindingCooperativityConformationFluorescenceNon‐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 newsProteinInteractionLabeling for Quantitative Comparison of Imaging Measurements in Vitro and in Cells
Davis CM, Gruebele M. Labeling for Quantitative Comparison of Imaging Measurements in Vitro and in Cells. Biochemistry 2018, 57: 1929-1938. PMID: 29546761, DOI: 10.1021/acs.biochem.8b00141.Peer-Reviewed Original ResearchConceptsCell biologyComplex dissociation constantsProtein structureBiophysical experimentsModification sitesCell proteinsSuch measurementsQualitative imagingImaging measurementsBiologyCellsPowerful techniqueMeasurementsQuantitative measurementsTarget moleculesDissociation constantsRNAProteinQuantitative comparisonVitroLocalizationConstantsLabelingTarget
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 composition