2024
Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos
Burke M, Batista V, Davis C. Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos. The Journal Of Physical Chemistry B 2024, 128: 8344-8354. PMID: 39186078, DOI: 10.1021/acs.jpcb.4c02859.Peer-Reviewed Original ResearchForster resonance energy transferProtein-RNA interactionsHigh-resolution microscopySubcellular localizationResonance energy transferSpecialized compartmentsSubcellular analysisMicroscopy dataCellsMolecular populationsCompartmentHigh-resolution microscopy dataMolecular environmentMicroscopy videosDynamic heterogeneityOleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes
Castillo H, Shuster S, Tarekegn L, Davis C. Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes. Chemical Communications 2024, 60: 3138-3141. PMID: 38329230, PMCID: PMC10939124, DOI: 10.1039/d3cc04829b.Peer-Reviewed Original Research
2023
Chemical 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 ResearchSpatiotemporal Heterogeneity of De Novo Lipogenesis in Fixed and Living Single Cells
Shuster S, Burke M, Davis C. Spatiotemporal Heterogeneity of De Novo Lipogenesis in Fixed and Living Single Cells. The Journal Of Physical Chemistry B 2023, 127: 2918-2926. PMID: 36976708, DOI: 10.1021/acs.jpcb.2c08812.Peer-Reviewed Original ResearchConceptsDe novo lipogenesisPanc1 pancreatic cancer cellsPancreatic cancer cellsLipid dropletsType II diabetesGlucose metabolismNovo lipogenesisII diabetesLipid droplet morphologyLiver tissueGlucose uptakeCancer cellsAdipocyte cellsHigh rateLipogenesisDNL ratesCritical metabolic processesAdipocytesMajority of lipidsCellsLipidsBetter preservationObesityDiabetesTriglycerides
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
2021
Cellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation
Davis C, Gruebele M. Cellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation. The Journal Of Physical Chemistry B 2021, 125: 3815-3823. PMID: 33826329, DOI: 10.1021/acs.jpcb.1c00950.Peer-Reviewed Original ResearchConceptsSpliceosomal protein U1APotential binding partnerMajor cellular effectsProtein U1ABinding partnerU1 snRNACellular environmentNonspecific interactionsFörster resonance energy transferProper bindingCellular componentsResonance energy transferU1ALive cellsLarge hydrophobic surface areaMacromolecular crowdingCellular effectsHydrophobic surface areaOS cellsModel systemComplex bindingHigh binding affinityWeak nonspecific interactionsBinding affinitiesCells
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 ResearchNon‐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