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 ResearchConceptsForster 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 acidsAminoSimilarity 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 heterogeneityExfoliation of a metal–organic framework enabled by post-synthetic cleavage of a dipyridyl dianthracene ligand
Logelin M, Schreiber E, Mercado B, Burke M, Davis C, Bartholomew A. Exfoliation of a metal–organic framework enabled by post-synthetic cleavage of a dipyridyl dianthracene ligand. Chemical Science 2024, 15: 15198-15204. PMID: 39246333, PMCID: PMC11378025, DOI: 10.1039/d4sc03524k.Peer-Reviewed Original ResearchMetal-organic frameworksZinc metal-organic frameworkStacking axisConductive 2D metal–organic frameworksThree-dimensional MOFsTwo-dimensional (2D) metal-organic frameworksCrystals of 2D materialsStimuli-responsive ligandsSynthetic tunabilityImproved crystal growthTwo-dimensional frameworkStacking directionMacroscopic crystalsDimeric ligandsLigandChemo-sensingCrystal growthStructural analysisNanoscale applicationsDianthraceneStackExfoliationAnthraceneDipyridylIncreasing orderIdentifying 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 pairsOrganellesOleic 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 ResearchOleic acid differentially affects de novo lipogenesis and global lipid levels in hepatocytes
Castillo H, Shuster S, Davis C. Oleic acid differentially affects de novo lipogenesis and global lipid levels in hepatocytes. Biophysical Journal 2024, 123: 411a. DOI: 10.1016/j.bpj.2023.11.2514.Peer-Reviewed Original ResearchTardigrade CAHS hydrogels protect proteins through concentration-dependent mechanism
Barilla M, Shuster S, Davis C. Tardigrade CAHS hydrogels protect proteins through concentration-dependent mechanism. Biophysical Journal 2024, 123: 75a-76a. DOI: 10.1016/j.bpj.2023.11.529.Peer-Reviewed Original ResearchMultispectral vibrational imaging for high resolution tracking of live cell metabolic processes
Shuster S, Castillo H, Davis C. Multispectral vibrational imaging for high resolution tracking of live cell metabolic processes. Biophysical Journal 2024, 123: 449a. DOI: 10.1016/j.bpj.2023.11.2740.Peer-Reviewed Original ResearchInsulin-resistant Huh-7 cells as a model for nonalcoholic fatty liver disease
Tarekegn L, Shuster S, Davis C. Insulin-resistant Huh-7 cells as a model for nonalcoholic fatty liver disease. Biophysical Journal 2024, 123: 411a. DOI: 10.1016/j.bpj.2023.11.2515.Peer-Reviewed Original ResearchStability vs. environmental sensitivity: The importance of protein surface charge adaptations
Knab E, Sternke M, Barrick D, Gruebele M, Davis C. Stability vs. environmental sensitivity: The importance of protein surface charge adaptations. Biophysical Journal 2024, 123: 302a. DOI: 10.1016/j.bpj.2023.11.1874.Peer-Reviewed Original ResearchConnecting simulation and experiment of protein folding inside cells with fast relaxation imaging
Sarker R, Knab E, Davis C. Connecting simulation and experiment of protein folding inside cells with fast relaxation imaging. Biophysical Journal 2024, 123: 31a. DOI: 10.1016/j.bpj.2023.11.284.Peer-Reviewed Original Research
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 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 ResearchSpliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM
Gopan G, Ghaemi Z, Davis C, Gruebele M. Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM. Nucleic Acids Research 2022, 50: 8193-8206. PMID: 35876068, PMCID: PMC9371917, DOI: 10.1093/nar/gkac599.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