2023
Identification of Efflux Substrates Using a Riboswitch-Based Reporter in Pseudomonas aeruginosa
Urdaneta-Páez V, Hamchand R, Anthony K, Crawford J, Sutherland A, Kazmierczak B. Identification of Efflux Substrates Using a Riboswitch-Based Reporter in Pseudomonas aeruginosa. MSphere 2023, 8: e00069-23. PMID: 36946743, PMCID: PMC10117056, DOI: 10.1128/msphere.00069-23.Peer-Reviewed Original ResearchConceptsLiquid chromatography-mass spectrometryCompound uptakeHigh-resolution liquid chromatography-mass spectrometryChromatography-mass spectrometryNovel antibioticsHigh-throughput screeningRational designMore rational designChemical librariesDiverse compoundsInitial hitsSelect compoundsPermeable compoundsDrug candidatesCompoundsStructural propertiesBacterial cellsPowerful methodAntifolate drugsSubstrateSpectrometrySynthesisPseudomonas aeruginosaClasses of antibioticsMembraneDecellularization compromises mechanical and structural properties of the native trachea
Greaney A, Ramachandra A, Yuan Y, Korneva A, Humphrey J, Niklason L. Decellularization compromises mechanical and structural properties of the native trachea. Biomaterials And Biosystems 2023, 9: 100074. PMID: 36967724, PMCID: PMC10036236, DOI: 10.1016/j.bbiosy.2023.100074.Peer-Reviewed Original ResearchMechanical behaviorGraft failureNative tracheaMechanical failureTissue engineering technologyDepletion of proteoglycansAirway narrowingAirway replacementClinical interventionsWestern blotTracheaMajor causeTracheal graftsEngineering technologyHistological stainingTracheal replacementDifferent decellularization protocolsSignificant differencesClinical implantationTissue repairCollagen IStructural deteriorationStructural propertiesDecellularization protocolGreat potential
2021
Chemsearch: collaborative compound libraries with structure-aware browsing
Gaffney S, Smaga S, Schepartz A, Townsend J. Chemsearch: collaborative compound libraries with structure-aware browsing. Bioinformatics Advances 2021, 1: vbab008. PMID: 36700113, PMCID: PMC9710581, DOI: 10.1093/bioadv/vbab008.Peer-Reviewed Original ResearchAccess controlServer applicationsWeb applicationDocker imageSource codeData storageEasy navigationRapid deploymentData filesCompound librariesCompounds of interestChemical compound librariesBrowsingLibraryNavigationSimilar compoundsDeploymentFilesApplicationsStructural propertiesImagesCompoundsImplementationCodeDocuments
2009
Reversible Visible-Light Photooxidation of an Oxomanganese Water-Oxidation Catalyst Covalently Anchored to TiO2 Nanoparticles
Li G, Sproviero EM, McNamara WR, Snoeberger RC, Crabtree RH, Brudvig GW, Batista VS. Reversible Visible-Light Photooxidation of an Oxomanganese Water-Oxidation Catalyst Covalently Anchored to TiO2 Nanoparticles. The Journal Of Physical Chemistry B 2009, 114: 14214-14222. PMID: 19924873, DOI: 10.1021/jp908925z.Peer-Reviewed Original ResearchPolynuclear transition metal complexesWater oxidation catalystsTransition metal complexesArtificial photosynthetic assembliesVisible-light photoexcitationInterfacial electron transferOxidation chemistryPhotosynthetic assembliesWater oxidationHomogeneous catalystsElectron transferEPR spectroscopyCharge separationManganese compoundsAmide bondCovalent attachmentVisible lightTiO2 nanoparticlesPhotocatalytic devicesNanoparticlesElectron scavengerInexpensive materialsElectron acceptorOxidative conditionsStructural propertiesThe MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules
Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynthesis Research 2009, 102: 455-470. PMID: 19633920, PMCID: PMC2954272, DOI: 10.1007/s11120-009-9467-6.Peer-Reviewed Original ResearchConceptsElectrostatic interactionsMM methodQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsForce fieldQM/MM hybrid methodsQM/MM methodologyQM/MM methodsMolecular mechanics force fieldQuantum chemistry techniquesMM force fieldsStructural refinementPhotosystem IIChemistry techniquesStructure/function relationsCharge transferQM layerMolecular fragmentsChemical modificationBiological macromoleculesSteric hindranceComputational protocolSpectroscopic dataMolecular domainsStructural propertiesHigh-resolution spectroscopic data
2007
Multi-Lamellar and Multi-Axial Maturation of Cell-Seeded Fiber-Reinforced Tissue Engineered Constructs
Baker B, O’Connell G, Sen S, Nathan A, Elliott D, Mauck R. Multi-Lamellar and Multi-Axial Maturation of Cell-Seeded Fiber-Reinforced Tissue Engineered Constructs. 2007, 1013-1014. DOI: 10.1115/sbc2007-176434.Peer-Reviewed Original ResearchFunctional tissue engineeringLength scalesLaminate structureCompressive loadingMultiple length scalesTensile deformationTensile propertiesCircumferential tensile propertiesTissue engineeringCentimeter length scalesFiber directionTransverse directionRadial tie fibersMechanical environmentKnee meniscusNanoscale interactionsAdjacent layersStructural propertiesCell patterningMechanical functionHorizontal axisAnnulus fibrosusMeniscusDeformationProperties
1996
Steady-State Characterization of Systems with Moiety-Conservations Made Easy: Matrix Equations of Metabolic Control Analysis and Biochemical System Theory
Cascante M, Puigjaner J, Kholodenko B. Steady-State Characterization of Systems with Moiety-Conservations Made Easy: Matrix Equations of Metabolic Control Analysis and Biochemical System Theory. Journal Of Theoretical Biology 1996, 178: 1-6. DOI: 10.1006/jtbi.1996.0001.Peer-Reviewed Original ResearchMatrix equationBiochemical systems theorySingle matrix inversionLocal propertiesMatrix inversionSystems theoryLink matrixMetabolic control analysisControl propertiesEquationsMoiety conservationSensitivity theoryControl analysisTheoryStructural propertiesMatrixPropertiesState characterizationInversion
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