2019
The EGFR Exon 19 Mutant L747-A750>P Exhibits Distinct Sensitivity to Tyrosine Kinase Inhibitors in Lung Adenocarcinoma
Truini A, Starrett JH, Stewart T, Ashtekar K, Walther Z, Wurtz A, Lu D, Park JH, DeVeaux M, Song X, Gettinger S, Zelterman D, Lemmon MA, Goldberg SB, Politi K. The EGFR Exon 19 Mutant L747-A750>P Exhibits Distinct Sensitivity to Tyrosine Kinase Inhibitors in Lung Adenocarcinoma. Clinical Cancer Research 2019, 25: 6382-6391. PMID: 31182434, PMCID: PMC6825535, DOI: 10.1158/1078-0432.ccr-19-0780.Peer-Reviewed Original ResearchThermodynamics of the S 2 -to-S 3 state transition of the oxygen-evolving complex of photosystem II
Amin M, Kaur D, Yang KR, Wang J, Mohamed Z, Brudvig GW, Gunner MR, Batista V. Thermodynamics of the S 2 -to-S 3 state transition of the oxygen-evolving complex of photosystem II. Physical Chemistry Chemical Physics 2019, 21: 20840-20848. PMID: 31517382, DOI: 10.1039/c9cp02308a.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexD1-E189Water/hydroxide moleculeOxygen evolution reactionWater/hydroxidePhotosystem IIVan der WaalsRedox isomersAdditional hydroxideHydroxide moleculeCatalytic intermediatesElectrostatic interactionsProton lossCoordination shellDer WaalsSerial femtosecond crystallographyHydroxide additionHydroxideConformational changesFree electron laser measurementXFEL structureAdditional oxygenMn4IntermediatesFemtosecond crystallography
2018
Artemether-lumefantrine dosing for malaria treatment in young children and pregnant women: A pharmacokinetic-pharmacodynamic meta-analysis
Kloprogge F, Workman L, Borrmann S, Tékété M, Lefèvre G, Hamed K, Piola P, Ursing J, Kofoed PE, Mårtensson A, Ngasala B, Björkman A, Ashton M, Hietala S, Aweeka F, Parikh S, Mwai L, Davis TME, Karunajeewa H, Salman S, Checchi F, Fogg C, Newton PN, Mayxay M, Deloron P, Faucher JF, Nosten F, Ashley EA, McGready R, van Vugt M, Proux S, Price RN, Karbwang J, Ezzet F, Bakshi R, Stepniewska K, White NJ, Guerin PJ, Barnes KI, Tarning J. Artemether-lumefantrine dosing for malaria treatment in young children and pregnant women: A pharmacokinetic-pharmacodynamic meta-analysis. PLOS Medicine 2018, 15: e1002579. PMID: 29894518, PMCID: PMC5997317, DOI: 10.1371/journal.pmed.1002579.Peer-Reviewed Original ResearchConceptsPregnant womenArtemether-lumefantrineCure rateClinical studiesYoung childrenCurrent standard treatment regimenUncomplicated Plasmodium falciparum malariaPharmacokinetic modelAbsorption of lumefantrinePre-treatment parasitaemiaVenous plasma dataAlternative dosing regimensPlasmodium falciparum malariaStandard treatment regimenProspective clinical studyNon-pregnant adultsLow cure ratePopulation pharmacokinetic modelRelevant clinical studiesUseful therapeutic lifeFrequency of dosingConcentration-time dataHigher individual dosesLumefantrine exposureLumefantrine levelsβ‑Lactam Biotransformations Activate Innate Immunity
Oh J, Patel J, Park HB, Crawford JM. β‑Lactam Biotransformations Activate Innate Immunity. The Journal Of Organic Chemistry 2018, 83: 7173-7179. PMID: 29616809, DOI: 10.1021/acs.joc.8b00241.Peer-Reviewed Original ResearchConceptsHuman microbiota compositionImmune responseImmune functionMicrobiota compositionInnate immunityBroad immunomodulatory mechanismPatient's immune responseClinical trial studyCommon resistance determinantsMicrobiome-dependent mannerImmunomodulatory mechanismsNF-κBTrial studyBacterial infectionsImmunomodulatory interactionsMinimal long-term impactAntibioticsΒ-lactamaseAmoxicillinHuman leukemic monocytesLeukemic monocytesResistance determinantsBiotransformation productsImmunityMolecular mechanisms
2017
Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima
An JY, Sharif H, Kang GB, Park KJ, Lee JG, Lee S, Jin MS, Song JJ, Wang J, Eom SH. Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima. Biochemical And Biophysical Research Communications 2017, 495: 1201-1207. PMID: 29180014, DOI: 10.1016/j.bbrc.2017.11.158.Peer-Reviewed Original ResearchConceptsPeriplasmic domainMisfolded membrane proteinsATP-dependent proteaseMembrane protein complexesResolution crystal structureHydrophobic membrane environmentMembrane homeostasisProtein complexesMembrane proteinsTransmembrane proteinMembrane environmentThermotoga maritimaStructural insightsFtsHProtease domainToxic proteinsProteinOligomerizationHigh energetic barrierDomainTranslocatesEnergetic barrierMaritimaHomeostasisCrystal structureHow 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
2016
Different modes of variation for each BG lineage suggest different functions
Chattaway J, Ramirez-Valdez R, Chappell P, Caesar J, Lea S, Kaufman J. Different modes of variation for each BG lineage suggest different functions. Open Biology 2016, 6: 160188. PMID: 27628321, PMCID: PMC5043582, DOI: 10.1098/rsob.160188.Peer-Reviewed Original ResearchConceptsComplementarity-determining region 1BG genesGenomic locationsSequence cassettesSequence diversityChromosome 2Phenotypic variationLipid bindingIntracellular regionImmunoglobulin variableAllelic polymorphismPolymorphic residuesImmune defenceGenesT cellsRegion 1ButyrophilinBG1Co-inhibitionTissue distributionDiversityImmune systemChromosomeHomologuesCDR2Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces
Levine ZA, Rapp MV, Wei W, Mullen RG, Wu C, Zerze GH, Mittal J, Waite JH, Israelachvili JN, Shea JE. Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 4332-4337. PMID: 27036002, PMCID: PMC4843488, DOI: 10.1073/pnas.1603065113.Peer-Reviewed Original ResearchConceptsSelf-assembled monolayersOrganic surfacesHydrophobic self-assembled monolayersReplica exchange molecular dynamics simulationsSurface force measurementsMolecular interactionsFree energy profilesMussel foot proteinsUmbrella sampling simulationsMolecular dynamics simulationsVan der WaalsPeptide adsorptionPeptide adhesionSFA measurementsUnderwater adhesivesAqueous adhesivesDer WaalsSurface forcesDynamics simulationsElectrostatic forcesFoot proteinsProtein analoguesSpecific interactionsAdsorptionAdhesive properties
2015
Accurate Line Shapes from Sub‑1 cm–1 Resolution Sum Frequency Generation Vibrational Spectroscopy of α‑Pinene at Room Temperature
Mifflin A, Velarde L, Ho J, Psciuk B, Negre C, Ebben C, Upshur M, Lu Z, Strick B, Thomson R, Batista V, Wang H, Geiger F. Accurate Line Shapes from Sub‑1 cm–1 Resolution Sum Frequency Generation Vibrational Spectroscopy of α‑Pinene at Room Temperature. The Journal Of Physical Chemistry A 2015, 119: 1292-1302. PMID: 25647092, DOI: 10.1021/jp510700z.Peer-Reviewed Original ResearchMeSH KeywordsBicyclic MonoterpenesModels, ChemicalMolecular Dynamics SimulationMonoterpenesSpectrum AnalysisTemperatureVibrationConceptsVibrational spectroscopySum frequency generation vibrational spectroscopyGeneration vibrational spectroscopySum frequency generation spectraMolecular dynamics calculationsΑ-pineneVibrational energy relaxationSFG spectroscopyRoom temperaturePhase-resolved spectraAccurate line shapesVibrational spectraFourier transformMolecular surfaceHigh spectral resolutionSpectroscopyRaman spectraDynamics calculationsSame moleculeCommon terpenesNew spectroscopyVibrational coherenceEnergy relaxationGeneration spectraSpectral lines
2014
Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions
Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR, Smith AB, Kwong PD, Blanchard SC, Mothes W. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 2014, 346: 759-763. PMID: 25298114, PMCID: PMC4304640, DOI: 10.1126/science.1254426.Peer-Reviewed Original ResearchA hypothesis-driven parametric study of effects of polymeric scaffold properties on tissue engineered neovessel formation
Miller KS, Khosravi R, Breuer CK, Humphrey JD. A hypothesis-driven parametric study of effects of polymeric scaffold properties on tissue engineered neovessel formation. Acta Biomaterialia 2014, 11: 283-294. PMID: 25288519, PMCID: PMC4256111, DOI: 10.1016/j.actbio.2014.09.046.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlood VesselsCompressive StrengthComputer SimulationComputer-Aided DesignElastic ModulusEndothelial CellsEquipment DesignEquipment Failure AnalysisHardnessHumansMaterials TestingModels, ChemicalNeovascularization, PhysiologicPolymersTensile StrengthTissue EngineeringTissue ScaffoldsConceptsScaffold parametersMaterial propertiesScaffold structureParametric studyFibrous scaffoldsScaffold propertiesBurst pressureConstitutive relationsSuture retentionNeotissue developmentTissue engineeringMechanobiological cuesNeovessel developmentFiber diameterNew modeling frameworkExperimental search spaceVascular graftsOptimal combinationPropertiesKey propertiesModeling frameworkParametersNumber of parametersComputational modelNative propertiesHypocoordinated solids in particulate media
Bertrand T, Schreck CF, O'Hern CS, Shattuck MD. Hypocoordinated solids in particulate media. Physical Review E 2014, 89: 062203. PMID: 25019766, DOI: 10.1103/physreve.89.062203.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationFourier AnalysisKineticsModels, ChemicalParticulate MatterTemperatureVibrationConceptsInput kinetic energyInterparticle contactsParticle rearrangementGranular mediaContact forceRepulsive contact forcesParticulate systemsHarmonic responseParticulate mediaDegrees of freedomKinetic energyIsostatic valueAverage contact numberFourier transformFraction deviationSolidsFrictionless disksChloride and Salicylate Influence Prestin-dependent Specific Membrane Capacitance SUPPORT FOR THE AREA MOTOR MODEL* * This work was supported, in whole or in part, by National Institutes of Health Grant NIDCD DC00273 (to J. S. S.).
Santos-Sacchi J, Song L. Chloride and Salicylate Influence Prestin-dependent Specific Membrane Capacitance SUPPORT FOR THE AREA MOTOR MODEL* * This work was supported, in whole or in part, by National Institutes of Health Grant NIDCD DC00273 (to J. S. S.). Journal Of Biological Chemistry 2014, 289: 10823-10830. PMID: 24554714, PMCID: PMC4036195, DOI: 10.1074/jbc.m114.549329.Peer-Reviewed Original Research
2013
Mechanistic Study of the Oxidative Coupling of Styrene with 2‑Phenylpyridine Derivatives Catalyzed by Cationic Rhodium(III) via C–H Activation
Brasse M, Cámpora J, Ellman JA, Bergman RG. Mechanistic Study of the Oxidative Coupling of Styrene with 2‑Phenylpyridine Derivatives Catalyzed by Cationic Rhodium(III) via C–H Activation. Journal Of The American Chemical Society 2013, 135: 6427-6430. PMID: 23590843, PMCID: PMC3677599, DOI: 10.1021/ja401561q.Peer-Reviewed Original ResearchInter-α/β subunits coupling mediating pre-inactivation and augmented activation of BKCa(β2)
Hou P, Zeng W, Gan G, Lv C, Guo X, Zhang Z, Liu H, Wu Y, Yao J, Wei A, Wang S, Ding J. Inter-α/β subunits coupling mediating pre-inactivation and augmented activation of BKCa(β2). Scientific Reports 2013, 3: 1666. PMID: 23588888, PMCID: PMC3627188, DOI: 10.1038/srep01666.Peer-Reviewed Original ResearchCell Shape Can Mediate the Spatial Organization of the Bacterial Cytoskeleton
Wang S, Wingreen NS. Cell Shape Can Mediate the Spatial Organization of the Bacterial Cytoskeleton. Biophysical Journal 2013, 104: 541-552. PMID: 23442905, PMCID: PMC3566457, DOI: 10.1016/j.bpj.2012.12.027.Peer-Reviewed Original ResearchConceptsBacterial cytoskeletonCell shapeCytoskeletal filamentsBacterial cytoskeletal proteinsRod-shaped cellsCytoskeletal proteinsCell wallCytoskeletal polymerizationCytoskeletonSpatial patterningMreBConformational transitionSpatial organizationFilament lengthSame membraneFilamentsMembraneFtsZSpatial patternsChemical energyFilament bendingProteinPatterningProper controlMicrofluidic approach
2012
Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end
Bai H, Kath J, Zörgiebel F, Sun M, Ghosh P, Hatfull G, Grindley N, Marko J. Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 16546-16551. PMID: 23011800, PMCID: PMC3478594, DOI: 10.1073/pnas.1203118109.Peer-Reviewed Original ResearchCholesterol-tethered platinum II-based supramolecular nanoparticle increases antitumor efficacy and reduces nephrotoxicity
Sengupta P, Basu S, Soni S, Pandey A, Roy B, Oh M, Chin K, Paraskar A, Sarangi S, Connor Y, Sabbisetti V, Kopparam J, Kulkarni A, Muto K, Amarasiriwardena C, Jayawardene I, Lupoli N, Dinulescu D, Bonventre J, Mashelkar R, Sengupta S. Cholesterol-tethered platinum II-based supramolecular nanoparticle increases antitumor efficacy and reduces nephrotoxicity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 11294-11299. PMID: 22733767, PMCID: PMC3396529, DOI: 10.1073/pnas.1203129109.Peer-Reviewed Original ResearchConceptsPlatinum-based chemotherapeuticsAntitumor efficacyMurine 4T1 breast cancerEnhanced in vivo antitumor efficacyOvarian cancer modelPlatinum-based agentsPolyethylene glycol)-2000Cisplatin in vitroDesign of active moleculesNanoscale drug delivery vehiclesFrontline therapyReduced nephrotoxicityToxicity profileCancer modelsBreast cancerCoordination environmentRational drug designSupramolecular assembliesNephro-toxicityIncreased efficacySupramolecular nanoparticlesCancer chemotherapeuticsPharmaceutical approachesCholesterol backboneNanoparticle assembliesCalculations of the structure of basin volumes for mechanically stable packings
Ashwin SS, Blawzdziewicz J, O'Hern CS, Shattuck MD. Calculations of the structure of basin volumes for mechanically stable packings. Physical Review E 2012, 85: 061307. PMID: 23005086, DOI: 10.1103/physreve.85.061307.Peer-Reviewed Original ResearchMeSH KeywordsColloidsComputer SimulationModels, ChemicalModels, MolecularMotionParticle SizeRheologyConceptsBasins of attractionMS packingsSystem size increasesFinite numberConfiguration spaceComplex geometric featuresInitial conditionsProfile functionGeometrical propertiesStable packingΓ distributionJammed systemsComputational methodsNovel computational methodSimple modelGeometric featuresFast quench ratesProbabilityComplex structureComputational model systemSmaller core volumeFrictionless particlesBasin volumeQuench rateSize increasesConstraints and vibrations in static packings of ellipsoidal particles
Schreck CF, Mailman M, Chakraborty B, O'Hern CS. Constraints and vibrations in static packings of ellipsoidal particles. Physical Review E 2012, 85: 061305. PMID: 23005084, DOI: 10.1103/physreve.85.061305.Peer-Reviewed Original ResearchConceptsStatic packingsEllipsoidal particlesFinite compressionMechanical propertiesStiffness matrixAspect ratioSpherical particlesHarmonic responseNumber of particlesAmorphous packingsParticlesAmplitude δPotential energy scalesMatrixInterparticle separationCompressionVibrationModePackingContact numberContactJamming
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