2024
Kinetic study of membrane protein interactions: from three to two dimensions
Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Scientific Reports 2024, 14: 882. PMID: 38195620, PMCID: PMC10776792, DOI: 10.1038/s41598-023-50827-5.Peer-Reviewed Original ResearchConceptsMembrane proteinsMembrane protein interactionsProtein-protein interactionsProtein complexesProtein interactionsMembrane environmentOpposite membranesBacterial efflux pumpsProtein behaviorProtein systemsMolecular interactionsEfflux pumpsProteinExploration distanceMembraneFluorescence recovery experimentsInteractionBinding rateBinding constantsComplexes
2023
Membrane Tubulation with a Biomembrane Force Probe
Pincet L, Pincet F. Membrane Tubulation with a Biomembrane Force Probe. Membranes 2023, 13: 910. PMID: 38132914, PMCID: PMC10744658, DOI: 10.3390/membranes13120910.Peer-Reviewed Original ResearchBiomembrane force probeOptical tweezersForce probeTweezersGiant unilamellar vesiclesMeasurement of forcesExperimental setupMicromanipulation techniqueUnilamellar vesiclesProbeSimilar tubesMaterial transportLocal geometryHigh curvatureMicromanipulationMolecular interactionsGUVsSetupEnergeticsInteractionMeasurementsFormationTubeNanospringsMolecular insights into the force-from-lipids gating of mechanosensitive channels
Bavi N, Cox C, Nikolaev Y, Martinac B. Molecular insights into the force-from-lipids gating of mechanosensitive channels. Current Opinion In Physiology 2023, 36: 100706. DOI: 10.1016/j.cophys.2023.100706.Peer-Reviewed Original ResearchMS channel gatingChannel gatingLipid bilayersMechanosensitive ion channelsLipid principleMechanosensitive channelsChannel proteinsPhysiological processesMolecular underpinningsMolecular insightsMembrane tensionIon channelsMolecular interactionsMechanical forcesCurrent understandingBilayer thinningNew insightsGatingBilayersBlood pressure regulationProteinRegulationInsightsCellsPressure regulationReframing macrophage diversity with network motifs
Pizzurro G, Miller-Jensen K. Reframing macrophage diversity with network motifs. Trends In Immunology 2023, 44: 965-970. PMID: 37949786, PMCID: PMC11057955, DOI: 10.1016/j.it.2023.10.009.Commentaries, Editorials and LettersConceptsNetwork motifsDistinct biological functionsSystems biology conceptsMacrophage stateMacrophage responseBiological functionsMacrophage diversityExtracellular networkMacrophage activationDisease contextsMotifLocal molecular interactionsMolecular interactionsFunctional modulesBiology conceptsDiversityActivationTissueIntracellularResponseModeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels
Shen Q, Feng Q, Wu C, Xiong Q, Tian T, Yuan S, Shi J, Bedwell G, Yang R, Aiken C, Engelman A, Lusk C, Lin C, Xiong Y. Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nature Structural & Molecular Biology 2023, 30: 425-435. PMID: 36807645, PMCID: PMC10121901, DOI: 10.1038/s41594-023-00925-9.Peer-Reviewed Original ResearchConceptsNuclear pore complexHIV-1 nuclear entryNuclear entryNuclear importNPC central channelPore complexHost nucleusCapsid dockingVirus genomeAffinity gradientNup153Central channelMechanistic insightsMolecular interactionsCapsidNucleoporinsNup358Nup62GenomeNucleusVirusDockingVirus-1 infectionImportComplexes
2022
TOP1-DNA Trapping by Exatecan and Combination Therapy with ATR Inhibitor.
Jo U, Murai Y, Agama KK, Sun Y, Saha LK, Yang X, Arakawa Y, Gayle S, Jones K, Paralkar V, Sundaram RK, Van Doorn J, Vasquez JC, Bindra RS, Choi WS, Pommier Y. TOP1-DNA Trapping by Exatecan and Combination Therapy with ATR Inhibitor. Molecular Cancer Therapeutics 2022, 21: 1090-1102. PMID: 35439320, PMCID: PMC9256811, DOI: 10.1158/1535-7163.mct-21-1000.Peer-Reviewed Original ResearchConceptsATR inhibitorsTop1 inhibitorsHomologous recombination deficiencyNovel molecular interactionApoptotic cell deathCancer cellsTop1 cleavage complexesAtaxia telangiectasiaCleavage complexesCell deathDNA damageHigher DNA damageMolecular interactionsDNA baseKinase inhibitorsI inhibitorMolecular pharmacologyMouse xenograftsTOP1Recombination deficiencyTopoisomerase I inhibitorInhibitorsTumor growthRad3Predictive biomarkers
2020
Interactions Between Ticks and Lyme Disease Spirochetes.
Pal U, Kitsou C, Drecktrah D, Yaş ÖB, Fikrig E. Interactions Between Ticks and Lyme Disease Spirochetes. Current Issues In Molecular Biology 2020, 42: 113-144. PMID: 33289683, PMCID: PMC8045411, DOI: 10.21775/cimb.042.113.Peer-Reviewed Original ResearchConceptsComplex enzootic life cycleEnzootic life cycleMammalian reservoir hostsMolecular interactionsLife cycleDiscrete molecular interactionsVariety of animalsRelated ticksVertebrate hostsLyme disease spirocheteArthropod vectorsSensu latoPathogen persistenceWild rodentsBacterial pathogensReservoir hostsCritical roleTick-transmitted infectionsMain vectorNortheastern United StatesPast discoveriesHostTicksArthropodsSpirochetesQuantitative Proteomic Analysis of Chikungunya Virus-Infected Aedes aegypti Reveals Proteome Modulations Indicative of Persistent Infection
Cui Y, Liu P, Mooney BP, Franz AWE. Quantitative Proteomic Analysis of Chikungunya Virus-Infected Aedes aegypti Reveals Proteome Modulations Indicative of Persistent Infection. Journal Of Proteome Research 2020, 19: 2443-2456. PMID: 32375005, PMCID: PMC7419016, DOI: 10.1021/acs.jproteome.0c00173.Peer-Reviewed Original ResearchConceptsSerine-type endopeptidasesMetabolism related pathwaysQuantitative proteomic analysisFunctional enrichment analysisChikungunya virusRibosome biogenesisLabel-free quantificationRNA machineryNonpathogenic relationshipsNovel proteinProteome modulationProteomic analysisVesicular transportEnrichment analysisCHIKV infectionOxidative phosphorylationBiological pathwaysRelated pathwaysMass spectrometry dataPresence of CHIKVProteinMosquito samplesProteomeOral acquisitionMolecular interactions
2018
Network Analysis as a Grand Unifier in Biomedical Data Science
McGillivray P, Clarke D, Meyerson W, Zhang J, Lee D, Gu M, Kumar S, Zhou H, Gerstein M. Network Analysis as a Grand Unifier in Biomedical Data Science. Annual Review Of Biomedical Data Science 2018, 1: 1-28. DOI: 10.1146/annurev-biodatasci-080917-013444.Peer-Reviewed Original Research
2016
Surface 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
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
Woo J, Shimoni Y, Yang W, Subramaniam P, Iyer A, Nicoletti P, Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell B, Bansal M, Califano A. Elucidating Compound Mechanism of Action by Network Perturbation Analysis. Cell 2015, 162: 441-451. PMID: 26186195, PMCID: PMC4506491, DOI: 10.1016/j.cell.2015.05.056.Peer-Reviewed Original ResearchConceptsGenome-wide identificationRegulatory network analysisBind target proteinsCompound's mechanism of actionNovel proteinsTarget proteinsCompound perturbationGlobal dysregulationSmall molecule compoundsCompound similarityProteinNetwork-based approachRepair activityMolecular interactionsTested compoundsCompoundsMechanism of actionNetwork analysisCompound analysisActivity modulationAnticancer drugsCompound efficacyPerturbation profilesSimilarityEffectorCoilin: The first 25 years
Machyna M, Neugebauer KM, Staněk D. Coilin: The first 25 years. RNA Biology 2015, 12: 590-596. PMID: 25970135, PMCID: PMC4615369, DOI: 10.1080/15476286.2015.1034923.Peer-Reviewed Original ResearchChapter 5 Molecular Events at Tissue–Biomaterial Interface
Kyriakides T. Chapter 5 Molecular Events at Tissue–Biomaterial Interface. 2015, 81-116. DOI: 10.1016/b978-0-12-800196-7.00005-0.Peer-Reviewed Original ResearchMolecular eventsIntracellular molecular pathwaysInteraction of proteinsKey inflammatory cell typeProduction of signalsAssociated proteinsProtein altersAltered conformationTissue-biomaterial interfaceConformational changesCell adhesionMolecular pathwaysCell typesProteinProteinaceous coatingsCell functionMolecular interactionsCell receptorCurrent understandingBiomaterial interactionsMatrix depositionActivationEventual encapsulationResident cellsCells
2014
Cell fate regulation during preimplantation development: A view of adhesion-linked molecular interactions
Sozen B, Can A, Demir N. Cell fate regulation during preimplantation development: A view of adhesion-linked molecular interactions. Developmental Biology 2014, 395: 73-83. PMID: 25176042, DOI: 10.1016/j.ydbio.2014.08.028.Peer-Reviewed Original ResearchConceptsCell fate regulationEarly mammalian embryoFate regulationCell fate specificationMammalian embryosJunctional complexesEvaluate transcriptional differencesTranscriptional networksFate specificationCell polarityIntercellular junctional complexesPreimplantation developmentCellular diversificationTranscriptional differencesDiversification processEmbryonic lineagesEarly embryosCell adhesionDevelopmental processesEarly morphogenesisLineage commitmentIdentical cellsCell positionMolecular interactionsCellsMolecular Mechanism of Selective Binding of Peptides to Silicon Surface
Ramakrishnan SK, Martin M, Cloitre T, Firlej L, Gergely C. Molecular Mechanism of Selective Binding of Peptides to Silicon Surface. Journal Of Chemical Information And Modeling 2014, 54: 2117-2126. PMID: 24936969, DOI: 10.1021/ci500260v.Peer-Reviewed Original ResearchConceptsMaterial-specific peptidesAdsorption energy calculationsExtensive recent research effortsInorganic surfacesAffinity of peptidesAdsorption mechanismPeptide conformationEnergy calculationsSelective bindingMolecular interactionsAmino acidsN-type silicon semiconductorSilicon surfacePeptide sequencesConformationAcidPeptidesAffinitySurfacePhage display technologySilicon semiconductorsRecent research effortsIndividual amino acidsDisplay technologyScanning analysisStructure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers
Opatowsky Y, Lax I, Tomé F, Bleichert F, Unger VM, Schlessinger J. Structure, domain organization, and different conformational states of stem cell factor-induced intact KIT dimers. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 1772-1777. PMID: 24449920, PMCID: PMC3918759, DOI: 10.1073/pnas.1323254111.Peer-Reviewed Original ResearchConceptsExtracellular regionConformational statesIg-like domainsReceptor tyrosine kinasesDifferent conformational statesTrans autophosphorylationTyrosine kinase domainMembrane-proximal Ig-like domainsTrans phosphorylationAutophosphorylation sitesDomain organizationKinase domainCytoplasmic regionHomotypic interactionsKinase activityReceptor dimersDimeric receptorTyrosine kinaseAsymmetric arrangementMolecular interactionsPrevalent conformationsCrystal structureAutophosphorylationDimersKinase
2013
Competing molecular interactions of aPKC isoforms regulate neuronal polarity
Parker SS, Mandell EK, Hapak SM, Maskaykina IY, Kusne Y, Kim JY, Moy JK, St. John PA, Wilson JM, Gothard KM, Price TJ, Ghosh S. Competing molecular interactions of aPKC isoforms regulate neuronal polarity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 14450-14455. PMID: 23940317, PMCID: PMC3761571, DOI: 10.1073/pnas.1301588110.Peer-Reviewed Original ResearchConceptsAtypical protein kinase CNeuronal polarityAPKC isoformsProtein kinase CCell polarityPolarized neuronsAlternative transcriptsKinase CPar3Supernumerary axonsIsoformsEmbryonic hippocampal neuronsMolecular interactionsOverexpressionPresumptive axonsMolecular modelHippocampal neuronsPolarityPKMTranscriptsRegulatorIntermolecular competitionInteractsNeuronsDisruptsInnovations of the Rule-Based Modeling Approach
Chylek L, Stites E, Posner R, Hlavacek W. Innovations of the Rule-Based Modeling Approach. 2013, 273-300. DOI: 10.1007/978-94-007-6803-1_9.Peer-Reviewed Original ResearchRule-based modeling approachRule-based modelProtein-protein interactionsCell engineering applicationsCell signaling systemsCell signaling mechanismsDynamics of molecular interactionsPhosphoproteomic dataRule-based approachSignaling mechanismsRule-basedSignaling systemCellular levelNetwork generationMolecular interactionsTraditional approachesNetworkModeling approachCellsReaction networkRulesModeling chemical kineticsSpecies
2009
Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function
Pawlicki JM, Steitz JA. Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function. Trends In Cell Biology 2009, 20: 52-61. PMID: 20004579, PMCID: PMC2821161, DOI: 10.1016/j.tcb.2009.10.004.Peer-Reviewed Original ResearchConceptsMature messenger RNAGene expressionRNA polymerase II transcriptsProtein-coding genesPolymerase II transcriptsRNA polymerase IIMessenger RNAPre-messenger RNARNA processing reactionsCotranscriptional eventsPolymerase IIProcessing eventsProcessing reactionsExtensive molecular interactionsEarly stepsTranscriptsRNAExquisite couplingMolecular interactionsMicroRNAsExpressionNuclear networkCrucial roleFinal fateSplicingUnderstanding Modularity in Molecular Networks Requires Dynamics
Alexander RP, Kim PM, Emonet T, Gerstein MB. Understanding Modularity in Molecular Networks Requires Dynamics. Science Signaling 2009, 2: pe44. PMID: 19638611, PMCID: PMC4243459, DOI: 10.1126/scisignal.281pe44.Peer-Reviewed Original ResearchConceptsMolecular networksBiological networksMolecular network analysisAnalysis of modularityCellular machinesMolecular partsSystems biologyFunctional analysisGenome sequencingCellular behaviorCollective functionsMolecular interactionsSmall moleculesNetwork analysisRecent advancesIntense researchBiologyFundamental goalSequencingMajor advancesMoleculesInteractionIsolationModularity
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