2002
Modular Response Analysis of Cellular Regulatory Networks
BRUGGEMAN F, WESTERHOFF H, HOEK J, KHOLODENKO B. Modular Response Analysis of Cellular Regulatory Networks. Journal Of Theoretical Biology 2002, 218: 507-520. PMID: 12384053, DOI: 10.1006/jtbi.2002.3096.Peer-Reviewed Original ResearchConceptsRegulatory networksMitogen-activated protein kinase cascadeEpidermal growth factor receptor (EGFR) networkGrowth factor receptor networkProtein kinase cascadeIntermodular interactionsCellular regulatory networksModular Response AnalysisIntracellular regulatory networksAmmonium assimilationKinase cascadeMolecular biological analysisGenetic circuitsInteraction mapSignal transducingEscherichia coliReceptor networkModular organizationMolecular interactionsBiological analysisSignal transferColiTransducingRegulationInteraction
1999
Live control of the living cell
van Heeswijk W, Bakker B, Teusink B, Kholodenko B, Somsen O, Snoep J, Westerhoff H. Live control of the living cell. Biochemical Society Transactions 1999, 27: 261-264. PMID: 10093744, DOI: 10.1042/bst0270261.Peer-Reviewed Original Research
1998
Implications of macromolecular crowding for signal transduction and metabolite channeling
Rohwer J, Postma P, Kholodenko B, Westerhoff H. Implications of macromolecular crowding for signal transduction and metabolite channeling. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 10547-10552. PMID: 9724740, PMCID: PMC27931, DOI: 10.1073/pnas.95.18.10547.Peer-Reviewed Original ResearchMeSH KeywordsCell-Free SystemEscherichia coliKineticsModels, BiologicalPhosphoenolpyruvate Sugar Phosphotransferase SystemSignal TransductionConceptsPhosphotransferase systemMacromolecular crowdingFlux response coefficientsCarbohydrate phosphotransferase systemGlucose phosphotransferase systemBacterial phosphoenolpyruvateSignal transductionMetabolite channelingCell-free extractsProtein concentrationEnzyme complexCarbohydrate phosphorylationPEG 6000 concentrationPolyethylene glycol 6000Total enzyme concentrationHigh protein concentrationsEscherichia coliLow protein concentrationsForm complexesGroup-transfer pathwaysMetabolic behaviorPEG 6000Crowded environmentsSubtleties in control by metabolic channelling and enzyme organization
Kholodenko B, Rohwer J, Cascante M, Westerhoff H. Subtleties in control by metabolic channelling and enzyme organization. Molecular And Cellular Biochemistry 1998, 184: 311-320. PMID: 9746327, DOI: 10.1023/a:1006809028612.Peer-Reviewed Original ResearchConceptsPhosphotransferase systemMetabolic control analysisBacterial phosphotransferase systemEnzyme-enzyme associationsDirect metabolite transferEnzyme organizationConcomitant phosphorylationTernary complex formationPTS pathwayMetabolite transferEnzyme sequestrationMetabolic channellingLiving cellsMacromolecular crowdingPhosphoryl groupEnzyme controlTernary complexCell functionPathwayEnzymeComplex formationIdeal systemEnzyme control coefficientsMetabolic systemsControl coefficients
1995
Molecular biology for flux control
Jensen P, Snoep J, Molenaar D, van Heeswijk W, Kholodenko B, van der Gugten A, Westerhoff H. Molecular biology for flux control. Biochemical Society Transactions 1995, 23: 367-370. PMID: 7672396, DOI: 10.1042/bst0230367.Peer-Reviewed Original Research
1993
The sum of the control coefficients of all enzymes on the flux through a group‐transfer pathway can be as high as two
van DAM K, van der VLAG J, KHOLODENKO B, WESTERHOFF H. The sum of the control coefficients of all enzymes on the flux through a group‐transfer pathway can be as high as two. The FEBS Journal 1993, 212: 791-799. PMID: 8462550, DOI: 10.1111/j.1432-1033.1993.tb17720.x.Peer-Reviewed Original ResearchMeSH KeywordsEnzymesEscherichia coliMathematicsModels, BiologicalPhosphoenolpyruvate Sugar Phosphotransferase SystemSalmonella typhimuriumConceptsGroup-transfer pathwaysReaction activityDissociation rate constantsElectron transfer chainAcceptor couplesEnzyme-enzyme interactionsEnzyme concentrationRate constantsEnzyme-enzyme complexEnzyme interactionsComplexesControl of enzymesEnzyme complexEnzymeConcentrationBacterial phosphoenolpyruvateMain pathwayInteractionConstantsChainControl analysisSimple metabolic pathwaysSugar phosphotransferase system