2003
Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law
Peletier M, Westerhoff H, Kholodenko B. Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. Journal Of Theoretical Biology 2003, 225: 477-487. PMID: 14615206, DOI: 10.1016/s0022-5193(03)00289-3.Peer-Reviewed Original ResearchConceptsMetabolic control analysisMembrane transportKinase/phosphatase systemCellular reaction networksIntracellular signaling pathwaysProtein networkIntracellular transportPhosphatase systemSignaling pathwaysControl coefficientsCell sizeSpherical cellsClassical metabolic control analysisActive mechanismProtein
2002
Control Analysis for Autonomously Oscillating Biochemical Networks
Reijenga K, Westerhoff H, Kholodenko B, Snoep J. Control Analysis for Autonomously Oscillating Biochemical Networks. Biophysical Journal 2002, 82: 99-108. PMID: 11751299, PMCID: PMC1302452, DOI: 10.1016/s0006-3495(02)75377-0.Peer-Reviewed Original ResearchConceptsSummation theoremYeast glycolytic oscillationsLimit cycle oscillationsDynamic systemsControl coefficientsBiochemical networksCycle oscillationsOscillatory propertiesControl analysisMetabolic control analysisTheoremGlycolytic oscillationsTime domainOscillationsModel outputDiscrete Fourier transformFrequency domainSteady stateData setsQualitative way
2000
Cellular information transfer regarded from a stoichiometry and control analysis perspective
Schuster S, Kholodenko B, Westerhoff H. Cellular information transfer regarded from a stoichiometry and control analysis perspective. Biosystems 2000, 55: 73-81. PMID: 10745111, DOI: 10.1016/s0303-2647(99)00085-4.Peer-Reviewed Original ResearchEngineering a Living Cell to Desired Metabolite Concentrations and Fluxes: Pathways with Multifunctional Enzymes
Kholodenko B, Westerhoff H, Schwaber J, Cascante M. Engineering a Living Cell to Desired Metabolite Concentrations and Fluxes: Pathways with Multifunctional Enzymes. Metabolic Engineering 2000, 2: 1-13. PMID: 10935931, DOI: 10.1006/mben.1999.0132.Peer-Reviewed Original ResearchConceptsMultifunctional enzymeRest of metabolismMetabolic engineeringMetabolic control analysisCellular pathwaysCellular metabolismMolecular geneticsCellular enzymesLiving cellsEnzymeMetabolismPathwayGeneticsMachineryMetabolic patternsEnzyme concentrationSingle intermediateModulationCellsMetabolite concentrationsPatterns
1998
Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes
Kholodenko B, Cascante M, Hoek J, Westerhoff H, Schwaber J. Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes. Biotechnology And Bioengineering 1998, 59: 239-247. PMID: 10099334, DOI: 10.1002/(sici)1097-0290(19980720)59:2<239::aid-bit11>3.0.co;2-9.Peer-Reviewed Original ResearchSubtleties 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 coefficientsSubtleties 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. Developments In Molecular And Cellular Biochemistry 1998, 311-320. DOI: 10.1007/978-1-4615-5653-4_20.Peer-Reviewed Original ResearchPhosphotransferase 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 coefficientsThermodynamics of complexity. The live cell
Westerhoff H, Jensen P, Snoep J, Kholodenko B. Thermodynamics of complexity. The live cell. Thermochimica Acta 1998, 309: 111-120. DOI: 10.1016/s0040-6031(97)00353-5.Peer-Reviewed Original ResearchNonequilibrium thermodynamicsNear-equilibrium assumptionsNonequilibrium systemsSingle moleculesControl theoremBehavior of systemsControl coefficientsIdeal gas mixtureMetabolic control analysisIndividual moleculesMacroscopic propertiesChemical systemsThermodynamic conceptsMolecular propertiesThermodynamicsEmergent propertiesFree energyControl analysisMoleculesTheoremLiving cellsGas mixtureBiological components
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
1995
Defining control coefficients in non-ideal metabolic pathways
Kholodenko B, Molenaar D, Schuster S, Heinrich R, Westerhoff H. Defining control coefficients in non-ideal metabolic pathways. Biophysical Chemistry 1995, 56: 215-226. PMID: 17023325, DOI: 10.1016/0301-4622(95)00039-z.Peer-Reviewed Original ResearchMetabolic pathwaysFlux control coefficientsHigh enzyme concentrationsMetabolic control analysisBiochemical pathwaysElemental stepsMetabolite channellingMetabolic channellingRelevant pathwaysEnzyme activityPathwayEnzymeControl coefficientsEnzyme concentrationMoiety-conserved cyclesEqual modulationsSpeciesReverse rateElemental processesModulationActivity
1994
How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox.
Snoep J, Jensen P, Groeneveld P, Molenaar D, Kholodenko B, Westerhoff H. How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox. IUBMB Life 1994, 33: 1023-32. PMID: 7987249.Peer-Reviewed Original Research