2019
Mapping connections in signaling networks with ambiguous modularity
Lill D, Rukhlenko O, Mc Elwee A, Kashdan E, Timmer J, Kholodenko B. Mapping connections in signaling networks with ambiguous modularity. Npj Systems Biology And Applications 2019, 5: 19. PMID: 31149348, PMCID: PMC6533310, DOI: 10.1038/s41540-019-0096-1.Peer-Reviewed Original ResearchConceptsModular Response AnalysisProtein abundanceProtein complexesNetwork reconstructionDownstream modulesRetroactive interactionsUpstream moduleComputational restorationNetwork modulesSuite of methodsAbundanceSuch complexesExperimental approachComplexesProteinEnzymePathwaySequestration effectNetwork responseDifferent modules
2001
Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase
DE ATAURI P, ACERENZA L, KHOLODENKO B, DE LA IGLESIA N, GUINOVART J, AGIUS L, CASCANTE M. Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase. Biochemical Journal 2001, 355: 787-793. PMID: 11311143, PMCID: PMC1221796, DOI: 10.1042/bj3550787.Peer-Reviewed Original ResearchConceptsRegulatory proteinsFlux control coefficientsParadoxical controlHigh flux control coefficientAllosteric enzymePathway fluxHepatic glucokinaseEnzymeEnzyme activitySigmoidal kineticsEnzyme kineticsControl coefficientsProteinEnzyme increasesGlucokinaseHill coefficientSubstrate concentrationEnzyme concentration
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
Subtleties 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 coefficients
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 processesModulationActivityComposite control of cell function: metabolic pathways behaving as single control units
Kholodenko B, Schuster S, Rohwer J, Cascante M, Westerhoff H. Composite control of cell function: metabolic pathways behaving as single control units. FEBS Letters 1995, 368: 1-4. PMID: 7615057, DOI: 10.1016/0014-5793(95)00562-n.Peer-Reviewed Original ResearchHow to reveal various aspects of regulation in group-transfer pathways
Kholodenko B, Westerhoff H. How to reveal various aspects of regulation in group-transfer pathways. Biochimica Et Biophysica Acta (BBA) - Bioenergetics 1995, 1229: 275-289. DOI: 10.1016/0005-2728(95)00013-9.Peer-Reviewed Original ResearchGroup-transfer pathwaysEnzyme-enzyme complexPathway componentsGene expressionMetabolic pathwaysAspects of regulationGenetic modulationSpecific inhibitorSuch inhibitorsEnzyme concentrationNon-competitive inhibitorEnzymeControl coefficientsPathwayIntact systemInhibitorsInhibited enzymeRegulationExpressionDYNAMIC ASPECTS OF CASCADE-TYPE METABOLIC REGULATION
MOLENAAR D, KHOLODENKO B, VAN HEESWIJK W, WESTERHOFF H. DYNAMIC ASPECTS OF CASCADE-TYPE METABOLIC REGULATION. Journal Of Biological System 1995, 3: 187-196. DOI: 10.1142/s0218339095000186.Peer-Reviewed Original ResearchThe macroworld versus the microworld of biochemical regulation and control
Kholodenko B, Westerhoff H. The macroworld versus the microworld of biochemical regulation and control. Trends In Biochemical Sciences 1995, 20: 52-54. PMID: 7701560, DOI: 10.1016/s0968-0004(00)88955-0.Peer-Reviewed Original Research
1994
Control theory of one enzyme
Kholodenko B, Westerhoff H. Control theory of one enzyme. Biochimica Et Biophysica Acta 1994, 1208: 294-305. PMID: 7947961, DOI: 10.1016/0167-4838(94)90116-3.Peer-Reviewed Original ResearchConceptsEnzyme catalytic cycleArbitrary kinetic schemesEnzyme catalyzed reactionsStandard free energy differenceControl of reactionsCatalytic cycleElemental stepsFree energy differenceCatalyzed reactionsFree energy dropForward rate constantElemental transitionsReaction rateEnzyme reactionRate constantsEnergy differenceEnzyme statesKinetic schemeReactionEnzyme cycleSingle enzymeEnzymeStepKineticsConstants
1993
‘Channelled’ pathways can be more sensitive to specific regulatory signals
Kholodenko B, Demin O, Westerhoff H. ‘Channelled’ pathways can be more sensitive to specific regulatory signals. FEBS Letters 1993, 320: 75-78. PMID: 8462681, DOI: 10.1016/0014-5793(93)81661-i.Peer-Reviewed Original ResearchThe 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 ResearchConceptsGroup-transfer pathwaysReaction activityDissociation rate constantsElectron transfer chainAcceptor couplesEnzyme-enzyme interactionsEnzyme concentrationRate constantsEnzyme-enzyme complexEnzyme interactionsComplexesControl of enzymesEnzyme complexEnzymeConcentrationBacterial phosphoenolpyruvateMain pathwayInteractionConstantsChainControl analysisSimple metabolic pathwaysSugar phosphotransferase systemMultiplicity of Control
Westerhoff H, Jensen P, van der Gugten A, Kahn D, Kholodenko B, Schuster S, Oldenburg N, van Dam K, van Heeswijk W. Multiplicity of Control. 1993, 263-268. DOI: 10.1007/978-1-4615-2962-0_41.Peer-Reviewed Original Research
1984
Control of mitochondrial oxidative phosphorylation
Kholodenko B. Control of mitochondrial oxidative phosphorylation. Journal Of Theoretical Biology 1984, 107: 179-188. PMID: 6717037, DOI: 10.1016/s0022-5193(84)80020-x.Peer-Reviewed Original Research