2007
Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and Space
Kholodenko B. Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and Space. 2007, 300-318. DOI: 10.1007/978-1-59745-531-2_16.Peer-Reviewed Original ResearchProtein phosphorylation networksReceptor tyrosine kinase signalingTrafficking of endosomesPivotal physiological processesTyrosine kinase signalingPlasma membrane receptorsPhosphorylation networksUltrasensitive switchPhosphorylated kinasesKinase signalingEnvironmental cuesCell motilitySystems biologyNegative feedback circuitPhysiological processesCellular responsesMembrane receptorsLiving cellsCellular architectureSpatiotemporal response patternsComputational approachIntricate relationshipEndosomesKinaseMitosis
2000
Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity
Westerhoff H, Teusink B, Mensonides F, Reijenga K, Esgalhado E, Kholodenko B, Somsen O, Van Heeswijk W, Boogerd F, Bruggeman F, Snoep J. Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity. NATO Science Partnership Subseries: 3 2000, 235-242. DOI: 10.1007/978-94-011-4072-0_26.Peer-Reviewed Original ResearchBacterial inner membraneElectron transfer chainImportant metabolic processesBiological free energy transductionFermentation of glucoseInner membraneATP hydrolysisPhysiological processesMetabolic processesMolecular biologyProton pumpLiving cellsStudy of metabolismProtein fractionsBiochemical reactionsIndependent chemical reactionsFree energy transductionBiochemistryChemical reactionsTransductionYeastBiocomplexityReactionBiologySubstantial progressEngineering 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 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
1995
Energy, control and DNA structure in the living cell
Wijker J, Jensen P, Snoep J, Gomes A, Guiral M, Jongsma A, de Waal A, Hoving S, van Dooren S, van der Weijden C, van Workum M, van Heeswijk W, Molenaar O, Wielinga P, Richard P, Diderich J, Bakker B, Teusink B, Hemker M, Rohwer J, van der Gugten A, Kholodenko B, Westerhoff H. Energy, control and DNA structure in the living cell. Biophysical Chemistry 1995, 55: 153-165. PMID: 7632875, DOI: 10.1016/0301-4622(94)00148-d.Peer-Reviewed Original ResearchConceptsHigh ATP/ADP ratiosATP/ADP ratioCell physiologyADP ratioCertain cell typesCellular functionsIntracellular ATP levelsTransduction pathwaysDNA structureLiving cellsCell typesIon gradientsHomeostatic control mechanismsATP levelsCell functionElaborate controlPhysiologyCellsControl mechanismsMaintenanceHIERARCHIES IN CONTROL
JENSEN P, VAN DER GUGTEN A, BIER M, VAN HEESWIJK W, ROHWER J, MOLENAAR D, VAN WORKUM M, RICHARD P, TEUSINK B, BAKKER B, KHOLODENKO B, WESTERHOFF H. HIERARCHIES IN CONTROL. Journal Of Biological System 1995, 3: 139-144. DOI: 10.1142/s0218339095000137.Peer-Reviewed Original Research