2008
Domain-oriented reduction of rule-based network models.
Borisov N, Chistopolsky A, Faeder J, Kholodenko B. Domain-oriented reduction of rule-based network models. IET Systems Biology 2008, 2: 342-51. PMID: 19045829, PMCID: PMC2628550, DOI: 10.1049/iet-syb:20070081.Peer-Reviewed Original ResearchConceptsMulti-domain proteinsAuxiliary proteinsMembrane-bound receptorsTranscriptional regulatorsProgenitor proteinsProtein interactionsComplex assemblyGrowth factor receptorProteinFactor receptorSpeciesCorrect mass balanceEffector functionsHeterodimerisationReceptorsSitesRegulatorAssemblyInteractionDomain
2005
Signaling through Receptors and Scaffolds: Independent Interactions Reduce Combinatorial Complexity
Borisov N, Markevich N, Hoek J, Kholodenko B. Signaling through Receptors and Scaffolds: Independent Interactions Reduce Combinatorial Complexity. Biophysical Journal 2005, 89: 951-966. PMID: 15923229, PMCID: PMC1366644, DOI: 10.1529/biophysj.105.060533.Peer-Reviewed Original ResearchConceptsProtein complexesComplex signaling networksDistinct physiological responsesSignaling networksAdaptor proteinDocking siteMolecular eventsTemporal dynamicsPhysiological responsesDistinct sitesIndependent interactionsBranched networkSeparate domainsMolecular speciesDomain-oriented approachCombinatorial increaseReceptorsIndividual sitesSitesComplexesScaffoldsSpeciesTens of thousandsProteinDifferent sites
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