Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle (Articolo in rivista)

Type
Label
  • Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle (Articolo in rivista) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1088/1367-2630/16/11/115018 (literal)
Alternative label
  • Daniele De Martino 1,3, Fabrizio Capuani 2,3 and Andrea De Martino 1,2 (2014)
    Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle
    in New journal of physics
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Daniele De Martino 1,3, Fabrizio Capuani 2,3 and Andrea De Martino 1,2 (literal)
Pagina inizio
  • 115018 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 16 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • 1 Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, I-00161 Roma, Italy 2 CNR-IPCF, Dipartimento di Fisica, Sapienza Università di Roma, p.le A. Moro 2, I-00185 Roma, Italy 3 Authors contributed equally (literal)
Titolo
  • Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle (literal)
Abstract
  • Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from minimal mass-balance assumptions upon prescribing in- and outtake fluxes. Here we consider the problem of inferring intracellular flux patterns from extracellular metabolite levels. Resorting to a thermodynamic out of equilibrium variational principle to describe the network at steady state, we show that the switch from fermentative to oxidative phenotypes in cells can be characterized in terms of the glucose, lactate, oxygen and carbon dioxide concentrations. Results obtained for an exactly solvable toy model are fully recovered for a large scale reconstruction of human catabolism. Finally we argue that, in spite of the many approximations involved in the theory, available data for several human cell types are well described by the predicted phenotypic map of the problem. (literal)
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