articleMolecular Systems BiologyAug 1, 2017GOLD OA

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

BJBenjamín J. SánchezCZCheng ZhangANAvlant NilssonPLPetri‐Jaan LahtveeEJEduard J. Kerkhoven

Chalmers University of Technology · East China University of Science and Technology · +4 more institutions

PubMed
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Abstract

Abstract Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could…

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Topics & keywords

Topics
Keywords
  • Biology
  • Phenotype
  • Computational biology
  • Yeast
  • Scale (ratio)
  • Enzyme
  • Saccharomyces cerevisiae
  • Genome
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