Parsimonious enzyme usage FBA (pFBA)

General concept

It is expected that when cells are growing exponentially, there will be selection for the fastest growers, and then among the fastest growers, there will be a fitness advantage to cells using the least amount of enzyme. This uses a bi-level LP to minimize enzyme-associated flux, subject to optimal biomass. With both of these constraints, flux variability analysis is used to assess the span of alternate optimal solutions, and then the genes and reactions are all classified into various groups according to their contribution to the optimal solutions. This approach uses a minimization of flux, similar to the Flux Minimization method, but without using thermodynamic parameters. It also includes a series of additional post-processing methods to classify the solutions.

Items to consider when implementing

Software packages with this method

Applications of interest

Description of study and link to study:

What was learned with this method:

Relevant references

Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. Lewis, et al. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol. 2010 Jul;6:390.

Related methods

Flux minimization

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