Metabolic Control and Response Analysis

controlAndResponseAnalysis(ensemble, saveResMatrices, conditionI, strucIdx)

Calculates both control coefficients and response coefficients. Response coefficients here answer the question: what happens if one increases a given enzyme’s concentration?

This is mostly important when modeling promiscuous enzymes, where increasing the enzyme’s concentration doesn’t necessarily lead to an equal increase in the flux of the reactions it catalyzes. Response and control coefficients are the same when enzymes are independent and an increase in enzyme concentration leads to a proportional increase in the reaction flux.

Response coefficients are calculated as

\[C_E^J = C_v^J\Pi\]

where \(C_v^J\) is the flux control coefficient matrix and \(\Pi\) is the parameter elasticity matrix.

The implementation is based on

For all models in the given ensemble it returns the average flux and concentration control coefficients across the ensemble as well as the average enzyme and concentration response coefficients.

It can also return the control and response coefficient matrices for each model in the ensemble if saveResMatrices is set to true. But keep in mind that for large models this can use a lot of RAM and CPU.

USAGE:

mcaResults = controlAndResponseAnalysis(ensemble, saveResMatrices, strucIdx)

INPUT:

ensemble (struct): model ensemble, see buildEnsemble for fields description saveResMatrices (logical): whether or not to save the elasticity and control coefficient matrices for all models

OPTIONAL INPUT:
conditionI (int): condition for which the user wants for run MCA when having multiple coniditions, by

default MCA is run for all conditions

strucIdx (int): number of the model structure considered

OUTPUT:

mcaResults (struct): control and response analysis results

  • xControlAvg (cell) : average concentration controls coefficient for the model ensemble

  • vControlAvg (cell) : average flux control coefficients for the model ensemble

  • eResponseAvg (cell) : average enzyme response coefficient for the model ensemble

  • xResponseAvg (cell) : average concentration response coefficients for the model ensemble

  • xcounter (cell) : number of models in the average concentration control coefficient calculation

  • vcounter (cell) : number of models in the average flux control coefficient calculation

  • xRcounter (cell) : number of models in the average concentration response coefficient calculation

  • eRcounter (cell) : number of models in the average enzyme response coefficient calculation

  • xControl (cell) : concentration control coefficient matrix for each model

  • vControl (cell) : flux control coefficient matrix for each model

  • xResponse (cell) : concentration response coefficient matrix for each model

  • eResponse (cell) : enzyme response coefficient matrix for each model