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