sybilccFBA (version 3.0.1)

cfba_moment_mr: Function: cfba_moment_mr: implement MOMENT method taking into account multifunctional enzymes

Description

This function uses GPR, kcat, and molecular weights to calculate fluxes according to MOMENT method taking into account multifunctional enzymes. Whenever a protein i was involved in more than one reaction, we introduced auxiliary concentration variables xi,j for each of these reactions. These xi,j replaced the global concentration variable gi for the protein in the corresponding equation that limits the flux through this reaction based on the enzyme concentration. The sum of the xi,j is then equal to the total concentration of protein gi included in the global enzyme solvent capacity constraint.

Usage

cfba_moment_mr(model,mod2=NULL, Kcat,MW=NULL,
selected_rxns=NULL,verboseMode=2,objVal=NULL,
RHS=NULL,solver=SYBIL_SETTINGS("SOLVER"),C_mu_coef = 0,medval=NULL,
                 runFVA = FALSE, fvaRxn = NULL)

Arguments

model

An object of class modelorg.

mod2

An object of class modelorg with only irreversible reactions. It can be sent to save time of recalculating it with each call.

Kcat

kcat values in unit 1/S. Contains three slots: reaction id,direction(dirxn),value(val)

MW

list of molecular weights of all genes, using function calc_MW, in units g/mol

selected_rxns

optional parameter used to select a set of reactions not all, list of react_id

verboseMode

An integer value indicating the amount of output to stdout: 0: nothing, 1: status messages, 2: like 1 plus with more details, 3: generates files of the LP problem. Default: 2.

RHS

the budget C, for EColi 0.27

objVal

when not null the problem will be to find the minimum budget that give the specified objective value(biomass)

solver

Single character string giving the solver package to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").

C_mu_coef

used to have C as a linear function of mu (biomass) : C = RHS + C_mu_coef*Biomass

medval

median of Kcat values , used for missing values

runFVA

flag to choose to run flux variability default FALSE

fvaRxn

optional parameter to choose set of reaction ids to run FVA on them. Ids are from the irreversible model default all reactions. Ignored when runFVA is not set.

Value

returns a list containing slots:

sol

solution of the problem.

prob

object of class sysBiolAlg that contains the linear problem, this can be used for further processing like adding more constraints. To save it, function writeProb can be used.

geneCol

mapping of genes to variables in the problem.

geneConc

the concentration of each gene, when the gene is catalyzing more than one reaction there will be a row with 'rxn' column set to NA containing the total.

rxnMC

for each reaction (GPR) the molecular crowding of it (total sum to budget)

rxnGeneMC

the contribution of each gene to all of its reactions.

Details

Main steps 1- Add variables for all genes 2- for each selected reaction: parse gpr, 3- Add variables accordingly and constraints 4- Add solvant constraint

References

Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters, 8(7). doi:10.1371/journal.pcbi.1002575

Gelius-Dietrich, G., Desouki, A. A., Fritzemeier, C. J., & Lercher, M. J. (2013). sybil<U+2013>Efficient constraint-based modelling in R. BMC systems biology, 7(1), 125.

See Also

modelorg, optimizeProb

Examples

# NOT RUN {
	library(sybilccFBA)
	data(iAF1260)
	model= iAF1260
 	data(mw)
 	data(kcat)
 	 mod2=mod2irrev(model)
  
	uppbnd(mod2)[react_id(mod2)=="R_EX_glc_e__b"]=1000
	uppbnd(mod2)[react_id(mod2)=="R_EX_glyc_e__b"]=0
	uppbnd(mod2)[react_id(mod2)=="R_EX_ac_e__b"]=0
	uppbnd(mod2)[react_id(mod2)=="R_EX_o2_e__b"]=1000
	lowbnd(mod2)[react_id(mod2)=="R_ATPM"]=0

  sol_mr=cfba_moment_mr(model,mod2,kcat,MW=mw,verbose=2,RHS=0.27,solver="glpkAPI",medval=3600*22.6) 
   bm_rxn = which(obj_coef(mod2)!=0)
   print(sprintf('biomass=%f',sol_mr$sol$fluxes[bm_rxn]))
  # Enzyme concentrations:
     gconc=sol_mr$geneConc
  
# }
# NOT RUN {
<!-- % end dontrun -->
# }
# NOT RUN {
# }