SCC

Get concentration ranges for metabolites with structurally constrained concentrations (SCC).

folders:

• F2C2
  • F2C2 toolbox from Larhlimi et al. 2002 used to calculate flux coupling matrix
• kinetic_model_predictions
  • code and data used for analysis based on a large-scale kinetic model of E. coli
  • includes the kinetic model used from Khodayari et al. 2014
  • compare predicted SCC concentration and concentration simulated from kinetic model (Correlation_prediction_simulation.m)
  • distribution of Euclidean distances between predicted and simulated SCC concentration over all samples (Distribution_euclidean_prediction_simulation.m)
  • get FBA based flux distribution for the kinetic model, which can be then used to predict SCC concentrations (FBA_flux_range.m)
  • SCC concentration of knock-out mutants predicted using MOMA (Moma_ko_analysis.m)
  • get samples of simulated steady-state data by simulations from different initial conditions (perturbationAnalysis.m)
  • effect of unknown kcat values on SCC concentration prediction (removal_kcat_knowledge.m)
  • compare prediction of concentration ranges obtained from SCC prediction to range obtained from shadow price (shadow_price_comparison.m)
  • compare simulated and predicted fold changes in SCC concentration upon reaction knock-ou (sim_pred_FoldChanges.m)
  • simulate knock-out mutants (Simulation_ko.m)
• Models
  • genome-scale metabolic models used in this study (format: .xml or .mat)
• Results
  • SCC metabolites for genome-scale models in Models/
  • SCC metabolites for genome-scale models in Models/ upon split into elementary reactions -Michaelis-Menten like format- (Results_MM_split/)

files:

• SCC concentration prediction for Gerosa data set (Gerosa_data_E_coli_metabolites.csv and Gerosa_data_E_coli_specific_rates.csv) and E. coli model iJO1366 (concentration_prediction_iJO1366_Gerosa.m)
• SCC concentration prediction for Ishii data set (Ishii_Quantitative_data_E_coli_metabolites.csv and Ishii_Quantitative_data_E_coli_specific_rates.csv) and E. coli model iJO1366 (concentration_prediction_iJO1366_Ishii.m)
• get cytosolic SCC metabolites for E coli model iJO1366 (E_coli_iJO1366_get_cytosolic_SCC.m)
• fractional LP used in SCC constant prediction (fractional_LP.m)
• find SCC metabolites (get_SCC.m)
• find SCC metabolites and calculate constants based on provided kcat values (get_SCC_kcat.m)
• model should be without blocked reactions and reversible reactions should be split into irreversible once model preprocessing (model_preprocessing.m) and SCC metabolite calculation (main.m)
• model preprocessing, MM-like split of reactions (model_preprocessing_MM.m) and SCC metabolite calculation (main_MM.m)
• MM-like split of reactions into their elementary reactions (MM_split_rxns.m)
• split reversible reactions into two irreversible once (spli_rxns.m)