A stoichiometric matrix, S (m × n), was constructed for iAF1260, where m is the number of metabolites and n is the number of reactions. The corresponding entry in the stoichiometric matrix, Sij, represents the stoichiometric coefficient for the participation of the ith metabolite in the jth reaction. FBA was then used to solve the linear programming problem under steady-state criteria (Price et al, 2004 (link)) represented by the equation:
where v (n × 1) is a vector of reaction fluxes. Since the linear problem is normally an underdetermined system for genome-scale metabolic models, there exist multiple solutions for v that satisfyequation 2 . To find a particular solution for v, the cellular objective of producing the maximal amount of biomass constituents, represented by the ratio of metabolites in the BOF, is optimized for in the linear system. Additionally, constraints that are imposed on the system are in the form of:
where α and β are the lower and upper limits placed on each reaction flux, vi, respectively. For reversible reactions, −∞⩽vi⩽∞, and for irreversible reactions, 0⩽vi⩽∞. The constraints on the reactions that allow metabolite entry into the extracellular space were set to 0⩽vi⩽∞ if the metabolite was not present in the medium, meaning that the compounds could leave, but not enter the system. For the metabolites that were in the medium, the constraints were set to −∞⩽vi⩽∞ for all except the limiting substrate(s) (e.g., glucose and/or oxygen). The reaction flux through the BOF was constrained from 0⩽vBOF⩽∞.
Linear programming calculations were performed using SimPheny™ (Genomatica, San Diego, CA) and the LINDO (Lindo Systems Inc., Chicago, IL) or TOMLAB (Tomlab Optimization Inc., San Diego, CA) solvers in MATLAB® (The MathWorks Inc., Natick, MA) with the COBRA Toolbox (Becker et al, 2007 (link)).
When comparing the flux distribution in central metabolism to experimentally reported values (Fischer et al, 2004 (link)), all of the comparisons were performed using computational results when optimal growth is predicted using the BOFCORE, the 152 regulated reactions under these conditions constrained to zero (see above), a split in the flux ratio between the two NADH dehydrogenases of 1:1, an NGAM value of 8.39 mmol ATP gDW−1 h−1, a GAM value of 59.81 mmol ATP gDW−1 and iAF1260. An FVA on the optimal flux distribution yielded no flexibility in the central metabolism pathways examined in this study. From the Fischer et al (2004) (link) study, data from E. coli growth in reactor conditions were used because the oxygen uptake and CO2 secretion rates were reported, and the flux values that were used were based off 13C-constrained flux balancing.
where v (n × 1) is a vector of reaction fluxes. Since the linear problem is normally an underdetermined system for genome-scale metabolic models, there exist multiple solutions for v that satisfy
where α and β are the lower and upper limits placed on each reaction flux, vi, respectively. For reversible reactions, −∞⩽vi⩽∞, and for irreversible reactions, 0⩽vi⩽∞. The constraints on the reactions that allow metabolite entry into the extracellular space were set to 0⩽vi⩽∞ if the metabolite was not present in the medium, meaning that the compounds could leave, but not enter the system. For the metabolites that were in the medium, the constraints were set to −∞⩽vi⩽∞ for all except the limiting substrate(s) (e.g., glucose and/or oxygen). The reaction flux through the BOF was constrained from 0⩽vBOF⩽∞.
Linear programming calculations were performed using SimPheny™ (Genomatica, San Diego, CA) and the LINDO (Lindo Systems Inc., Chicago, IL) or TOMLAB (Tomlab Optimization Inc., San Diego, CA) solvers in MATLAB® (The MathWorks Inc., Natick, MA) with the COBRA Toolbox (Becker et al, 2007 (link)).
When comparing the flux distribution in central metabolism to experimentally reported values (Fischer et al, 2004 (link)), all of the comparisons were performed using computational results when optimal growth is predicted using the BOFCORE, the 152 regulated reactions under these conditions constrained to zero (see above), a split in the flux ratio between the two NADH dehydrogenases of 1:1, an NGAM value of 8.39 mmol ATP gDW−1 h−1, a GAM value of 59.81 mmol ATP gDW−1 and iAF1260. An FVA on the optimal flux distribution yielded no flexibility in the central metabolism pathways examined in this study. From the Fischer et al (2004) (link) study, data from E. coli growth in reactor conditions were used because the oxygen uptake and CO2 secretion rates were reported, and the flux values that were used were based off 13C-constrained flux balancing.