The GRaPe tool assigns rate equations to all the reactions in the model based on the stoichiometry of the reaction. We successfully applied our methodology to the M. tuberculosis genome-scale metabolic network,

resulting in a kinetic model with 739 metabolites, 856 metabolic reactions and 856 enzymes. Predicting cellular behaviours in silico by examining the dynamics and properties of cellular processes has the potential to increase our INCB-018424 understanding of biological systems. This makes it necessary to advance towards kinetic modelling in our drive to understand the detailed dynamics of cellular functions and their Inhibitors,research,lifescience,medical regulation. However, it is time-consuming and costly to experimentally measure all metabolite concentrations, reaction Inhibitors,research,lifescience,medical fluxes

and kinetic parameters at the genome scale. Additionally, many kinetic equations are unknown and thus, standard rate laws have been used to Tofacitinib alopecia describe metabolism. Liebermeister et al. [12], Adiamah et al. [7] and Ao et al. [10] have all shown that using generic rate equations, the dynamical behaviour of systems can be predicted without experimentally measuring all kinetic parameters. Constraint-based modelling fails in capturing the dynamics of cellular behaviour and is insufficient to provide insights into changes in metabolite concentrations. Inhibitors,research,lifescience,medical Beste et al. [15] produced a constraint-based simulation of a genome-scale metabolic model of M. tuberculosis which was capable of predicting different growth conditions using FBA. The phenotype growth of 78% of mutant strains was correctly predicted by the Beste model. We built a genome-scale kinetic model of M. tuberculosis based on this stoichiometric model and showed Inhibitors,research,lifescience,medical that our model accurately reproduced genome-scale flux distributions under different growth

conditions. The kinetic parameters used in our model were estimated using only flux values, therefore there remains a degree of redundancy in parameter values as illustrated by PVA. The results from PVA indicate that Vf, the velocity of the Inhibitors,research,lifescience,medical forward reaction, is the most constrained parameter. The rest of the parameters in our model exhibit a high degree of redundancy. Banga [13] suggests that global optimisation methods are needed in an attempt to avoid finding local solutions. Additionally, there are suggestions indicating that due to the stochastic nature of biological systems, parameter estimation must account for this degree of stochasticity [33]. Reducing the value of the objective function in parameter estimation improves the quality Dacomitinib of the kinetic parameters. However, we observed a significant increase in computing time when the objective function was reduced beyond 10-8. The compromise between computing time and more precise parameter values must always be considered when performing parameter estimation. Furthermore, our results also show that computing time increases non-linearly with the number of data points in the parameter estimation training data.