How reliable are thermodynamic feasibility statements of biochemical pathways?
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Engineering of large-scale metabolic pathways to maximize production of a certain substance or to minimize creation of undesired chemicals require explicit information about the underlying enzyme kinetics. Unfortunately, such information is frequently not ...
The engineering of the metabolism requires the building of reliable kinetic models of the metabolic pathways through the integration of the information from heterogeneous data sources. Unfortunately, the quantitative knowledge about fluxes, mechanisms or k ...
Thermodynamic feasibility analysis (TFA) has been used as a toot capable of providing additional constraints to the mass balance-based methods of analysis of Metabolic networks (e.g., flux balance analysis). Several publications have recently appeared in w ...
ABSTRACT A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involve ...
Motivation: Metab., the network of chem. reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochem. reaction from a given ...
Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual react ...
Advancement of genomic research and anal. techniques enables an in-depth understanding of individual components in the cellular metab. The crit. subject is the integration of massive exptl. details and the quantification of the contributions of individual ...
Precise information about kinetic properties of enzymes within a biochemical network is a necessary ingredient of any successful metabolic engineering design. Such information inevitably involves uncertainty due to changes in cellular and process parameter ...
With the sequencing and annotation of the entire genomes of numerous microorganisms has come the advent of the genome scale metabolic models such as the iJR904 model of E. coli from Palsson and coworkers. Metabolic flux anal. (MFA) is widely employed to ge ...
A precise quantification of the effect of perturbations in a metabolic network depends on explicit knowledge of the kinetic properties of the enzymes of the individual reactions. However, a comprehensive knowledge of enzymes kinetics in a metabolic network ...