Incorporating metabolic control analysis

As briefly outlined in Section 6.3, one of the theoretical frameworks in quantitative analysis of metabolic networks is metabolic control analysis. In metabolic control analysis, the enzyme elasticity coefficients provide empirical constraints between the metabolites concentrations and the reaction fluxes. These constraints can be considered in concert with the interdependencies in the J and c spaces that are imposed by the network stoichiometry. If the coefficients elk = (c / Ji)dJi/dck are known, then these values bind the fluxes and concentrations to a hyperplane in the (J, c) space. 

One can view biochemical systems as represented at the most basic level as networks of given stoichiometry. Whether the steady state or the kinetic behavior is explored, the stoichiometry constrains the feasible behavior according to mass balance and the laws of thermodynamics. As we have seen in this chapter, some analysis is possible based solely on the stoichiometric structure of a given system. Mass balance provides linear constraints on reaction fluxes non-linear thermodynamic constraints provide information about feasible flux directions and reactant concentrations. 

Applying mass-balance and thermodynamic constraints typically leaves one without a precisely defined (unique) solution for reaction fluxes and reactant concentration, but instead with a mathematically constrained feasible space for these variables. Exploration of this feasible space is the purview of constraint-based analysis. It has so far been left unstated that any application in this area starts with the determination of the reactions in a system, from which the stoichiometric matrix arises. This first step, network reconstruction, integrates genomic and proteomic data to determine carefully the enzymes present in an organism, cell, or subcellular compartment. The network reconstruction process is described elsewhere [107]. 

Construct the stoichiometric matrix for this system, given the reaction numbering defined in the figure. Assume that internal reactions 1 through 4 are irreversible with feasible directions indicated in the figure. Reactions 6 and 7 are transport reactions, also irreversible with directions indicated. If the maximum uptake rate of A is 1 (in arbitrary units), what is the maximal output of D Given that production of D is optimal, is the internal flux distribution unique  

3 Use the flux balance constraint and the thermodynamic feasibility to show that for a closed chemical reaction system, i.e., b = 0 in Equation (9.2), the only possible steady state is J = A/u = 0. That is, the steady state of a closed chemical reaction system is necessarily a chemical equilibrium. 

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Fig. 25 Characterization and luciferase expression of PGP DNA condensates in vivo. These results show that luciferase expression is dependent on galactose incorporation but independent of amount of melittin. (a) Represents the input mol ratio of Cys-terminated melittin, PEG-peptide, and glycopeptide. (b) Represents the measured mol ratio of Cys-terminated melittin, PEG-peptide, and glycopeptide for each purified PGP. (c) Values are the calculated MW based on polylysine standards, (d) Values are the calculated MW based on PEG standards, (e) The mean particle size determined at a stoichiometry of 0.3 nmol of PGP per mg of DNA. The value represents the mean diameter (nm) based on unimodal analysis, (f) The zeta potential of PGP DNA condensates at a stoichiometry of 0.3 nmol of PGP per mg of DNA. (g) The metabolic half-life of PGP 125I-DNA in triplicate mice. The results are derived from Fig. 6. (h) The PC/NPC ratio of DNA-targeted liver, (i) Represents a control PGP 3 in which galactose has been removed. Figure adapted with permission from [182], 2007 American Chemical Society...

Figure 4.10. Proteomic analysis by SILAC. Proteomic analysis by SILAC or stable isotope labeling of amino acids in cell culture utilize de novo metabolic incorporation of stable-isotope-labeled amino acids during protein synthesis. Cells can be cultured with various combinations of stable-isotope-labeled amino acids such as lysine or arginine. Tyrosine has been used in phosphoprotein studies of tyrosine residues. About five or six cell divisions are needed for complete labeling of proteins in cell cultures prior to experimentation. Labeled cells from control and treatment(s) lysates are combined and digested. Quantitation and identification are performed by LC-MS/MS.

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