Topological analysis, complex reactions

Nonetheless, the topological and stoichiometric analysis of metabolic networks is probably the most powerful computational approach to large-scale metabolic networks that is currently available. Stoichiometric analysis draws upon extensive work on the structure of complex reaction systems in physical chemistry in the 1970s and 1980s [59], and can be considered as one of the few theoretically mature areas of Systems Biology. While the variety and amount of applications of stoichiometric analysis prohibit any comprehensive summary, we briefly address some essential aspects in the following. 

Stoichiometric analysis goes beyond topological arguments and takes the specific physicochemical properties of metabolic networks into account. As noted above, based on the analysis of the nullspace of complex reaction networks, stoichiometric analysis has a long history in the chemical and biochemical sciences [59 62]. At the core of all stoichiometric approaches is the assumption of a stationary and time-invariant state of the metabolite concentrations S°. As already specified in Eq. (6), the steady-state condition... 

We may model complex systems by top-down or bottom-up approaches. In the top-down approach, we describe the components from the systemic behavior of the actual system. For example, from the flow balance analysis in a steady-state bacterium, we learn the input and output flows, topology of the network, and the rates of maty metabolic reactions. 

Figure 15.4. Principle of HDX-MS analysis The protein complex is diluted in deuterium oxide to start the exchange reaction. After the incubation time at room temperature, the exchange reaction is quenched by lowering both pH and temperature. To study the topology of deuterium incorporation, the protein complex is digested with pepsin under quenched conditions. The peptides generated can be analyzed using ESI or MALDI ionization. During the mass spectrometric analysis the number of deuterium atoms incorporated is determined to calculate the exchange rate along the sequence of the protein (See color insert).

---