Team/CINVESTAV-IPN-UNAM MX/Model.htm
From 2012.igem.org
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![]() Construction of Model The mathematical model is based on the ODEs and kinetic parameters outlined in Pandey et al 2011. The following are its assumptions and basis: In vitro experiments showed that AppA inhibits the DNA-binding activity of oxidized PpsR by two mechanisms (1,2): 1. By reducing a disulfide bond in PpsR. At the first stage, the reduced form of AppA (A-) reduces a disulfide bond in oxidized PpsR (P4+), which occurs independently of the light conditions. The molecular mechanism of this two-electron transfer is not yet clear. Redox titration experiments have shown that both PpsR and AppA have two redox-active thiol groups that can form intramolecular disulfide bonds with a similar midpoint potential, according to this equation:
At the second level of regulation, the reduced form of AppA can form a complex with reduced PpsR. Experiments based on size exclusion chromatography have revealed that, in the complex, one AppA molecule is associated with two PpsR monomers corresponding to half of a PpsR molecule, which exists as a stable tetramer in solution (1). The same study showed that complex formation is inhibited by high intensities of blue-light irradiation (LI ¼ 900mmol/m2s). However, a subsequent study found that AppA responds to blue light over several orders of magnitude down to 0.2 mmol/m2s (3). Other experiments indicate that light absorption induces a structural change in the BLUF domain of AppA (5), which results in interactions with its C-terminal part, thereby causing the dissociation of PpsR (4).
To implement the redox-sensing capabilities of AppA, we use the model proposed by Han et al. (4), according to which AppA utilizes heme as a cofactor, bound to its C-terminal domain, to sense the cytosolic redox conditions, according to this equation:
If the electron transfer from AppA to PpsR in Eq. 1 was indeed effectively irreversible (kPr -<< kPr+), as suggested by the experiments of Masuda and Bauer (1), PpsR would have to be reoxidized through an AppA-independent mechanism. To account for this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen concentration as:
Finally assuming mass-action kinetics for the reactions in Eq. 1 and Eqs. 3–5 the following are the set of ordinary differential equations established:
Were the total amounts of PpsR and AppA molecules are conserved according to:
1. Masuda, S., and C. E. Bauer. 2002. AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides. Cell. 110:613–623.
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