Team/CINVESTAVIPNUNAM MX/Model.htm
From 2012.igem.org
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 DNAbinding 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 twoelectron transfer is not yet clear. Redox titration experiments have shown that both PpsR and AppA have two redoxactive 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 bluelight 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 Cterminal part, thereby causing the dissociation of PpsR (4).
To implement the redoxsensing 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 Cterminal 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 AppAindependent mechanism. To account for this possibility, the assumption is that PpsR is reoxidized proportional to the oxygen concentration as:
Finally assuming massaction 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.
