Symbol | Definition & Comments |
---|---|
A | concentration of the activator (nM) |
R | concentration of the repressor (nM) |
t | model time (hours) |
| DNA-binding constant of the activator A |
| DNA-binding constant of the repressor R |
| dimerization constant of the activator A to A2 |
| dimerization constant of the repressor R to R2 |
| multimerization constant of the activator A to A n |
| dimerization constant of the repressor R to R m |
δ A | degradation rate of the activator A |
δ R | degradation rate of the repressor R |
Δ | δ A /δR,non-dimensional parameter of the model |
x | , the nondimensional variable associated to the activator, when the activator is a dimer |
y | , the nondimensional variable associated to the repressor, when the repressor is a dimer |
τ | tδ R , the nondimensional time variable of the model |
α | the transcriptional synergy conferred by the activator bound to DNA |
β | , the nondimensional parameter of the transcriptional response from the activator promoter, with γ A , the translation rate of the activator A; β A , the transcription rate of the mRNA of the activator; α A , activator mRNA degradation; , total activator promoter number. The root order n denotes the multimerization degree of the TF binding to DNA (i.e. n = 2, dimer; n = 4, tetramer). The subscript from , the equilibrium constant for multimer formation, also denotes its dependence on the multimerization of the binding factor. |
γ | , the nondimensional parameter of the transcriptional response from the repressor promoter, similar to β. See also [18]. Notice also the multimerization degree appears here as m with similar consequences as for the β parameter. |
σ | , the binding ratio of the repressor compared to the activator. |