Construction and analysis of a modular model of caspase activation in apoptosis

Table 2 Reactions for the model equations

Number	Reaction	Forward rate (nM^-1 s^-1)	Reverse rate (s^-1)
DISC	(FasL, FasR) → DISC	f _DISC
1	DISC + Casp8 → DISC + Casp8*	10^-4 (k₂)
2	Casp3* + Casp8 → Casp3* + Casp8*	10^-4 [65]
3	Casp8* + Casp3 → Casp8* + Casp3*	5.8 × 10^-4 [65]
4	Casp3* + XIAP ⇌ Casp3*-XIAP	3 × 10^-3 [65]	0.035 [65]
5	Casp3* + XIAP → Casp3*	3 × 10^-3 [65]
6	Casp8* + BAR ⇌ Casp8*-BAR	5 × 10^-3 [65]	0.035 [65]
7	Casp8* + Bid → Casp8* + tBid	5 × 10^-4 (est. [70, 71])
tBid-Bax₂	(tBid, Bax) → tBid-Bax₂	$f_{{tBid-Bax}_{2}}$
8	tBid-Bax₂ + Cytc → tBid-Bax₂ + Cytc*	10^-3 [70, 71]
9	tBid-Bax₂ + Smac → tBid-Bax₂ + Smac*	10^-3 [70, 71]
10	Smac* + XIAP ⇌ Smac*-XIAP	7 × 10^-3 [70, 71]	2.21 × 10^-3 [70, 71]
Apop	(Cytc*; Apaf) → Apop	f _Apop
11	Apop + Casp9 → Apop + Casp9*	2 × 10^-4 (est. [66])
12	Casp3* + Casp9 → Casp3* + Casp9*	2 × 10^-4 [66]
13	Casp9* + Casp3 → Casp9* + Casp3*	5 × 10^-5 [66]
14	Casp9* + XIAP ⇌ Casp9*-XIAP	1.06 × 10^-4 [70, 71]	10^-3 [70, 71]

Each reaction described highlights whether the reaction is a forward or reversible reaction by the arrows. The rates are provided from previous work. Reaction are illustrated in Figure 1.

ISSN: 1742-4682