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

Table 1 Species description, synthesis and degradation rates for the model equations

Species	Description	Synthesis rate (nM/s)	Degradation rate (s^-1)
DISC	DISC		8.807 × 10^-3
Casp8	procaspase-8	adjusted	6.5 × 10^-5 [65]
Casp8*	caspase-8		9.667 × 10^-5 [65]
Casp3	procaspase-3	adjusted	6.5 × 10^-5 [65]
Casp3*	caspase-3		9.667 × 10^-5 [65]
XIAP	XIAP	adjusted	1.933 × 10^-4 [65]
Casp3*-XIAP	Casp3*-XIAP complex		2.883 × 10^-4 [65]
BAR	BAR	1.111 × 10^-3 ([BAR]₀ = 66.67 nM [65])	1.667 × 10^-5 [65]
Casp8*-BAR	Casp8*-BAR complex		1.933 × 10^-4 [65]
Bid	Bid	4.168 × 10^-4 ([Bid]₀ = 25 nM [70, 71])	1.667 × 10^-5 (μ_BAR)
tBid	truncated Bid		1.667 × 10^-5 (μ_Bid)
tBid-Bax₂	tBid-Bax₂ complex		0.0264
Cytc	cytochrome c (mitochondrial)	10^-3 ([Cytc]₀ = 100 nM [70, 71])	10^-5
Cytc*	cytochrome c (cytosolic)		10^-5
Smac	Smac (mitochondrial)	0.0167 ([Smac]₀ = 100 nM [70, 71])	1.667 × 10^-5 (μ_BAR)
Smac*	Smac (cytosolic)		1.667 × 10^-5 (μ_Smac)
Smac*-XIAP	Smac-XIAP complex		1.933 × 10^-4 (μ_Casp8*-BAR)
Apop	apoptosome		1.487 × 10^-5
Casp9	procaspase-9	1.3 × 10^-3 ([Casp9]₀ = 20 nM [70, 71])	6.5 × 10^-5 (μ_Casp8)
Casp9*	caspase-9		9.667 × 10^-5 (μ_Casp8*)
Casp9*-XIAP	Casp9*-XIAP complex		2.883 × 10^-4 (μ_Casp3*-XIAP)

Model species and description are given. In the model, synthesis and degradation rates are given for the model system and labeled α and μ, respectively.

ISSN: 1742-4682