Biochemical reactions
| Reactant Aa . | Reactant B . | Reactant C . | Forward Reaction Rate . | Reverse Reaction Rate . | Comment . |
|---|---|---|---|---|---|
| FasL | Fas | FasC | k1_f | k1_r | |
| FasC | FADD | FasC:FADD | k2_f | k2_r | Assume noncooperative binding between FADD and Fas, which means that regardless of other molecules in the complex, the FADD-Fas interaction always has the same rate constant. |
| FasC:FADD | FADD | FasC:FADD_2 | k2_f | k2_r | |
| FasC:FADD_2 | FADD | FasC:FADD_3 | k2_f | k2_r | |
| FasC:FADD_2:Casp8 | FADD | FasC:FADD_3:Casp8 | k2_f | k2_r | |
| FasC:FADD_2:FLIP | FADD | FasC:FADD_3:FLIP | k2_f | k2_r | |
| FasC:FADD_2:Casp8_2 | FADD | FasC:FADD_3:Casp8_2 | k2_f | k2_r | |
| FasC:FADD_2:Casp8:FLIP | FADD | FasC:FADD_3:Casp8:FLIP | k2_f | k2_r | |
| FasC:FADD_2:FLIP_2 | FADD | FasC:FADD_3:FLIP_2 | k2_f | k2_r | |
| FasC:FADD:Casp8 | FADD | FasC:FADD_2:Casp8 | k2_f | k2_r | |
| FasC:FADD:FLIP | FADD | FasC:FADD_2:FLIP | k2_f | k2_r | |
| FasC:FADD_3 | Casp8 | FasC:FADD_3:Casp8 | k3_f | k3_r | Assume caspase-8 and FLIP have the same binding rate constants for FADD, because their death effector domains (FADD binding domain) have high homology (38). |
| FasC:FADD_3 | FLIP | FasC:FADD_3:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8 | Casp8 | FasC:FADD_3:Casp8_2 | k3_f | k3_r | |
| FasC:FADD_3:Casp8 | FLIP | FasC:FADD_3:Casp8_FLIP | k3_f | k3_r | |
| FasC:FADD_3:FLIP | Casp8 | FasC:FADD_3:Casp8:FLIP | k3_f | k3_r | Similar to binding between FADD and Fas, assume noncooperative binding between FADD and caspase-8 and between FADD and FLIP. |
| FasC:FADD_3:FLIP | FLIP | FasC:FADD_3:FLIP_2 | k3_f | k3_r | |
| FasC:FADD_3:Casp8_2 | Casp8 | FasC:FADD_3:Casp8_3 | k3_f | k3_r | |
| FasC:FADD_3:Casp8_2 | FLIP | FasC:FADD_3:Casp8_2:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8:FLIP | Casp8 | FasC:FADD_3:Casp8_2:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8:FLIP | FLIP | FasC:FADD_3:Casp8:FLIP_2 | k3_f | k3_r | |
| FasC:FADD3:FLIP_2 | Casp8 | FasC:FADD_3:Casp8:FLIP_2 | k3_f | k3_r | |
| FasC:FADD_3:FLIP_2 | FLIP | FasC:FADD_3:FLIP_3 | k3_f | k3_r | |
| FasC:FADD_2 | Casp8 | FasC:FADD_2:Casp8 | k3_f | k3_r | |
| FasC:FADD_2 | FLIP | FasC:FADD_2:FLIP | k3_f | k3_r | |
| FasC:FADD_2:Casp8 | Casp8 | FasC:FADD_2:Casp8_2 | k3_f | k3_r | |
| FasC:FADD_2:Casp8 | FLIP | FasC:FADD_2:Casp8:FLIP | k3_f | k3_r | |
| FasC:FADD_2:FLIP | Casp8 | FasC:FADD_2:Casp8:FLIP | k3_f | k3_r | |
| FasC:FADD_2:FLIP | FLIP | FasC:FADD_2:FLIP_2 | k3_f | k3_r | |
| FasC:FADD | Casp8 | FasC:FADD:Casp8 | k3_f | k3_r | |
| FasC:FADD | FLIP | FasC:FADD:FLIP | k3_f | k3_r | |
| FasC:FADD_2 | Casp8_2_p41 | FasC:FADD-2:Casp8_2 | k4 | ||
| FasC:FADD_3:Casp8 | Casp8_2_p41 | FasC:FADD-3:Casp8_3 | k4 | ||
| FasC:FADD_3:FLIP | Casp8_2_p41 | FasC:FADD-3:Casp8_2:FLIP | k4 | ||
| FasC:FADD_3 | Casp8_2_p41 | FasC:FADD-3:Casp8_2 | k4 | ||
| Casp8_2_p41 | Casp8_2* | k5 | Nongeneral reaction: \[A\ {\rightarrow}kfA{\ast}\] | ||
| Casp8_2* | Casp3 | Casp8_2*:Casp3 | k6_f | k6_r | |
| Casp8_2* | Casp3* | Casp8_2*:Casp3 | k7 | Assume the catalytic reaction rate of caspase_8 is the same regardless of the substrate. | |
| Casp8_2* | tBid | Cas8_2*:Bid | k7 | ||
| Casp8_2* | Bid | Cas8_2*:Bid | k8_f | k8_r | |
| tBid | Bax | tBid:Bax | k9_f | k9_r | Assume the first Bax and the second Bax binding to tBid have the same rate constants. |
| tBid:Bax | Bax | tBid:Bax_2 | k9_f | k9_r | |
| Smac | tBid:Bax_2 | Smac* | k10 | Assume Smac and Cyto.c have the same release rate and nongeneral reaction. | |
| Cyto.c | tBid:Bax_2 | Cyto.c* | k10 | \[A\ {\rightarrow}kf{\cdot}BA{\ast}\] | |
| Smac* | XIAP | Smac*:XIAP | k11_f | k11_r | Nongeneral reaction: \[A\ {\rightarrow}kf{\cdot}BA{\ast}\] |
| Cyto.c* | Apaf | Cyto.c*:Apaf:ATP | k12_f | k12_r | |
| Cyto.c*:Apaf:ATP | Casp9 | Cyto.c*:Apaf:ATP:Casp9 | k13_f | k13_r | |
| Cyto.c*:Apaf:ATP:Casp9 | Casp9 | Cyto.c*:Apaf:ATP:Casp9_2 | k14_f | k14_r | |
| Cyto.c*:Apaf:ATP:Casp9 | Casp9* | Cyto.c*:Apaf:ATP:Casp9_2 | k15 | ||
| Casp9* | Casp3 | Casp9*:Casp3 | k16_f | k16_r | |
| (Table continues) |
| Reactant Aa . | Reactant B . | Reactant C . | Forward Reaction Rate . | Reverse Reaction Rate . | Comment . |
|---|---|---|---|---|---|
| FasL | Fas | FasC | k1_f | k1_r | |
| FasC | FADD | FasC:FADD | k2_f | k2_r | Assume noncooperative binding between FADD and Fas, which means that regardless of other molecules in the complex, the FADD-Fas interaction always has the same rate constant. |
| FasC:FADD | FADD | FasC:FADD_2 | k2_f | k2_r | |
| FasC:FADD_2 | FADD | FasC:FADD_3 | k2_f | k2_r | |
| FasC:FADD_2:Casp8 | FADD | FasC:FADD_3:Casp8 | k2_f | k2_r | |
| FasC:FADD_2:FLIP | FADD | FasC:FADD_3:FLIP | k2_f | k2_r | |
| FasC:FADD_2:Casp8_2 | FADD | FasC:FADD_3:Casp8_2 | k2_f | k2_r | |
| FasC:FADD_2:Casp8:FLIP | FADD | FasC:FADD_3:Casp8:FLIP | k2_f | k2_r | |
| FasC:FADD_2:FLIP_2 | FADD | FasC:FADD_3:FLIP_2 | k2_f | k2_r | |
| FasC:FADD:Casp8 | FADD | FasC:FADD_2:Casp8 | k2_f | k2_r | |
| FasC:FADD:FLIP | FADD | FasC:FADD_2:FLIP | k2_f | k2_r | |
| FasC:FADD_3 | Casp8 | FasC:FADD_3:Casp8 | k3_f | k3_r | Assume caspase-8 and FLIP have the same binding rate constants for FADD, because their death effector domains (FADD binding domain) have high homology (38). |
| FasC:FADD_3 | FLIP | FasC:FADD_3:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8 | Casp8 | FasC:FADD_3:Casp8_2 | k3_f | k3_r | |
| FasC:FADD_3:Casp8 | FLIP | FasC:FADD_3:Casp8_FLIP | k3_f | k3_r | |
| FasC:FADD_3:FLIP | Casp8 | FasC:FADD_3:Casp8:FLIP | k3_f | k3_r | Similar to binding between FADD and Fas, assume noncooperative binding between FADD and caspase-8 and between FADD and FLIP. |
| FasC:FADD_3:FLIP | FLIP | FasC:FADD_3:FLIP_2 | k3_f | k3_r | |
| FasC:FADD_3:Casp8_2 | Casp8 | FasC:FADD_3:Casp8_3 | k3_f | k3_r | |
| FasC:FADD_3:Casp8_2 | FLIP | FasC:FADD_3:Casp8_2:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8:FLIP | Casp8 | FasC:FADD_3:Casp8_2:FLIP | k3_f | k3_r | |
| FasC:FADD_3:Casp8:FLIP | FLIP | FasC:FADD_3:Casp8:FLIP_2 | k3_f | k3_r | |
| FasC:FADD3:FLIP_2 | Casp8 | FasC:FADD_3:Casp8:FLIP_2 | k3_f | k3_r | |
| FasC:FADD_3:FLIP_2 | FLIP | FasC:FADD_3:FLIP_3 | k3_f | k3_r | |
| FasC:FADD_2 | Casp8 | FasC:FADD_2:Casp8 | k3_f | k3_r | |
| FasC:FADD_2 | FLIP | FasC:FADD_2:FLIP | k3_f | k3_r | |
| FasC:FADD_2:Casp8 | Casp8 | FasC:FADD_2:Casp8_2 | k3_f | k3_r | |
| FasC:FADD_2:Casp8 | FLIP | FasC:FADD_2:Casp8:FLIP | k3_f | k3_r | |
| FasC:FADD_2:FLIP | Casp8 | FasC:FADD_2:Casp8:FLIP | k3_f | k3_r | |
| FasC:FADD_2:FLIP | FLIP | FasC:FADD_2:FLIP_2 | k3_f | k3_r | |
| FasC:FADD | Casp8 | FasC:FADD:Casp8 | k3_f | k3_r | |
| FasC:FADD | FLIP | FasC:FADD:FLIP | k3_f | k3_r | |
| FasC:FADD_2 | Casp8_2_p41 | FasC:FADD-2:Casp8_2 | k4 | ||
| FasC:FADD_3:Casp8 | Casp8_2_p41 | FasC:FADD-3:Casp8_3 | k4 | ||
| FasC:FADD_3:FLIP | Casp8_2_p41 | FasC:FADD-3:Casp8_2:FLIP | k4 | ||
| FasC:FADD_3 | Casp8_2_p41 | FasC:FADD-3:Casp8_2 | k4 | ||
| Casp8_2_p41 | Casp8_2* | k5 | Nongeneral reaction: \[A\ {\rightarrow}kfA{\ast}\] | ||
| Casp8_2* | Casp3 | Casp8_2*:Casp3 | k6_f | k6_r | |
| Casp8_2* | Casp3* | Casp8_2*:Casp3 | k7 | Assume the catalytic reaction rate of caspase_8 is the same regardless of the substrate. | |
| Casp8_2* | tBid | Cas8_2*:Bid | k7 | ||
| Casp8_2* | Bid | Cas8_2*:Bid | k8_f | k8_r | |
| tBid | Bax | tBid:Bax | k9_f | k9_r | Assume the first Bax and the second Bax binding to tBid have the same rate constants. |
| tBid:Bax | Bax | tBid:Bax_2 | k9_f | k9_r | |
| Smac | tBid:Bax_2 | Smac* | k10 | Assume Smac and Cyto.c have the same release rate and nongeneral reaction. | |
| Cyto.c | tBid:Bax_2 | Cyto.c* | k10 | \[A\ {\rightarrow}kf{\cdot}BA{\ast}\] | |
| Smac* | XIAP | Smac*:XIAP | k11_f | k11_r | Nongeneral reaction: \[A\ {\rightarrow}kf{\cdot}BA{\ast}\] |
| Cyto.c* | Apaf | Cyto.c*:Apaf:ATP | k12_f | k12_r | |
| Cyto.c*:Apaf:ATP | Casp9 | Cyto.c*:Apaf:ATP:Casp9 | k13_f | k13_r | |
| Cyto.c*:Apaf:ATP:Casp9 | Casp9 | Cyto.c*:Apaf:ATP:Casp9_2 | k14_f | k14_r | |
| Cyto.c*:Apaf:ATP:Casp9 | Casp9* | Cyto.c*:Apaf:ATP:Casp9_2 | k15 | ||
| Casp9* | Casp3 | Casp9*:Casp3 | k16_f | k16_r | |
| (Table continues) |