TABLE 2.
Reactions and rates used to simulate the bifan motif
| Reaction | Rate (expression) | OR | AND | Ordered AND | Rate (value) | Reference |
|---|---|---|---|---|---|---|
| Signal1 + p38 → p38* | [signal1][p38] | X | X | X | Included in signal | |
| p38* → p38 | k1 [p38*] | X | X | X | k1 = 0.1 | |
| Signal2 + JNK → JNK* | [signal2][JNK] | X | X | X | Included in signal | |
| JNK* → JNK | k2 [JNK*] | X | X | X | k2 = 0.1 | |
| p38* + ATF2 → p38*:ATF2 | k3 [p38*][ATF2] | X | X | X | k3 = 3.9 | (58) |
| p38* + ATF2JNK → p38*:ATF2JNK | k3 [p38*][ATF2JNK] | X | ||||
| p38*:ATF2 → p38* + ATF2 | k4 [p38*:ATF2] | X | X | X | k4 = 19.2 | |
| p38*:ATF2JNK → p38* + ATF2JNK | k4 [p38*:ATF2JNK] | X | ||||
| p38*:ATF2 → p38* + ATF2* | k5 [p38*:ATF2] | X | k5 = 4.8 | |||
| p38*:ATF2 → p38* + ATF2p38 | k5 [p38*:ATF2] | X | X | |||
| p38*:ATF2JNK → p38* + ATF2* | k5 [p38*:ATF2JNK] | X | ||||
| JNK* + ATF2 → JNK*ATF2 | k6 [JNK*][ATF2] | X | X | k6 = 20 | (47) (assumed to be the same as JNK-c-Jun rates) | |
| JNK* + ATF2p38 → JNK*:ATF2p38 | k6 [JNK*][ATF2p38] | X | X | |||
| JNK*:ATF2 → JNK* + ATF2 | k7 [JNK*:ATF2] | X | X | k7 = 40 | ||
| JNK*:ATF2p38 → JNK* + ATF2p38 | k7 [JNK*:ATF2p38] | X | X | |||
| JNK*:ATF2 → JNK* + ATF2* | k8 [JNK*:ATF2] | X | k8 = 10 | |||
| JNK*:ATF2 → JNK* + ATF2JNK | k8 [JNK*:ATF2] | X | ||||
| JNK*:ATF2p38 → JNK* + ATF2* | k8 [JNK*:ATF2p38] | X | X | |||
| p38* + ELK-1 → p38*:ELK-1 | k9 [p38*][ELK-1] | X | X | k9 = 16.02 | (59) | |
| p38* + ELK-1JNK → p38*:ELK-1JNK | k9 [p38*][ELK-1JNK] | X | X | |||
| p38*:ELK-1 → p38* + ELK-1 | k10 [p38*:ELK-1] | X | X | k10 = 35 | ||
| p38*:ELK-1JNK → p38* + ELK-1JNK | k10 [p38*:ELK-1JNK] | X | X | |||
| p38*:ELK-1 → p38* + ELK-1* | k11 [p38*:ELK-1] | X | k11 = 8.75 | |||
| p38*:ELK-1 → p38* + ELK-1p38 | k11 [p38*:ELK-1] | X | ||||
| p38*:ELK-1JNK → p38* + ELK-1* | k11 [p38*:ELK-1JNK] | X | X | |||
| JNK* + ELK-1 → JNK*:ELK-1 | k12 [JNK*][ELK-1] | X | X | X | k12 = 20 | (47) (assumed to be the same as JNK-c-Jun rates) |
| JNK* + ELK-1p38 → JNK*:ELK-1p38 | k12 [JNK*][ELK-1p38] | X | ||||
| JNK*:ELK-1 → JNK* + ELK-1 | k13 [JNK*:ELK-1] | X | X | X | k13 = 40 | |
| JNK*:ELK-1p38 → JNK* + ELK-1p38 | k13 [JNK*:ELK-1p38] | X | ||||
| JNK*:ELK-1 → JNK* + ELK-1* | k14 [JNK*:ELK-1] | X | k14 = 10 | |||
| JNK*:ELK-1 → JNK* + ELK-1JNK | k14 [JNK*:ELK-1] | X | X | |||
| JNK*:ELK-1p38 → JNK* + ELK-1* | k14 [JNK*:ELK-1p38] | X | ||||
| ATF2* + ATF2* → ATF2*:ATF2* | k15 [ATF2*]2 | X | X | X | k15 = 0.02 | |
| ELK-1* + ELK-1* → ELK-1*:ELK-1* | k16 [ELK-1*]2 | X | X | X | k16 = 0.02 |
Some of the reactions occur at all variants of the motif whereas others are used only at one or two configurations. XY represents a substrate X that is phosphorylated by kinase Y. This substrate is not considered activated until a second phosphorylation by another kinase. Full activation is denoted by X*. This may be either activation by a single kinase in the OR gate configuration, or double phosphorylation in the AND gate cases. All rates for the reactions of the form A + B→… are in μM−1 min−1. Rates for the A→… reactions are in min−1.