Table 1.
Biochemical reactions and their associated reaction rate constants in the computational model of the NF-κB signaling network
| Reactions | I | II | III | IV | V |
|---|---|---|---|---|---|
| IKKa + IкBα → IKKa:IкBα |
Aα |
[a] |
0.2 |
[1] |
0.1813 |
| IKKa + IкBβ → IKKa:IкBβ |
Aβ |
[a] |
0.05 |
[3] |
0.02997 |
| IKKa + IкBϵ → IKKa:IкBϵ |
Aϵ |
[a] |
0.05 |
[3] |
0.04244 |
| IKKa + IkBα:NF-кB → IKKa:IкBα:NF-кB |
Bα |
[a] |
1 |
[1] |
1.024 |
| IKKa + IkBβ:NF-кB → IKKa:IкBβ:NF-кB |
Bβ |
[a] |
0.25 |
[3] |
0.3683 |
| IKKa + IkBϵ:NF-кB → IKKa:IкBϵ:NF-кB |
Bϵ |
[a] |
0.25 |
[3] |
0.42 |
| NF-кBn → NF-кBn + A20t |
C1 |
[b] |
0.0000005 |
[1] |
0.000000506 |
| 0 → A20t |
C2 |
[c] |
0 |
[1] |
0 |
| A20t → 0 |
C3 |
[b] |
0.0004 |
[1] |
0.0002438 |
| A20t → A20t + A20 |
C4 |
[b] |
0.5 |
[1] |
0.5807 |
| A20 → 0 |
C5 |
[b] |
0.0003 |
[1] |
0.0003769 |
| IKKa:IкBα → IKKa + IкBα |
Dα |
[b] |
0.00125 |
[2] |
0.002046 |
| IKKa:IкBβ → IKKa + IкBβ |
Dβ |
[b] |
0.00175 |
[2] |
0.0005609 |
| IKKa:IкBϵ → IKKa + IкBϵ |
Dϵ |
[b] |
0.00175 |
[2] |
0.002142 |
| IKKa:IкBα:NF-кB → IKKa + IккBα:NF-кB |
Dα |
[b] |
0.00125 |
[2] |
0.002046 |
| IKKa:IkBβ:NF-кB → IKKa + IкBβ:NF-кB |
Dβ |
[b] |
0.00175 |
[2] |
0.000561 |
| IKKa:IкBϵ:NF-кB → IKKa + IкBϵ:NF-кB |
Dϵ |
[b] |
0.00175 |
[2] |
0.002142 |
| IKKa:IкBα:NF-кB → IKKa:IкBα + NF-кB |
Eα |
[b] |
0.000001 |
[2] |
0.00000144 |
| IKKa:IкBβ:NF-кB → IKKa:IкBβ + NF-кB |
Eβ |
[b] |
0.000001 |
[2] |
0.00000124 |
| IKKa:IкBϵ:NF-кB → IKKa:IкBϵ + NF-кB |
Eϵ |
[b] |
0.000001 |
[2] |
0.00000064 |
| IKKa:IкBα + NF-кB → IKKa:IкBα:NF-кB |
Fα |
[a] |
0.5 |
[2] |
0.3789 |
| IKKa:IкBβ + NF-кB → IKKa:IкBβ:NF-кB |
Fβ |
[a] |
0.5 |
[2] |
0.2135 |
| IKKa:IкBϵ + NF-кB → IKKa:IкBϵ:NF-кB |
Fϵ |
[a] |
0.5 |
[2] |
0.3528 |
| IкBα:NF-кB → NF-кB + IкBα |
Gα |
[b] |
0.000001 |
[2] |
0.00000064 |
| IкBβ:NF-кB → NF-кB + IкBβ |
Gβ |
[b] |
0.000001 |
[2] |
0.00000044 |
| IкBϵ:NF-кB → NF-кB + IкBϵ |
Gϵ |
[b] |
0.000001 |
[2] |
0.00000069 |
| IкBαn:NF-кBn → NF-кBn + IкBαn |
Gα |
[b] |
0.000001 |
[2] |
0.00000064 |
| IкBβn:NF-кBn → NF-кBn + IкBβn |
Gβ |
[b] |
0.000001 |
[2] |
0.00000044 |
| IкBϵn:NF-кBn → NF-кBn + IкBϵn |
Gϵ |
[b] |
0.000001 |
[2] |
0.00000069 |
| IкBα + NF-кB → IкBα:NF-кB |
Hα |
[a] |
0.5 |
[2] |
0.4593 |
| IкBβ + NF-кB → IкBβ:NF-кB |
Hβ |
[a] |
0.5 |
[2] |
0.7753 |
| IкBϵ + NF-кB → IкBϵ:NF-кB |
Hϵ |
[a] |
0.5 |
[2] |
0.2895 |
| IкBαn + NF-кBn → IкBαn:NF-кBn |
Hα |
[a] |
0.5 |
[2] |
0.4593 |
| IкBβn + NF-кBn → IкBβn:NF-кBn |
Hβ |
[a] |
0.5 |
[2] |
0.7753 |
| IкBϵn + NF-кBn → IкBϵn:NF-кBn |
Hϵ |
[a] |
0.5 |
[2] |
0.2895 |
| NF-кB → NF-кBn |
I1 |
[b] |
0.0025 |
[1] |
0.003037 |
| NF-кBn → NF-кB |
K01 |
[b] |
0.00005 |
[3] |
0.00005537 |
| IKKn → IKKa |
K1 |
[b] |
0.0025 |
[1] |
0.003273 |
| A20 + IKKa → A20 + IKKi |
K2 |
[a] |
0.1 |
[1] |
0.07075 |
| IKKa → IKKi |
K3 |
[b] |
0.0015 |
[1] |
0.00202 |
| 0 → IKKn |
Kprod |
[c] |
0.000025 |
[1] |
0.000009752 |
| IKKn, IKKa, or IKKi → 0 |
Kdeg |
[b] |
0.000125 |
[1] |
0.0001561 |
| Volume ratio of cytoplasm to nucleus |
Kv |
1 |
5 |
[1] |
5 |
| IкBαn:NF-кBn → IкBα:NF-кB |
Lα |
[b] |
0.01 |
[1] |
0.013979 |
| IкBβn:NF-кBn → IкBβ:NF-кB |
Lβ |
[b] |
0.005 |
[3] |
0.001567 |
| IкBϵn:NF-кBn → IкBϵ:NF-кB |
Lϵ |
[b] |
0.005 |
[3] |
0.006583 |
| IкBα:NF-кB → NF-кB |
Mα |
[b] |
0.000025 |
[1] |
0.00002837 |
| IкBβ:NF-кB → NF-кB |
Mβ |
[b] |
0.000025 |
[3] |
0.00003609 |
| IкBϵ:NF-кB → NF-кB |
Mϵ |
[b] |
0.000025 |
[3] |
0.00000866 |
| Total NF-кB concentration |
NF-кB |
[d] |
0.06 |
[1] |
0.06 |
| IKKa:IкBα:NF-кB → IKKa + NF-кB |
Pα |
[b] |
0.1 |
[1] |
0.12928 |
| IKKa:IкBβ:NF-кB → IKKa + NF-кB |
Pβ |
[b] |
0.05 |
[3] |
0.06454 |
| IKKa:IкBϵ:NF-кB → IKKa + NF-кB |
Pϵ |
[b] |
0.05 |
[3] |
0.08434 |
| IкBαn → IкBα |
Qα |
[b] |
0.0005 |
[1] |
0.0005123 |
| IкBβn → IкBβ |
Qβ |
[b] |
0.0005 |
[3] |
0.0007398 |
| IkBϵn → IkBϵ |
Qϵ |
[b] |
0.0005 |
[3] |
0.0002184 |
| IKKa:IкBα → IKKa |
Rα |
[b] |
0.1 |
[1] |
0.123 |
| IKKa:IкBβ → IKKa |
Rβ |
[b] |
0.1 |
[3] |
0.03837 |
| IKKa:IкBϵ → IKKa |
Rϵ |
[b] |
0.1 |
[3] |
0.1571 |
| IкBαn:NF-кBn → NF-кBn |
Sα |
[b] |
0.000001 |
[2] |
0.00000037 |
| IкBβn:NF-кBn → NF-кBn |
Sβ |
[b] |
0.000001 |
[2] |
0.000001131 |
| IкBϵn:NF-кBn → NF-кBn |
Sϵ |
[b] |
0.000001 |
[2] |
0.000001037 |
| NF-кBn → NF-кBn + IкBαt |
Uα |
[b] |
0.0000005 |
[1] |
0.000000279 |
| NF-кBn → NF-кBn + IкBβt |
Uβ |
[b] |
0 |
[2] |
0 |
| NF-кBn → NF-кBn + IкBϵt |
Uϵ |
[b] |
0.00000005 |
[3] |
0.000000059 |
| IкBα → IкBαn |
Vα |
[b] |
0.001 |
[1] |
0.0009786 |
| IкBβ → IкBβn |
Vβ |
[b] |
0.001 |
[3] |
0.0004871 |
| IkBϵ → IkBϵn |
Vϵ |
[b] |
0.001 |
[3] |
0.00147 |
| IкBα, IкBαn → 0 |
Wα |
[b] |
0.0001 |
[1] |
0.000132 |
| IкBβ, IкBβn → 0 |
Wβ |
[b] |
0.0001 |
[3] |
0.000133 |
| IкBϵ, IкBϵn → 0 |
Wϵ |
[b] |
0.0001 |
[3] |
0.000042 |
| IкBαt → IkBαt + IkBα |
Xα |
[b] |
0.5 |
[1] |
0.4552 |
| IкBβt → IкBαt + IкBβ |
Xβ |
[b] |
0.5 |
[3] |
0.3828 |
| IкBϵt → IкBαt + IкBϵ |
Xϵ |
[b] |
0.5 |
[3] |
0.3304 |
| 0 → IкBαt |
Yα |
[c] |
0.00000005 |
[3] |
0.000000084 |
| 0 → IкBβt |
Yβ |
[c] |
0.000000005 |
[3] |
0.00000000414 |
| 0 → IкBϵt |
Yϵ |
[c] |
0.000000005 |
[3] |
0.00000000508 |
| IкBαt → 0 |
Zα |
[b] |
0.0004 |
[1] |
0.0003375 |
| IкBβt → 0 |
Zβ |
[b] |
0.0004 |
[3] |
0.0002031 |
| IкBϵt → 0 | Zϵ | [b] | 0.0004 | [3] | 0.0004742 |
The far left column denotes biochemical reactions. The symbols for reaction rate constants are in the column I. Their units and their published nominal values are in columns II and III respectively. Column IV denotes the reference: [1] for Ref. [21], [2] for Ref. [20], and [3] for the average of values from Refs. [20,21]. Column V lists values used in this paper. The units for [a] are μM-1 s-1, for [b] are s-1, for [c] are μM s-1, and for [d] are μM.