Table 1.
Model ℳ(39, 65, 90).
| reaction | kinetic constants |
| IKK → IKK|active | k1 = 0.0025 |
| IKK → null | k2 = 0.000125 |
| null → IKK | k3 = 1e-005 |
| IKK|active + A20 → A20 + IKK|inactive | k4 = 0.1 |
| IKK|active → IKK|inactive | k5 = 0.0015 |
| IKK|active → null | k6 = 0.000125 |
| IKK|active + IkBa@csl → IKK|active:IkBa | k7 = 0.24 |
| IKK|active:IkBa → IKK|active | k8 = 0.1 |
| IKK|active + IkBa:p50:p65@csl → IKK|active:IkBa:p50:p65 | k9 = 1.2 |
| IKK|active:IkBa:p50:p65 → IKK|active + p50:p65@csl | k10 = 0.1 |
| IKK|inactive → null | k11 = 0.000125 |
| IkBa:p50:p65@csl → p50:p65@csl | k12 = 2e-005 |
| p50:p65@csl + IkBa@csl ⇌ IkBa:p50:p65@csl | kf13 = 0.5 kr13 = 0 |
| p50:p65@ncl + IkBn ⇌ IkBa:p50:p65@ncl | kf14 = 0.5 kr14 = 0 |
| p50:p65@csl ⇌ kv p50:p65@ncl | kf15 = 0.0025 kr15 = 8e-005 |
| mRNAA20 → mRNAA20 + A20 | k16 = 0.5 |
| mRNAA20 → null | k17 = 0.0004 |
| A20 → null | k18 = 0.0003 |
| null → mRNAA20 | k19 = 0 |
| p50:p65@ncl → p50:p65@ncl + mRNAA20 | k20 = 5e-007 |
| IkBa@csl → null | k21 = 0.0001 |
| mRNAIkBa → mRNAIkBa + IkBa@csl | k22 = 0.5 |
| IkBa@csl ⇌ kv IkBn | kf23 = 0.001 kr23 = 0.0005 |
| null → mRNAIkBa | k25 = 0 |
| mRNAIkBa → null | k27 = 0.0004 |
| kv IkBa:p50:p65@ncl → IkBa:p50:p65@csl | kf28 = 0.01 kr28 = 0 |
| Prop105:RNAP + FTAx ⇌ Prop105:RNAP:FTAx | kf32 = 10 kr32 = 0.0001 |
| Prop105:RNAP → Prop105:RNAP + RNAP1|active | k33 = 0.0005 |
| Prop105:RNAP:FTAx → Prop105:RNAP:FTAx + RNAP1|active | k34 = 0.1 |
| RNAP1|active → mRNAp105 | k35 = 0.01 |
| mRNAp105 → mRNAp105 + p105 | k36 = 0.0041 |
| mRNAp105 → null | k37 = 5e-005 |
| p105 → null | k38 = 6e-005 |
| p105 → p50 | k39 = 0.00013 |
| p50 → null | k40 = 6.4e-005 |
| FTAy + Prop65:RNAP ⇌ Prop65:RNAP:FTAy | kf41 = 10 kr41 = 0.0001 |
| Prop65:RNAP → Prop65:RNAP + RNAP2|active | k42 = 0.0005 |
| Prop65:RNAP:FTAy → Prop65:RNAP:FTAy + RNAP2|active | k43 = 0.1 |
| RNAP2|active → mRNAp65 | k44 = 0.016 |
| mRNAp65 → mRNAp65 + p65 | k45 = 0.0053 |
| mRNAp65 → null | k46 = 5e-005 |
| p65 → null | k47 = 6.4e-005 |
| FTAz + ProIkBa:RNAP ⇌ ProIkBa:RNAP:FTAz | kf48 = 10 kr48 = 0.0001 |
| ProIkBa:RNAP → ProIkBa:RNAP + RNAP3|active | k49 = 0.0005 |
| ProIkBa:RNAP:FTAz → ProIkBa:RNAP:FTAz + RNAP3|active | k50 = 0.02 |
| RNAP3|active → mRNAIkBa | k51 = 0.025 |
| p50 + p65 ⇌ p50:p65@csl | kf52 = 0.003 kr52 = 0.001 |
| p50:p65@csl → null | k53 = 0.0002 |
| p50:p65@ncl → null | k54 = 0.0002 |
| p50:p65@ncl + ProIkBa:RNAP ⇌ ProIkBa:RNAP:p50:p65 | kf55 = 0.62 kr55 = 0.00048 |
| p50:p65@ncl + ProIkBa:RNAP:FTAz ⇌ ProIkBa:RNAP:FTAz:p50:p65 | kf56 = 0.62 kr56 = 0.00048 |
| IkBn + p50:p65@nclProIkBa:RNAP ⇌ ProIkBa:RNAP:p50:p65:IkBa | kf57 = 18.4 kr57 = 0.055 |
| IkBn + ProIkBa:RNAP:FTAz:p50:p65 ⇌ IkBnProIkBa:RNAP:FTAz:p50:p65 | kf58 = 18.4 kr58 = 0.055 |
| ProIkBa:RNAP:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + ProIkBa:RNAP | kf59 = 0.0038 kr59 = 8e-013 |
| IkBnProIkBa:RNAP:FTAz:p50:p65 ⇌ IkBa:p50:p65@ncl + ProIkBa:RNAP:FTAz | kf60 = 0.0038 kr60 = 8e-013 |
| p50:p65@nclProIkBa:RNAP → p50:p65@nclProIkBa:RNAP + RNAP3|active | k61 = 0.06 |
| ProIkBa:RNAP:FTAz:p50:p65 → ProIkBa:RNAP:FTAz:p50:p65 + RNAP3|active | k62 = 0.6 |
| p50:p65@ncl + Prop105:RNAP ⇌ Prop105:RNAP:p50:p65 | kf63 = 0.62 kr63 = 0.00048 |
| p50:p65@ncl + Prop105:RNAP:FTAx ⇌ Prop105:RNAP:FTAx:p50:p65 | kf64 = 0.62 kr64 = 0.00048 |
| IkBn + Prop105:RNAP:p50:p65 ⇌ Prop105:RNAP:p50:p65:IkBa | kf65 = 18.4 kr65 = 0.055 |
| IkBn + Prop105:RNAP:FTAx:p50:p65 ⇌ Prop105:RNAP:FTAx:p50:p65:IkBa | kf66 = 18.4 kr66 = 0.055 |
| Prop105:RNAP:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + Prop105:RNAP | kf67 = 0.0038 kr67 = 8e-013 |
| Prop105:RNAP:FTAx:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + Prop105:RNAP:FTAx | kf68 = 0.0038 kr68 = 8e-013 |
| Prop105:RNAP:p50:p65 → Prop105:RNAP:p50:p65 + RNAP1|active | k69 = 0.006 |
| Prop105:RNAP:FTAx:p50:p65 → Prop105:RNAP:FTAx:p50:p65 + RNAP1|active | k70 = 0.06 |
| IkBa:p50:p65@csl → null | k71 = 0.0002 |
| IkBa:p50:p65@ncl → null | k72 = 0.0002 |
Detailed description of the complex model for NF-κB signalling. The names of the species are provided following the template similar to that proposed in B7676: Entity1name|Modifications ...: Entity2name|Modifications...[|active]@compartment. Here, the colon symbol ':' delimitates components of a complex. Optional suffix 'active' describes the active state of the protein. The localization information (@compartment suffix) is provided when a protein or complex exists in both nucleus (@ncl) and cytoplasm (@csl). Mass action law constants are either in s-1 or in μMs-1 units. kv parameter (cytoplasm/nucleus volume ratio) is set up to 5. First reactions in the list (Re1–Re28) correspond to the Lipniacky's model.