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Table 1 Model (39, 65, 90).

From: Robust simplifications of multiscale biochemical networks

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 k v 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 k v IkBn kf23 = 0.001 kr23 = 0.0005
null → mRNAIkBa k25 = 0
mRNAIkBa → null k27 = 0.0004
k v 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
  1. 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.