Table 1 |
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Model ℳ(39, 65, 90). |
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reaction |
kinetic constants |
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IKK → IKK|active |
k1 = 0.0025 |
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IKK → null |
k2 = 0.000125 |
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null → IKK |
k3 = 1e-005 |
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IKK|active + A20 → A20 + IKK|inactive |
k4 = 0.1 |
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IKK|active → IKK|inactive |
k5 = 0.0015 |
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IKK|active → null |
k6 = 0.000125 |
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IKK|active + IkBa@csl → IKK|active:IkBa |
k7 = 0.24 |
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IKK|active:IkBa → IKK|active |
k8 = 0.1 |
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IKK|active + IkBa:p50:p65@csl → IKK|active:IkBa:p50:p65 |
k9 = 1.2 |
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IKK|active:IkBa:p50:p65 → IKK|active + p50:p65@csl |
k10 = 0.1 |
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IKK|inactive → null |
k11 = 0.000125 |
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IkBa:p50:p65@csl → p50:p65@csl |
k12 = 2e-005 |
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p50:p65@csl + IkBa@csl ⇌ IkBa:p50:p65@csl |
kf13 = 0.5 kr13 = 0 |
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p50:p65@ncl + IkBn ⇌ IkBa:p50:p65@ncl |
kf14 = 0.5 kr14 = 0 |
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p50:p65@csl ⇌ kv p50:p65@ncl |
kf15 = 0.0025 kr15 = 8e-005 |
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mRNAA20 → mRNAA20 + A20 |
k16 = 0.5 |
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mRNAA20 → null |
k17 = 0.0004 |
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A20 → null |
k18 = 0.0003 |
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null → mRNAA20 |
k19 = 0 |
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p50:p65@ncl → p50:p65@ncl + mRNAA20 |
k20 = 5e-007 |
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IkBa@csl → null |
k21 = 0.0001 |
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mRNAIkBa → mRNAIkBa + IkBa@csl |
k22 = 0.5 |
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IkBa@csl ⇌ kv IkBn |
kf23 = 0.001 kr23 = 0.0005 |
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null → mRNAIkBa |
k25 = 0 |
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mRNAIkBa → null |
k27 = 0.0004 |
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kv IkBa:p50:p65@ncl → IkBa:p50:p65@csl |
kf28 = 0.01 kr28 = 0 |
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Prop105:RNAP + FTAx ⇌ Prop105:RNAP:FTAx |
kf32 = 10 kr32 = 0.0001 |
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Prop105:RNAP → Prop105:RNAP + RNAP1|active |
k33 = 0.0005 |
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Prop105:RNAP:FTAx → Prop105:RNAP:FTAx + RNAP1|active |
k34 = 0.1 |
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RNAP1|active → mRNAp105 |
k35 = 0.01 |
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mRNAp105 → mRNAp105 + p105 |
k36 = 0.0041 |
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mRNAp105 → null |
k37 = 5e-005 |
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p105 → null |
k38 = 6e-005 |
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p105 → p50 |
k39 = 0.00013 |
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p50 → null |
k40 = 6.4e-005 |
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FTAy + Prop65:RNAP ⇌ Prop65:RNAP:FTAy |
kf41 = 10 kr41 = 0.0001 |
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Prop65:RNAP → Prop65:RNAP + RNAP2|active |
k42 = 0.0005 |
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Prop65:RNAP:FTAy → Prop65:RNAP:FTAy + RNAP2|active |
k43 = 0.1 |
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RNAP2|active → mRNAp65 |
k44 = 0.016 |
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mRNAp65 → mRNAp65 + p65 |
k45 = 0.0053 |
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mRNAp65 → null |
k46 = 5e-005 |
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p65 → null |
k47 = 6.4e-005 |
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FTAz + ProIkBa:RNAP ⇌ ProIkBa:RNAP:FTAz |
kf48 = 10 kr48 = 0.0001 |
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ProIkBa:RNAP → ProIkBa:RNAP + RNAP3|active |
k49 = 0.0005 |
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ProIkBa:RNAP:FTAz → ProIkBa:RNAP:FTAz + RNAP3|active |
k50 = 0.02 |
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RNAP3|active → mRNAIkBa |
k51 = 0.025 |
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p50 + p65 ⇌ p50:p65@csl |
kf52 = 0.003 kr52 = 0.001 |
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p50:p65@csl → null |
k53 = 0.0002 |
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p50:p65@ncl → null |
k54 = 0.0002 |
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p50:p65@ncl + ProIkBa:RNAP ⇌ ProIkBa:RNAP:p50:p65 |
kf55 = 0.62 kr55 = 0.00048 |
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p50:p65@ncl + ProIkBa:RNAP:FTAz ⇌ ProIkBa:RNAP:FTAz:p50:p65 |
kf56 = 0.62 kr56 = 0.00048 |
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IkBn + p50:p65@nclProIkBa:RNAP ⇌ ProIkBa:RNAP:p50:p65:IkBa |
kf57 = 18.4 kr57 = 0.055 |
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IkBn + ProIkBa:RNAP:FTAz:p50:p65 ⇌ IkBnProIkBa:RNAP:FTAz:p50:p65 |
kf58 = 18.4 kr58 = 0.055 |
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ProIkBa:RNAP:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + ProIkBa:RNAP |
kf59 = 0.0038 kr59 = 8e-013 |
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IkBnProIkBa:RNAP:FTAz:p50:p65 ⇌ IkBa:p50:p65@ncl + ProIkBa:RNAP:FTAz |
kf60 = 0.0038 kr60 = 8e-013 |
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p50:p65@nclProIkBa:RNAP → p50:p65@nclProIkBa:RNAP + RNAP3|active |
k61 = 0.06 |
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ProIkBa:RNAP:FTAz:p50:p65 → ProIkBa:RNAP:FTAz:p50:p65 + RNAP3|active |
k62 = 0.6 |
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p50:p65@ncl + Prop105:RNAP ⇌ Prop105:RNAP:p50:p65 |
kf63 = 0.62 kr63 = 0.00048 |
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p50:p65@ncl + Prop105:RNAP:FTAx ⇌ Prop105:RNAP:FTAx:p50:p65 |
kf64 = 0.62 kr64 = 0.00048 |
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IkBn + Prop105:RNAP:p50:p65 ⇌ Prop105:RNAP:p50:p65:IkBa |
kf65 = 18.4 kr65 = 0.055 |
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IkBn + Prop105:RNAP:FTAx:p50:p65 ⇌ Prop105:RNAP:FTAx:p50:p65:IkBa |
kf66 = 18.4 kr66 = 0.055 |
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Prop105:RNAP:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + Prop105:RNAP |
kf67 = 0.0038 kr67 = 8e-013 |
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Prop105:RNAP:FTAx:p50:p65:IkBa ⇌ IkBa:p50:p65@ncl + Prop105:RNAP:FTAx |
kf68 = 0.0038 kr68 = 8e-013 |
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Prop105:RNAP:p50:p65 → Prop105:RNAP:p50:p65 + RNAP1|active |
k69 = 0.006 |
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Prop105:RNAP:FTAx:p50:p65 → Prop105:RNAP:FTAx:p50:p65 + RNAP1|active |
k70 = 0.06 |
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IkBa:p50:p65@csl → null |
k71 = 0.0002 |
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IkBa:p50:p65@ncl → null |
k72 = 0.0002 |
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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. |
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Radulescu et al. BMC Systems Biology 2008 2:86 doi:10.1186/1752-0509-2-86 |
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