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BIOMD0000000489 - Sharp2013 - Lipopolysaccharide induced NFkB activation

 

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Reference Publication
Publication ID: 23936158
Sharp GC, Ma H, Saunders PT, Norman JE.
A computational model of lipopolysaccharide-induced nuclear factor kappa B activation: a key signalling pathway in infection-induced preterm labour.
PLoS ONE 2013; 8(7): e70180
Medical Research Council (MRC) Centre for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom. Gemma.sharp@ed.ac.uk  [more]
Model
Original Model: BIOMD0000000489.xml.origin
Submitter: Gemma Sharp
Submission ID: MODEL1303230000
Submission Date: 23 Mar 2013 21:03:45 UTC
Last Modification Date: 08 Mar 2014 20:25:20 UTC
Creation Date: 24 Sep 2013 15:42:05 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Gemma Sharp
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqmodel:isDerivedFrom BioModels Database Hoffmann2002_WT_IkBNFkB_Signaling
BioModels Database Hoffmann2002_KnockOut_IkBNFkB_Signaling
PubMed 16166516
set #3
bqbiol:isVersionOf Gene Ontology release of cytoplasmic sequestered NF-kappaB
Gene Ontology lipopolysaccharide metabolic process
set #4
bqbiol:hasTaxon Taxonomy Mus musculus
Notes
Model
Publication ID: 23936158 Submission Date: 23 Mar 2013 21:03:45 UTC Last Modification Date: 08 Mar 2014 20:25:20 UTC Creation Date: 24 Sep 2013 15:42:05 UTC
Mathematical expressions
Reactions
MYD881) Receptor Complex Formation MYD882) IRAK1 and TRAF6 Phosphorylation MYD883) TAK/TAB Binds to TRAF6 MYD884) IKK Phosphorylation by TAK1
MYD885) IKK[P] Dephosphorylation TRIF01) Receptor Complex Formation TRIF02) IRF3 Phosphorylation TRIF03) IRF3 Dephosphorylation
TRIF04) IRF3 Nuclear Import/Export TRIF05) Inducible TNFa Synthesis TRIF06) Constitutive TNFa Synthesis TRIF09) TNFa Degradation
TRIF10) TNFa Receptor Complex Formation TRIF11) IKK Phosphorylation by RIP1 NFkB01) IkBa:NFkB Binding NFkB02) IKK:IkBa:NFkB Binding (1)
NFkB03) IkBb:NFkB Binding NFkB04) IKK:IkBb:NFkB Binding (1) NFkB05) IkBe:NFkB Binding NFkB06) IKK:IkBe:NFkB Binding (1)
NFkB07) IKK:IkBa:NFkB Catalysis NFkB08) IKK:IkBb:NFkB Catalysis NFkB09) IKK:IkBe:NFkB Catalysis NFkB10) IkBa:NFkB Constitutive Degradation
NFkB11) IkBb:NFkB Constitutive Degradation NFkB12) IkBe:NFkB Constitutive Degradation NFkB13) NFkB Nuclear Import/Export NFkB14) Nuclear IkBa:NFkB Binding
NFkB15) Nuclear IkBb:NFkB Binding NFkB16) Nuclear IkBe:NFkB Binding NFkB17) Constitutive IkBa mRNA Synthesis NFkB18) Inducible IkBa mRNA Synthesis
NFkB19) IkBa mRNA degradation NFkB20) Constitutive IkBb mRNA Synthesis NFkB21) IkBb mRNA degradation NFkB22) Constitutive IkBe mRNA Synthesis
NFkB23) IkBe mRNA degradation NFkB24) IKK:IkBa Binding NFkB25) IkBa Translation NFkB26) IkBa Degradation
NFkB27) IkBa Nuclear Import/Export NFkB28) IKK:IkBb Binding NFkB29) IkBb Translation NFkB30) IkBb Degradation
NFkB31) IkBb Nuclear Import/Export NFkB32) IKK:IkBe Binding NFkB33) IkBe Translation NFkB34) IkBe Degradation
NFkB35) IkBe Nuclear Import/Export NFkB36) IKK:IkBa:NFkB Binding (2) NFkB37) IkBa:NFkB Nuclear Export NFkB38) IKK:IkBb:NFkB Binding (2)
NFkB39) IkBb:NFkB Nuclear Export NFkB40) IKK:IkBe:NFkB Binding (2) NFkB41) IkBe:NFkB Nuclear Export NFkB42) IKK:IkBa Catalysis
NFkB43) IKK:IkBb Catalysis NFkB44) IKK:IkBe Catalysis TRIF06a)Inducible TNFa Synthesis by NFkB  
Physical entities
Compartments Species
compartment CD14 IRAK4 LBP
LPS LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4 MyD88
TIRAP TLR4 IRAK1
TRAF6 TRAF6:IRAK1[P] TAK1:TAB1:TAB2
TAK1:TAB1:TAB2:TRAF6 IKK IKK[P]
RIP1 TRAM TRIF
IRF3 IRF3[P] IRF3[P](nuc)
source sink TNFa
TNFR1 TRADD TRAF2
TNFa:TNFR1:TRAF2:TRADD:RIP1 IkBa IkBa:NFkB
NFkB IKK[P]:IkBa:NFkB IkBb
IkBb:NFkB IKK[P]:IkBb:NFkB IkBe
IkBe:NFkB IKK[P]:IkBe:NFkB NFkB(nuc)
IkBa(nuc) IkBa:NFkB(nuc) IkBb(nuc)
IkBb:NFkB(nuc) IkBe(nuc) IkBe:NFkB(nuc)
IkBa_mRNA IkBb_mRNA IkBe_mRNA
IKK[P]:IkBa IKK[P]:IkBb IKK[P]:IkBe
LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe TBK1/IKKe  
Reactions (59)
 
 MYD881) Receptor Complex Formation [LPS] + [LBP] + [CD14] + [TLR4] + [MyD88] + [IRAK4] + [TIRAP] ↔ [LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4];   {LPS} , {LBP} , {CD14} , {TLR4} , {MyD88} , {IRAK4} , {TIRAP} , {LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4}
 
 MYD882) IRAK1 and TRAF6 Phosphorylation [IRAK1] + [TRAF6] ↔ [TRAF6:IRAK1[P]];   {LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4} , {LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4} , {IRAK1} , {TRAF6} , {TRAF6:IRAK1[P]}
 
 MYD883) TAK/TAB Binds to TRAF6 [TRAF6:IRAK1[P]] + [TAK1:TAB1:TAB2] ↔ [TAK1:TAB1:TAB2:TRAF6];   {TRAF6:IRAK1[P]} , {TAK1:TAB1:TAB2} , {TAK1:TAB1:TAB2:TRAF6}
 
 MYD884) IKK Phosphorylation by TAK1 [IKK] → [IKK[P]];   {TAK1:TAB1:TAB2:TRAF6} , {TAK1:TAB1:TAB2:TRAF6} , {IKK}
 
 MYD885) IKK[P] Dephosphorylation [IKK[P]] → [IKK];   {IKK[P]}
 
 TRIF01) Receptor Complex Formation [LPS] + [LBP] + [CD14] + [TLR4] + [TRIF] + [TRAM] + [RIP1] + [TBK1/IKKe] ↔ [LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe];   {LPS} , {LBP} , {CD14} , {TLR4} , {TRIF} , {TRAM} , {RIP1} , {TBK1/IKKe} , {LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe}
 
 TRIF02) IRF3 Phosphorylation [IRF3] → [IRF3[P]];   {LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe} , {LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe} , {IRF3}
 
 TRIF03) IRF3 Dephosphorylation [IRF3[P]] → [IRF3];   {IRF3[P]}
 
 TRIF04) IRF3 Nuclear Import/Export [IRF3[P]] ↔ [IRF3[P](nuc)];   {IRF3[P]} , {IRF3[P](nuc)}
 
 TRIF05) Inducible TNFa Synthesis 2.0 × [IRF3[P](nuc)] → [TNFa] + 2.0 × [IRF3[P](nuc)];   {IRF3[P](nuc)}
 
 TRIF06) Constitutive TNFa Synthesis [source] → [TNFa];   {source}
 
 TRIF09) TNFa Degradation [TNFa] → [sink];   {TNFa}
 
 TRIF10) TNFa Receptor Complex Formation [TNFa] + [TNFR1] + [TRAF2] + [TRADD] + [RIP1] ↔ [TNFa:TNFR1:TRAF2:TRADD:RIP1];   {TNFa} , {TNFR1} , {TRAF2} , {TRADD} , {RIP1} , {TNFa:TNFR1:TRAF2:TRADD:RIP1}
 
 TRIF11) IKK Phosphorylation by RIP1 [IKK] → [IKK[P]];   {TNFa:TNFR1:TRAF2:TRADD:RIP1} , {TNFa:TNFR1:TRAF2:TRADD:RIP1} , {IKK}
 
 NFkB01) IkBa:NFkB Binding [IkBa] + [NFkB] ↔ [IkBa:NFkB];   {IkBa} , {NFkB} , {IkBa:NFkB}
 
 NFkB02) IKK:IkBa:NFkB Binding (1) [IKK[P]] + [IkBa:NFkB] ↔ [IKK[P]:IkBa:NFkB];   {IKK[P]} , {IkBa:NFkB} , {IKK[P]:IkBa:NFkB}
 
 NFkB03) IkBb:NFkB Binding [IkBb] + [NFkB] ↔ [IkBb:NFkB];   {IkBb} , {NFkB} , {IkBb:NFkB}
 
 NFkB04) IKK:IkBb:NFkB Binding (1) [IKK[P]] + [IkBb:NFkB] ↔ [IKK[P]:IkBb:NFkB];   {IKK[P]} , {IkBb:NFkB} , {IKK[P]:IkBb:NFkB}
 
 NFkB05) IkBe:NFkB Binding [IkBe] + [NFkB] ↔ [IkBe:NFkB];   {IkBe} , {NFkB} , {IkBe:NFkB}
 
 NFkB06) IKK:IkBe:NFkB Binding (1) [IKK[P]] + [IkBe:NFkB] ↔ [IKK[P]:IkBe:NFkB];   {IKK[P]} , {IkBe:NFkB} , {IKK[P]:IkBe:NFkB}
 
 NFkB07) IKK:IkBa:NFkB Catalysis [IKK[P]:IkBa:NFkB] → [IKK[P]] + [NFkB];   {IKK[P]:IkBa:NFkB}
 
 NFkB08) IKK:IkBb:NFkB Catalysis [IKK[P]:IkBb:NFkB] → [IKK[P]] + [NFkB];   {IKK[P]:IkBb:NFkB}
 
 NFkB09) IKK:IkBe:NFkB Catalysis [IKK[P]:IkBe:NFkB] → [IKK[P]] + [NFkB];   {IKK[P]:IkBe:NFkB}
 
 NFkB10) IkBa:NFkB Constitutive Degradation [IkBa:NFkB] → [NFkB];   {IkBa:NFkB}
 
 NFkB11) IkBb:NFkB Constitutive Degradation [IkBb:NFkB] → [NFkB];   {IkBb:NFkB}
 
 NFkB12) IkBe:NFkB Constitutive Degradation [IkBe:NFkB] → [NFkB];   {IkBe:NFkB}
 
 NFkB13) NFkB Nuclear Import/Export [NFkB] ↔ [NFkB(nuc)];   {NFkB} , {NFkB(nuc)}
 
 NFkB14) Nuclear IkBa:NFkB Binding [IkBa(nuc)] + [NFkB(nuc)] ↔ [IkBa:NFkB(nuc)];   {IkBa(nuc)} , {NFkB(nuc)} , {IkBa:NFkB(nuc)}
 
 NFkB15) Nuclear IkBb:NFkB Binding [IkBb(nuc)] + [NFkB(nuc)] ↔ [IkBb:NFkB(nuc)];   {IkBb(nuc)} , {NFkB(nuc)} , {IkBb:NFkB(nuc)}
 
 NFkB16) Nuclear IkBe:NFkB Binding [IkBe(nuc)] + [NFkB(nuc)] ↔ [IkBe:NFkB(nuc)];   {IkBe(nuc)} , {NFkB(nuc)} , {IkBe:NFkB(nuc)}
 
 NFkB17) Constitutive IkBa mRNA Synthesis [source] → [IkBa_mRNA];   {source}
 
 NFkB18) Inducible IkBa mRNA Synthesis 2.0 × [NFkB(nuc)] → [IkBa_mRNA] + 2.0 × [NFkB(nuc)];   {NFkB(nuc)}
 
 NFkB19) IkBa mRNA degradation [IkBa_mRNA] → [sink];   {IkBa_mRNA}
 
 NFkB20) Constitutive IkBb mRNA Synthesis [source] → [IkBb_mRNA];   {source}
 
 NFkB21) IkBb mRNA degradation [IkBb_mRNA] → [sink];   {IkBb_mRNA}
 
 NFkB22) Constitutive IkBe mRNA Synthesis [source] → [IkBe_mRNA];   {source}
 
 NFkB23) IkBe mRNA degradation [IkBe_mRNA] → [sink];   {IkBe_mRNA}
 
 NFkB24) IKK:IkBa Binding [IKK[P]] + [IkBa] ↔ [IKK[P]:IkBa];   {IKK[P]} , {IkBa} , {IKK[P]:IkBa}
 
 NFkB25) IkBa Translation [IkBa_mRNA] → [IkBa] + [IkBa_mRNA];   {IkBa_mRNA}
 
 NFkB26) IkBa Degradation [IkBa] → [sink];   {IkBa}
 
 NFkB27) IkBa Nuclear Import/Export [IkBa] ↔ [IkBa(nuc)];   {IkBa} , {IkBa(nuc)}
 
 NFkB28) IKK:IkBb Binding [IKK[P]] + [IkBb] ↔ [IKK[P]:IkBb];   {IKK[P]} , {IkBb} , {IKK[P]:IkBb}
 
 NFkB29) IkBb Translation [IkBb_mRNA] → [IkBb] + [IkBb_mRNA];   {IkBb_mRNA}
 
 NFkB30) IkBb Degradation [IkBb] → [sink];   {IkBb}
 
 NFkB31) IkBb Nuclear Import/Export [IkBb] ↔ [IkBb(nuc)];   {IkBb} , {IkBb(nuc)}
 
 NFkB32) IKK:IkBe Binding [IKK[P]] + [IkBe] ↔ [IKK[P]:IkBe];   {IKK[P]} , {IkBe} , {IKK[P]:IkBe}
 
 NFkB33) IkBe Translation [IkBe_mRNA] → [IkBe] + [IkBe_mRNA];   {IkBe_mRNA}
 
 NFkB34) IkBe Degradation [IkBe] → [sink];   {IkBe}
 
 NFkB35) IkBe Nuclear Import/Export [IkBe] ↔ [IkBe(nuc)];   {IkBe} , {IkBe(nuc)}
 
 NFkB36) IKK:IkBa:NFkB Binding (2) [IKK[P]:IkBa] + [NFkB] ↔ [IKK[P]:IkBa:NFkB];   {IKK[P]:IkBa} , {NFkB} , {IKK[P]:IkBa:NFkB}
 
 NFkB37) IkBa:NFkB Nuclear Export [IkBa:NFkB(nuc)] → [IkBa:NFkB];   {IkBa:NFkB(nuc)}
 
 NFkB38) IKK:IkBb:NFkB Binding (2) [IKK[P]:IkBb] + [NFkB] ↔ [IKK[P]:IkBb:NFkB];   {IKK[P]:IkBb} , {NFkB} , {IKK[P]:IkBb:NFkB}
 
 NFkB39) IkBb:NFkB Nuclear Export [IkBb:NFkB(nuc)] → [IkBb:NFkB];   {IkBb:NFkB(nuc)}
 
 NFkB40) IKK:IkBe:NFkB Binding (2) [IKK[P]:IkBe] + [NFkB] ↔ [IKK[P]:IkBe:NFkB];   {IKK[P]:IkBe} , {NFkB} , {IKK[P]:IkBe:NFkB}
 
 NFkB41) IkBe:NFkB Nuclear Export [IkBe:NFkB(nuc)] → [IkBe:NFkB];   {IkBe:NFkB(nuc)}
 
 NFkB42) IKK:IkBa Catalysis [IKK[P]:IkBa] → [IKK[P]];   {IKK[P]:IkBa}
 
 NFkB43) IKK:IkBb Catalysis [IKK[P]:IkBb] → [IKK[P]];   {IKK[P]:IkBb}
 
 NFkB44) IKK:IkBe Catalysis [IKK[P]:IkBe] → [IKK[P]];   {IKK[P]:IkBe}
 
 TRIF06a)Inducible TNFa Synthesis by NFkB 2.0 × [NFkB(nuc)] → [TNFa] + 2.0 × [NFkB(nuc)];   {NFkB(nuc)}
 
Functions (2)
 
 Modified Michaelis Menten lambda(k, Enzyme, Substrate, Km, k*Enzyme*Substrate/(Km+Substrate))
 
 Modified Mass Action lambda(k1, Enzyme, Substrate1, Substrate2, k2, Product, k1*Enzyme*Substrate1*Substrate2-k2*Product)
 
 compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 CD14
Compartment: compartment
Initial concentration: 1.0
Constant
 
 IRAK4
Compartment: compartment
Initial concentration: 1.0
Constant
 
 LBP
Compartment: compartment
Initial concentration: 1.0
Constant
 
 LPS
Compartment: compartment
Initial concentration: 1.0
Constant
 
 LPS:LBP:CD14:TLR4:TIRAP:MyD88:IRAK4
Compartment: compartment
Initial concentration: 0.0
 
 MyD88
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TIRAP
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TLR4
Compartment: compartment
Initial concentration: 1.0
Constant
 
 IRAK1
Compartment: compartment
Initial concentration: 1.0
 
 TRAF6
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TRAF6:IRAK1[P]
Compartment: compartment
Initial concentration: 0.0
 
 TAK1:TAB1:TAB2
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TAK1:TAB1:TAB2:TRAF6
Compartment: compartment
Initial concentration: 0.0
 
 IKK
Compartment: compartment
Initial concentration: 0.1
 
 IKK[P]
Compartment: compartment
Initial concentration: 0.0
 
 RIP1
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TRAM
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TRIF
Compartment: compartment
Initial concentration: 1.0
Constant
 
 IRF3
Compartment: compartment
Initial concentration: 1.0
 
 IRF3[P]
Compartment: compartment
Initial concentration: 0.0
 
 IRF3[P](nuc)
Compartment: compartment
Initial concentration: 0.0
 
 source
Compartment: compartment
Initial concentration: 1.0
Constant
 
 sink
Compartment: compartment
Initial concentration: 0.0
Constant
 
 TNFa
Compartment: compartment
Initial concentration: 0.0
 
 TNFR1
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TRADD
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TRAF2
Compartment: compartment
Initial concentration: 1.0
Constant
 
 TNFa:TNFR1:TRAF2:TRADD:RIP1
Compartment: compartment
Initial concentration: 0.0
 
 IkBa
Compartment: compartment
Initial concentration: 0.0
 
 IkBa:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 NFkB
Compartment: compartment
Initial concentration: 0.1
 
 IKK[P]:IkBa:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 IkBb
Compartment: compartment
Initial concentration: 0.0
 
 IkBb:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 IKK[P]:IkBb:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 IkBe
Compartment: compartment
Initial concentration: 0.0
 
 IkBe:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 IKK[P]:IkBe:NFkB
Compartment: compartment
Initial concentration: 0.0
 
 NFkB(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBa(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBa:NFkB(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBb(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBb:NFkB(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBe(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBe:NFkB(nuc)
Compartment: compartment
Initial concentration: 0.0
 
 IkBa_mRNA
Compartment: compartment
Initial concentration: 0.0
 
 IkBb_mRNA
Compartment: compartment
Initial concentration: 0.0
 
 IkBe_mRNA
Compartment: compartment
Initial concentration: 0.0
 
 IKK[P]:IkBa
Compartment: compartment
Initial concentration: 0.0
 
 IKK[P]:IkBb
Compartment: compartment
Initial concentration: 0.0
 
 IKK[P]:IkBe
Compartment: compartment
Initial concentration: 0.0
 
 LPS:LBP:CD14:TLR4:RIP1:TRAM:TRIF:TBK/IKKe
Compartment: compartment
Initial concentration: 0.0
 
 TBK1/IKKe
Compartment: compartment
Initial concentration: 1.0
Constant
 
MYD881) Receptor Complex Formation (2)
 
   k1
Value: 1.0E-4
Constant
 
   k2
Value: 1.0E-4
Constant
 
MYD882) IRAK1 and TRAF6 Phosphorylation (2)
 
   k1
Value: 0.0010
Constant
 
   k2
Value: 0.0010
Constant
 
MYD883) TAK/TAB Binds to TRAF6 (2)
 
   k1
Value: 0.0030
Constant
 
   k2
Value: 0.01
Constant
 
MYD884) IKK Phosphorylation by TAK1 (2)
 
   k
Value: 0.1
Constant
 
   Km
Value: 0.1
Constant
 
MYD885) IKK[P] Dephosphorylation (1)
 
   k1
Value: 0.1
Constant
 
TRIF01) Receptor Complex Formation (2)
 
   k1
Value: 1.0E-4
Constant
 
   k2
Value: 1.0E-4
Constant
 
TRIF02) IRF3 Phosphorylation (2)
 
   k
Value: 0.1
Constant
 
   Km
Value: 0.1
Constant
 
TRIF03) IRF3 Dephosphorylation (1)
 
   k1
Value: 0.1
Constant
 
TRIF04) IRF3 Nuclear Import/Export (2)
 
   k1
Value: 0.1
Constant
 
   k2
Value: 0.1
Constant
 
TRIF05) Inducible TNFa Synthesis (1)
 
   k1
Value: 0.02
Constant
 
TRIF06) Constitutive TNFa Synthesis (1)
 
   k1
Value: 0.0010
Constant
 
TRIF09) TNFa Degradation (1)
 
   k1
Value: 0.1
Constant
 
TRIF10) TNFa Receptor Complex Formation (2)
 
   k1
Value: 0.1
Constant
 
   k2
Value: 0.1
Constant
 
TRIF11) IKK Phosphorylation by RIP1 (2)
 
   k
Value: 0.1
Constant
 
   Km
Value: 0.1
Constant
 
NFkB01) IkBa:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB02) IKK:IkBa:NFkB Binding (1) (2)
 
   k1
Value: 0.185
Constant
 
   k2
Value: 0.0125
Constant
 
NFkB03) IkBb:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB04) IKK:IkBb:NFkB Binding (1) (2)
 
   k1
Value: 0.048
Constant
 
   k2
Value: 0.00175
Constant
 
NFkB05) IkBe:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB06) IKK:IkBe:NFkB Binding (1) (2)
 
   k1
Value: 0.07
Constant
 
   k2
Value: 0.00175
Constant
 
NFkB07) IKK:IkBa:NFkB Catalysis (1)
 
   k1
Value: 0.0204
Constant
 
NFkB08) IKK:IkBb:NFkB Catalysis (1)
 
   k1
Value: 0.0075
Constant
 
NFkB09) IKK:IkBe:NFkB Catalysis (1)
 
   k1
Value: 0.011
Constant
 
NFkB10) IkBa:NFkB Constitutive Degradation (1)
 
   k1
Value: 2.25E-5
Constant
 
NFkB11) IkBb:NFkB Constitutive Degradation (1)
 
   k1
Value: 2.25E-5
Constant
 
NFkB12) IkBe:NFkB Constitutive Degradation (1)
 
   k1
Value: 2.25E-5
Constant
 
NFkB13) NFkB Nuclear Import/Export (2)
 
   k1
Value: 0.09
Constant
 
   k2
Value: 8.0E-5
Constant
 
NFkB14) Nuclear IkBa:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB15) Nuclear IkBb:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB16) Nuclear IkBe:NFkB Binding (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB17) Constitutive IkBa mRNA Synthesis (1)
 
   k1
Value: 1.54E-6
Constant
 
NFkB18) Inducible IkBa mRNA Synthesis (1)
 
   k1
Value: 0.0165
Constant
 
NFkB19) IkBa mRNA degradation (1)
 
   k1
Value: 2.8E-4
Constant
 
NFkB20) Constitutive IkBb mRNA Synthesis (1)
 
   k1
Value: 1.78E-7
Constant
 
NFkB21) IkBb mRNA degradation (1)
 
   k1
Value: 2.8E-4
Constant
 
NFkB22) Constitutive IkBe mRNA Synthesis (1)
 
   k1
Value: 1.27E-7
Constant
 
NFkB23) IkBe mRNA degradation (1)
 
   k1
Value: 2.8E-4
Constant
 
NFkB24) IKK:IkBa Binding (2)
 
   k1
Value: 0.0225
Constant
 
   k2
Value: 0.00125
Constant
 
NFkB25) IkBa Translation (1)
 
   k1
Value: 0.00408
Constant
 
NFkB26) IkBa Degradation (1)
 
   k1
Value: 1.13E-4
Constant
 
NFkB27) IkBa Nuclear Import/Export (2)
 
   k1
Value: 3.0E-4
Constant
 
   k2
Value: 2.0E-4
Constant
 
NFkB28) IKK:IkBb Binding (2)
 
   k1
Value: 0.0060
Constant
 
   k2
Value: 0.00175
Constant
 
NFkB29) IkBb Translation (1)
 
   k1
Value: 0.00408
Constant
 
NFkB30) IkBb Degradation (1)
 
   k1
Value: 1.13E-4
Constant
 
NFkB31) IkBb Nuclear Import/Export (2)
 
   k1
Value: 1.5E-4
Constant
 
   k2
Value: 1.0E-4
Constant
 
NFkB32) IKK:IkBe Binding (2)
 
   k1
Value: 0.0090
Constant
 
   k2
Value: 0.00175
Constant
 
NFkB33) IkBe Translation (1)
 
   k1
Value: 0.00408
Constant
 
NFkB34) IkBe Degradation (1)
 
   k1
Value: 1.13E-4
Constant
 
NFkB35) IkBe Nuclear Import/Export (2)
 
   k1
Value: 1.5E-4
Constant
 
   k2
Value: 1.0E-4
Constant
 
NFkB36) IKK:IkBa:NFkB Binding (2) (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB37) IkBa:NFkB Nuclear Export (1)
 
   k1
Value: 0.0138
Constant
 
NFkB38) IKK:IkBb:NFkB Binding (2) (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB39) IkBb:NFkB Nuclear Export (1)
 
   k1
Value: 0.0052
Constant
 
NFkB40) IKK:IkBe:NFkB Binding (2) (2)
 
   k1
Value: 0.5
Constant
 
   k2
Value: 5.0E-4
Constant
 
NFkB41) IkBe:NFkB Nuclear Export (1)
 
   k1
Value: 0.0052
Constant
 
NFkB42) IKK:IkBa Catalysis (1)
 
   k1
Value: 0.00407
Constant
 
NFkB43) IKK:IkBb Catalysis (1)
 
   k1
Value: 0.0015
Constant
 
NFkB44) IKK:IkBe Catalysis (1)
 
   k1
Value: 0.0022
Constant
 
TRIF06a)Inducible TNFa Synthesis by NFkB (1)
 
   k1
Value: 0.0010
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000489

Curator's comment: (updated: 24 Sep 2013 16:46:06 BST)

Figures 3 and 4 of the reference publication has been reproduced here. The model time is in seconds, for 400 mins, the simulation should be run for 24000 secs. Further the concentration are plotted in microMolar units whereas in the paper it is in nanoMolar.
The simulation was done using SBML odeSolver. The plots were generated using Gnuplot.

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