begin name beuke3 end name begin reactions Complexassociationc {1.0}p65cytoplasm + {1.0}IkBacytoplasm = {1.0}s19 ComplexdegradationIkBac {1.0}s19 = {1.0}p65cytoplasm ComplexdegradationIkBan {1.0}p65IkBanucleus = {1.0}p65nucleus Complexdegradationp65c {1.0}s19 = {1.0}IkBacytoplasm Complexdegradationp65n {1.0}p65IkBanucleus = {1.0}s11 Complexnuclearshuttle {1.0}p65IkBanucleus = {1.0}s19 IKKphosphorylation {1.0}s14 = {1.0}s15 IkBadegradationc {1.0}IkBacytoplasm = {1.0}$EXTERNAL IkBadegradationn {1.0}s11 = {1.0}$EXTERNAL IkBamRNAdegradationc {1.0}IkBamRNAcytoplasm = {1.0}$EXTERNAL IkBamRNAdegradationn {1.0}IkBamRNAnucleus = {1.0}$EXTERNAL IkBamRNAtransport {1.0}IkBamRNAnucleus = {1.0}IkBamRNAcytoplasm IkBanuclearshuttle {1.0}IkBacytoplasm = {1.0}s11 IkBaphosphorylation {1.0}IkBacytoplasm = {1.0}s5 IkBatranscriptionelongation1 {1.0}IkBapremRNA1 = {1.0}IkBapremRNA2 IkBatranscriptionelongation2 {1.0}IkBapremRNA2 = {1.0}IkBamRNAnucleus IkBatranslation {1.0}IkBamRNAcytoplasm = {1.0}IkBamRNAcytoplasm + {1.0}IkBacytoplasm JNKactivephosphorylation {1.0}JNK = {1.0}JNKP JNKbasalphosphorylation {1.0}JNK = {1.0}JNKP JNKdephosphorylation {1.0}JNKP = {1.0}JNK LPSLSECdegradation {1.0}LPS = {1.0}$EXTERNAL LPSMCdegradation {1.0}LPS = {1.0}$EXTERNAL MSK1activation {1.0}MSK1 = {1.0}MSK1P MSK1deactivation {1.0}MSK1P = {1.0}MSK1 TNFR1shuttle {1.0}TNFR1cytoplasm = {1.0}TNFR1EL TNFaLSECtranscriptionelongation {1.0}TNFapremRNALSEC = {1.0}TNFamRNALSEC TNFaLSECtranscriptioninitiation {1.0}$EXTERNAL = {2.0}TNFapremRNALSEC TNFaLSECtranslation {1.0}TNFamRNALSEC = {1.0}TNFamRNALSEC + {1.0}s16 TNFaMCtranscriptionelongation {1.0}TNFapremRNAMC = {1.0}TNFamRNAMC TNFaMCtranscriptioninitiation {1.0}$EXTERNAL = {2.0}TNFapremRNAMC TNFaMCtranslation {1.0}TNFamRNAMC = {1.0}TNFamRNAMC + {1.0}s16 TNFaTNFR1association {1.0}TNFR1EL + {1.0}s16 = {1.0}TNFaTNFR1EL TNFaTNFR1internalisation {1.0}TNFaTNFR1EL = {1.0}TNFaTNFR1cytoplasm TNFadegradation {1.0}s16 = {1.0}$EXTERNAL TNFainternaldegradation {1.0}TNFaTNFR1cytoplasm = {1.0}TNFR1cytoplasm TNFamRNALSECdegradation {1.0}TNFamRNALSEC = {1.0}$EXTERNAL TNFamRNAMCdegradation {1.0}TNFamRNAMC = {1.0}$EXTERNAL basalIKKbphosphorylation {1.0}s14 = {1.0}s15 p38activephosphorylation {1.0}p38 = {1.0}p38P p38basalphosphorylation {1.0}p38 = {1.0}p38P p38dephosphorylation {1.0}p38P = {1.0}p38 p652Pdegradation {1.0}p652P = {1.0}$EXTERNAL p652Pdephosphorylation0 {1.0}p652P = {1.0}p65nucleus p65Pdegradationc {1.0}s3 = {1.0}$EXTERNAL p65Pdegradationn {1.0}s8 = {1.0}$EXTERNAL p65Pdephosphorylationc {1.0}s8 = {1.0}p65nucleus p65Pdephosphorylationn {1.0}s3 = {1.0}p65cytoplasm p65PphosphorylationMSK1 {1.0}s8 = {1.0}p652P p65nuclearshuttle {1.0}p65cytoplasm = {1.0}p65nucleus p65phosphorylationMSK1 {1.0}p65nucleus = {1.0}p652P p65translation {1.0}$p65mRNA = {1.0}$p65mRNA + {1.0}p65cytoplasm re10 {1.0}$EXTERNAL = {1.0}IkBapremRNA1 re14 {1.0}s5 = {1.0}$EXTERNAL re15 {1.0}s19 = {1.0}s3 + {1.0}s5 re17 {1.0}s15 = {1.0}s14 re19 {1.0}p65nucleus + {1.0}s11 = {1.0}p65IkBanucleus re3 {1.0}s3 = {1.0}s8 end reactions begin rate equations Complexassociationc = default*(IkBap65associationk*IkBacytoplasm[t]*p65cytoplasm[t] - IkBap65dissociationk*s19[t]) ComplexdegradationIkBac = default*IkBadegcomplexcytk*s19[t] ComplexdegradationIkBan = c1*IkBadegcomplexnuck*p65IkBanucleus[t] Complexdegradationp65c = default*p65degradationk*s19[t] Complexdegradationp65n = c1*p65degradationk*p65IkBanucleus[t] Complexnuclearshuttle = IkBap65nuclearexportk*p65IkBanucleus[t] - IkBap65nuclearimportk*s19[t] IKKphosphorylation = default*Catalyticactivationirrev[s14[t], TNFaTNFR1EL[t], IKKbactivephosphorylationkM, IKKbactivephosphorylationvmax, IKKbactivephosphorylationkA] IkBadegradationc = default*IkBadegcytk*IkBacytoplasm[t] IkBadegradationn = c1*IkBadegnuck*s11[t] IkBamRNAdegradationc = default*IkBamRNAdegcytk*IkBamRNAcytoplasm[t] IkBamRNAdegradationn = c1*IkBamRNAdegnuck*IkBamRNAnucleus[t] IkBamRNAtransport = IkBamRNAtransportk*IkBamRNAnucleus[t] IkBanuclearshuttle = IkBanuclearimportk*IkBacytoplasm[t] - IkBanuclearexportk*s11[t] IkBaphosphorylation = default*HenriMichaelisMentenirreversible[IkBacytoplasm[t], IkBaphosphorylationkM, IkBaphosphorylationvmax] IkBatranscriptionelongation1 = c1*IkBatranscriptionelongationkbasal*IkBapremRNA1[t] IkBatranscriptionelongation2 = c1*IkBatranscriptionelongationkbasal*IkBapremRNA2[t] IkBatranslation = default*HenriMichaelisMentenirreversible[IkBamRNAcytoplasm[t], IkBatranslationKm, IkBatranslationvmax] JNKactivephosphorylation = default*HenriMichaelisMentenirreversible[JNK[t], JNKactivephoshorylationKm, JNKactivephosphorylationvmax] JNKbasalphosphorylation = default*JNKbasalphosphorylationk*JNK[t] JNKdephosphorylation = default*JNKdephosphorylationk*JNKP[t] LPSLSECdegradation = EL*LPSLSECdegradationk*LPS[t] LPSMCdegradation = EL*LPSMCdegradationk*LPS[t] MSK1activation = c1*HenriMichaelisMentenirreversible[MSK1[t], MSK1activationkM, MSK1activationvmax] MSK1deactivation = c1*MSK1dephosphorylationk*MSK1P[t] TNFR1shuttle = kTNFR1vessicle2outermembraneshuttle*TNFR1cytoplasm[t] - kTNFR1outermembrane2vessicleshuttle*TNFR1EL[t] TNFaLSECtranscriptionelongation = LSEC*TNFaLSECtranscriptionelongationk*TNFapremRNALSEC[t] TNFaLSECtranscriptioninitiation = LSEC*TNFatranscriptioninitiation[TNFaLSECtranscriptioninitiationkbasal, TNFaLSECtranscriptioninitiationvALPS, LPS[t], TNFaLSECtranscriptioninitiationkALPS] TNFaLSECtranslation = TNFaLSECtranslationk*TNFamRNALSEC[t] TNFaMCtranscriptionelongation = MC*TNFaMCtranscriptionelongationk*TNFapremRNAMC[t] TNFaMCtranscriptioninitiation = MC*TNFatranscriptioninitiation[TNFaMCtranscriptioninitiationkbasal, TNFaMCtranscriptioninitiationvALPS, LPS[t], TNFaMCtranscriptioninitiationkALPS] TNFaMCtranslation = TNFaMCtranslationk*TNFamRNAMC[t] TNFaTNFR1association = EL*(-(kTNFaTNFR1dissociation*TNFaTNFR1EL[t]) + kTNFaTNFR1association*s16[t]*TNFR1EL[t]) TNFaTNFR1internalisation = kTNFaTNFR1internalisation*TNFaTNFR1EL[t] TNFadegradation = EL*TNFadegradationk*s16[t] TNFainternaldegradation = default*kTNFainternaldegradation*TNFaTNFR1cytoplasm[t] TNFamRNALSECdegradation = LSEC*TNFamRNALSECdegradationk*TNFamRNALSEC[t] TNFamRNAMCdegradation = MC*TNFamRNAMCdegradationk*TNFamRNAMC[t] basalIKKbphosphorylation = default*IKKbbasalphosphoylationk*s14[t] p38activephosphorylation = default*HenriMichaelisMentenirreversible[p38[t], p38activephoshorylationKm, p38activephosphorylationvmax] p38basalphosphorylation = default*p38basalphosphorylationk*p38[t] p38dephosphorylation = default*p38dephosphorylationk*p38P[t] p652Pdegradation = c1*p65degradationk*p652P[t] p652Pdephosphorylation0 = c1*p652Pdephosphorylation*p652P[t] p65Pdegradationc = default*p65degradationk*s3[t] p65Pdegradationn = c1*p65degradationk*s8[t] p65Pdephosphorylationc = c1*p65Pdephosphorylationk*s8[t] p65Pdephosphorylationn = default*p65Pdephosphorylationk*s3[t] p65PphosphorylationMSK1 = c1*HenriMichaelisMentenirreversible[s8[t], p65PMSK1phosphrylationkM, p65PMSK1phosphrylationvmax] p65nuclearshuttle = p65nuclearimportk*p65cytoplasm[t] - p65nuclearexportk*p65nucleus[t] p65phosphorylationMSK1 = c1*HenriMichaelisMentenirreversible[p65nucleus[t], p65MSK1phosphorylationkM, p65MSK1phosphrylationvmax] p65translation = default*p65mRNA*p65translationk re10 = c1*activatedTranscription1[IkBatranscriptioninitiationkbasal, IkBatranscriptionkA2p65P, s8[t], IkBatranscriptionkAp65, p65nucleus[t], p652P[t], IkBatranscriptionkA3p652P] re14 = default*IkBapactivedegradationk*s5[t] re15 = default*HenriMichaelisMentenirreversible[s19[t], IkBap65phosphorylationkM, IkBap65phosphorylationvmax] re17 = default*IKKbdephopshorylationk*s15[t] re19 = c1*(-(IkBap65dissociationk*p65IkBanucleus[t]) + IkBap65associationk*p65nucleus[t]*s11[t]) re3 = p65nuclearimportk*s3[t] - p65nuclearexportk*s8[t] end rate equations begin parameters IKKbactivephosphorylationkA = 0.0458734293398926 IKKbactivephosphorylationkM = 5.0 IKKbactivephosphorylationvmax = 63.375821737573 IKKbbasalphosphoylationk = "1.00000000222045e-07" IKKbdephopshorylationk = 0.00240839365117589 IkBadegcomplexcytk = "1e-05" IkBadegcomplexnuck = "1.00000000002221e-05" IkBadegcytk = "4.51627599206577e-05" IkBadegnuck = "1e-05" IkBamRNAdegcytk = 0.000203995909577407 IkBamRNAdegnuck = "5e-05" IkBamRNAtransportk = 0.0001 IkBanuclearimportk = 0.005 IkBap65associationk = 0.0334296587563766 IkBap65nuclearexportk = 0.000100000000000222 IkBap65nuclearimportk = 0.00199999999999978 IkBap65phosphorylationkM = 0.5 IkBap65phosphorylationkcat = 23.7842490714247 IkBapactivedegradationk = 0.00388933983234716 IkBaphosphorylationkM = 0.141052340885947 IkBatranscriptionelongationkbasal = 0.00229785212051148 IkBatranscriptioninitiationkbasal = "1e-06" IkBatranscriptionkA2p65P = 0.000100000000000222 IkBatranscriptionkA3p652P = 0.000100000000000222 IkBatranscriptionkAp65 = 0.0650941195667352 IkBatranslationKm = 0.673943661414537 IkBatranslationvmax = 0.000831353763043219 JNKactivephoshorylationKm = 0.00100000000000022 JNKactivephosphorylationkcat = 129397.251691883 JNKbasalphosphorylationk = 0.000288246429277155 JNKdephosphorylationk = 0.000439860502037341 LPSLSECdegradationk = 0.00022691990763365 LPSMCdegradationk = 0.000116872398310443 MSK1activationkM = 0.332175 MSK1dephosphorylationk = 0.00999999999999978 MSK1phosphorylationkcat = 0.000999999999999778 TNFaLSECtranscriptionelongationk = "1.00000000022204e-06" TNFaLSECtranscriptioninitiationkALPS = 1.08607178915101 TNFaLSECtranscriptioninitiationkbasal = 0.0 TNFaLSECtranscriptioninitiationvALPS = "1.22414196552364e-05" TNFaLSECtranslationk = "2.17362661072005e-05" TNFaMCtranscriptionelongationk = "1.00000000022204e-06" TNFaMCtranscriptioninitiationkALPS = 0.829523383541807 TNFaMCtranscriptioninitiationkbasal = 0.0 TNFaMCtranscriptioninitiationvALPS = "5.92893637443215e-06" TNFaMCtranslationk = "2.17249481768177e-06" TNFadegradationk = 0.000165457369506909 TNFamRNALSECdegradationk = 0.588609608498249 TNFamRNAMCdegradationk = 0.0511300421668375 kIkBa = 142322.590983584 kIkBaP = 581912.595265984 kIkBamRNA = 83954.031290434 kJNKP = 132488.100842004 kMSKP = 79505430.5973529 kTNFR1outermembrane2vessicleshuttle = "1.8e-05" kTNFR1vessicle2outermembraneshuttle = 0.0004 kTNFaTNFR1association = 16.833 kTNFaTNFR1internalisation = 0.00077 kTNFainternaldegradation = "7.22595577481172e-05" kp38P = 604822.527788398 kp65 = 0.102372088824604 kp65P = 3058419.22306038 p38activephoshorylationKm = 1.16996274736508 p38activephosphorylationkcat = 71235.2777766154 p38basalphosphorylationk = "8.53615616997532e-05" p38dephosphorylationk = 0.000730127683728513 p65MSK1phosphorylationkM = 0.723076219021569 p65MSK1phosphrylationkcat = 0.085311347603303 p65Pdephosphorylationk = 0.000995614225497409 p65degradationk = "1.328912101e-05" p65nuclearimportk = 0.0005 p65translationk = "1.68e-06" p65mRNA = 1.0 EL = "2.59e-06" LSEC = "4.7e-07" MC = "3.5e-07" c1 = "8e-07" default = "1.3e-05" end parameters begin initial conditions IkBacytoplasm[0] = IkBacytoplasmi IkBamRNAcytoplasm[0] = IkBamRNAcytoplasmi IkBamRNAnucleus[0] = IkBamRNAnucleusi IkBapremRNA1[0] = IkBapremRNA1i IkBapremRNA2[0] = IkBapremRNA2i JNK[0] = JNKi JNKP[0] = JNKPi LPS[0] = LPSi MSK1[0] = MSK1i MSK1P[0] = MSK1Pi TNFR1EL[0] = TNFR1ELi TNFR1cytoplasm[0] = TNFR1cytoplasmi TNFaTNFR1EL[0] = TNFaTNFR1ELi TNFaTNFR1cytoplasm[0] = TNFaTNFR1cytoplasmi TNFamRNALSEC[0] = TNFamRNALSECi TNFamRNAMC[0] = TNFamRNAMCi TNFapremRNALSEC[0] = TNFapremRNALSECi TNFapremRNAMC[0] = TNFapremRNAMCi p38[0] = p38i p38P[0] = p38Pi p652P[0] = p652Pi p65IkBanucleus[0] = p65IkBanucleusi p65cytoplasm[0] = p65cytoplasmi p65nucleus[0] = p65nucleusi s11[0] = s11i s14[0] = s14i s15[0] = s15i s16[0] = s16i s19[0] = s19i s3[0] = s3i s5[0] = s5i s8[0] = s8i end initial conditions begin initial values IkBacytoplasmi = 0.471089717173928 IkBamRNAcytoplasmi = 0.333896464790274 IkBamRNAnucleusi = 8.85475669514445e-06 IkBapremRNA1i = 0.48168679774942 IkBapremRNA2i = 0.48168679774942 JNKi = 0.604115251647494 JNKPi = 0.395884748352507 LPSi = 5.0 MSK1i = 14.9897594053151 MSK1Pi = 0.0102405946849511 TNFR1ELi = 0.00122834645669293 TNFR1cytoplasmi = 5.52755905511816e-05 TNFaTNFR1ELi = 0.0 TNFaTNFR1cytoplasmi = 0.0 TNFamRNALSECi = 0.0 TNFamRNAMCi = 0.0 TNFapremRNALSECi = 0.0 TNFapremRNAMCi = 0.0 p38i = 0.895324724172268 p38Pi = 0.104675275827732 p652Pi = 0.186188426712606 p65IkBanucleusi = 0.904439631339684 p65cytoplasmi = 0.000328869555044952 p65nucleusi = 0.0164370718721187 s11i = 0.942179298536235 s14i = 0.299987544081733 s15i = 1.24559182673988e-05 s16i = 0.0 s19i = 0.0452218191890392 s3i = 0.00345444129388382 s5i = 0.0649370850531866 s8i = 0.172694651888365 end initial values begin assignment rules unscaledIkBaP := default*s5[t] p38activephosphorylationvmax := p38activephosphorylationkcat*TNFaTNFR1EL[t] IkBaphosphorylationvmax := IkBaphosphorylationkcat*s15[t] unscaledp38P := default*p38P[t] scaledp65P := kp65P*unscaledp65P IkBap65phosphorylationvmax := IkBap65phosphorylationkcat*s15[t] scaledIkBa := kIkBa*unscaledIkBa scaledp65 := kp65*unscaledp65 p65PMSK1phosphrylationkM := p65MSK1phosphorylationkM scaledIkBamRNA := kIkBamRNA*unscaledIkBamRNA unscaledJNKP := default*JNKP[t] p652Pdephosphorylation := p65Pdephosphorylationk kTNFaTNFR1dissociation := 0.000019*kTNFaTNFR1association scaledMSKP := kMSKP*unscaledMSKP p65PMSK1phosphrylationkcat := p65MSK1phosphrylationkcat p65nuclearexportk := 0.02*p65nuclearimportk IkBanuclearexportk := 0.5*IkBanuclearimportk unscaledIkBamRNA := default*IkBamRNAcytoplasm[t] + c1*IkBamRNAnucleus[t] IkBaphosphorylationkcat := IkBap65phosphorylationkcat unscaledp65P := default*s3[t] + c1*s8[t] scaledp38P := kp38P*unscaledp38P scaledIkBaP := kIkBaP*unscaledIkBaP IkBap65dissociationk := 0.003*IkBap65associationk MSK1activationvmax := MSK1phosphorylationkcat*p38P[t] p65MSK1phosphrylationvmax := p65MSK1phosphrylationkcat*MSK1P[t] JNKactivephosphorylationvmax := JNKactivephosphorylationkcat*TNFaTNFR1EL[t] p65PMSK1phosphrylationvmax := p65PMSK1phosphrylationkcat*MSK1P[t] unscaledMSKP := c1*MSK1P[t] scaledJNKP := kJNKP*unscaledJNKP unscaledIkBa := c1*(p65IkBanucleus[t] + s11[t]) + default*(IkBacytoplasm[t] + s19[t] + s5[t]) unscaledp65 := default*(p65cytoplasm[t] + s19[t] + s3[t]) + c1*(p652P[t] + p65IkBanucleus[t] + p65nucleus[t] + s8[t]) end assignment rules begin function definitions Catalyticactivationirrev[substrate_,Activator_,Kms_,V_,Ka_] := (Activator*substrate*V)/((Activator + Ka)*(Kms + substrate)) HenriMichaelisMentenirreversible[substrate_,Km_,V_] := (substrate*V)/(Km + substrate) TNFatranscriptioninitiation[kbasal_,vA_,A_,kA_] := kbasal + (A*vA)/(A + kA) activatedTranscription1[k1_,k2_,Modifier_,k3_,Modifier2_,Modifier3_,k4_] := k1 + k2*Modifier + k3*Modifier2 + k4*Modifier3 end function definitions begin events end events begin process annotations end process annotations begin species annotations end species annotations begin units end units