#schliemann1 #reactions J1: {1.0}TNFR = {1.0}TNFR_E ka_1 * TNFR J10: {1.0}TNFRC1 = $pool ka_10 * TNFRC1 J11: {1.0}TNFRC2 = $pool ka_11 * TNFRC2 J12: {1.0}TNFRC2_FLIP = $pool ka_12 * TNFRC2_FLIP J13: {1.0}TNFRC2_FLIP_FLIP = $pool ka_13 * TNFRC2_FLIP_FLIP J14: {1.0}TNFRC2_pCasp8 = $pool ka_14 * TNFRC2_pCasp8 J15: {1.0}TNFRC2_pCasp8_pCasp8 = $pool ka_15 * TNFRC2_pCasp8_pCasp8 J16: {1.0}TNFRC2_FLIP_pCasp8 = $pool ka_16 * TNFRC2_FLIP_pCasp8 J17: {1.0}TNFRC2_FLIP_pCasp8_RIP_TRAF2 = $pool ka_17 * TNFRC2_FLIP_pCasp8_RIP_TRAF2 J18: {1.0}TNFR_E + {1.0}TNF_E = {1.0}TNF_TNFR_E ka_18 * TNFR_E * TNF_E - kd_18 * TNF_TNFR_E J19: {1.0}TNF_TNFR_E + {1.0}TRADD = {1.0}TNF_TNFR_TRADD ka_19 * TNF_TNFR_E * TRADD J2: $pool = {1.0}TNFR ka_2 J20: {1.0}RIP + {1.0}TRAF2 + {1.0}TNF_TNFR_TRADD = {1.0}TNFRC1 ka_20 * RIP * TRAF2 * TNF_TNFR_TRADD J21: {1.0}TNFRC1 = {1.0}TNFRCint1 ka_21 * TNFRC1 J22: {1.0}TNFRCint1 = {1.0}RIP + {1.0}TRAF2 + {1.0}TNFRCint2 ka_22 * TNFRCint1 J23: {2.0}FADD + {1.0}TNFRCint2 = {1.0}TNFRCint3 ka_23 * pow(FADD, 2) * TNFRCint2 J24: {1.0}TNFRCint3 = {1.0}TNFRC2 ka_24 * TNFRCint3 J25: {1.0}TNFRC2 + {1.0}FLIP = {1.0}TNFRC2_FLIP ka_25 * TNFRC2 * FLIP J26: {1.0}FLIP + {1.0}TNFRC2_FLIP = {1.0}TNFRC2_FLIP_FLIP ka_26 * FLIP * TNFRC2_FLIP J27: {1.0}TNFRC2 + {1.0}pCasp8 = {1.0}TNFRC2_pCasp8 ka_27 * TNFRC2 * pCasp8 J28: {1.0}TNFRC2_pCasp8 + {1.0}pCasp8 = {1.0}TNFRC2_pCasp8_pCasp8 ka_28 * TNFRC2_pCasp8 * pCasp8 J29: {1.0}TNFRC2_pCasp8_pCasp8 = {1.0}TNFRC2 + {1.0}Casp8 ka_29 * TNFRC2_pCasp8_pCasp8 J3: {1.0}TNFR_E = $pool ka_3 * TNFR_E J30: {1.0}FLIP + {1.0}TNFRC2_pCasp8 = {1.0}TNFRC2_FLIP_pCasp8 ka_30 * FLIP * TNFRC2_pCasp8 J31: {1.0}TNFRC2_FLIP + {1.0}pCasp8 = {1.0}TNFRC2_FLIP_pCasp8 ka_31 * TNFRC2_FLIP * pCasp8 J32: {1.0}TNFRC2_FLIP_pCasp8 = {1.0}TNFRC2 + {1.0}Casp8 ka_32 * TNFRC2_FLIP_pCasp8 J33: {1.0}RIP + {1.0}TRAF2 + {1.0}TNFRC2_FLIP_pCasp8 = {1.0}TNFRC2_FLIP_pCasp8_RIP_TRAF2 ka_33 * RIP * TRAF2 * TNFRC2_FLIP_pCasp8 J34: {1.0}IKK = {1.0}IKKa ka_34 * TNFRC2_FLIP_pCasp8_RIP_TRAF2 * IKK J35: $pool = {1.0}IKK ka_35 - kd_35 * IKK J36: $pool = {1.0}NFkB ka_36 - kd_36 * NFkB J37: $pool = {1.0}FLIP ka_37 - kd_37 * FLIP J38: $pool = {1.0}XIAP ka_38 - kd_38 * XIAP J39: $pool = {1.0}A20 ka_39 - kd_39 * A20 J4: $pool = {1.0}RIP ka_4 - kd_4 * RIP J40: {1.0}IKKa = $pool ka_40 * IKKa J41: {1.0}IkBa_NFkB = $pool ka_41 * IkBa_NFkB J42: {1.0}NFkB_N = $pool ka_42 * NFkB_N J43: {1.0}IkBa_mRNA = $pool ka_43 * IkBa_mRNA J44: {1.0}IkBa = $pool ka_44 * IkBa J45: {1.0}IkBa_N = $pool ka_45 * IkBa_N J46: {1.0}IkBa_NFkB_N = $pool ka_46 * IkBa_NFkB_N J47: {1.0}PIkBa = $pool ka_47 * PIkBa J48: {1.0}A20_mRNA = $pool ka_48 * A20_mRNA J49: {1.0}XIAP_mRNA = $pool ka_49 * XIAP_mRNA J5: $pool = {1.0}TRADD ka_5 - kd_5 * TRADD J50: {1.0}FLIP_mRNA = $pool ka_50 * FLIP_mRNA J51: {1.0}IKK = {1.0}IKKa ka_51 * TNFRC1 * IKK J52: {1.0}IKKa = {1.0}IKK ka_52 * IKKa J53: {1.0}TNFRC1 = {1.0}TRAF2 + {1.0}TNF_TNFR_TRADD ka_53 * TNFRC1 * A20 J54: {1.0}NFkB + {1.0}IkBa = {1.0}IkBa_NFkB ka_54 * NFkB * IkBa J55: {1.0}IkBa_NFkB = {1.0}NFkB + {1.0}PIkBa ka_55 * IKKa * IkBa_NFkB J56: {1.0}NFkB = {1.0}NFkB_N ka_56 * NFkB J57: $pool = {1.0}IkBa_mRNA ka_57 * NFkB_N J58: $pool = {1.0}IkBa ka_58 * IkBa_mRNA J59: {1.0}IkBa = {1.0}IkBa_N ka_59 * IkBa - kd_59 * IkBa_N J6: $pool = {1.0}TRAF2 ka_6 - kd_6 * TRAF2 J60: {1.0}NFkB_N + {1.0}IkBa_N = {1.0}IkBa_NFkB_N ka_60 * NFkB_N * IkBa_N J61: {1.0}IkBa_NFkB_N = {1.0}IkBa_NFkB ka_61 * IkBa_NFkB_N J62: $pool = {1.0}A20_mRNA ka_62 * NFkB_N J63: $pool = {1.0}A20 ka_63 * A20_mRNA J64: $pool = {1.0}XIAP_mRNA ka_64 * NFkB_N J65: $pool = {1.0}XIAP ka_65 * XIAP_mRNA J66: $pool = {1.0}FLIP_mRNA ka_66 * NFkB_N J67: $pool = {1.0}FLIP ka_67 * FLIP_mRNA J68: $pool = {1.0}pCasp8 ka_68 - kd_68 * pCasp8 J69: $pool = {1.0}pCasp3 ka_69 - kd_69 * pCasp3 J7: $pool = {1.0}FADD ka_7 - kd_7 * FADD J70: $pool = {1.0}pCasp6 ka_70 - kd_70 * pCasp6 J71: {1.0}Casp8 = $pool ka_71 * Casp8 J72: {1.0}Casp3 = $pool ka_72 * Casp3 J73: {1.0}Casp6 = $pool ka_73 * Casp6 J74: {1.0}XIAP_Casp3 = $pool ka_74 * XIAP_Casp3 J75: $pool = {1.0}BAR ka_75 - kd_75 * BAR J76: {1.0}BAR_Casp8 = $pool ka_76 * BAR_Casp8 J77: {1.0}PARP = $pool ka_77 * PARP - kd_77 J78: {1.0}cPARP = $pool ka_78 * cPARP J79: {1.0}pCasp3 = {1.0}Casp3 ka_79 * pCasp3 * Casp8 J8: {1.0}TNF_TNFR_E = $pool ka_8 * TNF_TNFR_E J80: {1.0}pCasp6 = {1.0}Casp6 ka_80 * pCasp6 * Casp3 J81: {1.0}pCasp8 = {1.0}Casp8 ka_81 * pCasp8 * Casp6 J82: {1.0}XIAP + {1.0}Casp3 = {1.0}XIAP_Casp3 ka_82 * XIAP * Casp3 - kd_82 * XIAP_Casp3 J83: {1.0}XIAP = $pool ka_83 * XIAP * Casp3 J84: {1.0}XIAP_Casp3 = {1.0}XIAP ka_84 * XIAP_Casp3 J85: {1.0}RIP = $pool ka_85 * RIP * Casp3 J86: {1.0}FLIP = $pool ka_86 * FLIP * Casp3 J87: {1.0}PARP = {1.0}cPARP ka_87 * Casp3 * PARP J88: {1.0}BAR + {1.0}Casp8 = {1.0}BAR_Casp8 ka_88 * BAR * Casp8 - kd_88 * BAR_Casp8 J9: {1.0}TNF_TNFR_TRADD = $pool ka_9 * TNF_TNFR_TRADD #parameters J1_ka_1 = 0.001 J2_ka_2 = 2.8e-07 J3_ka_3 = 5.6e-05 J4_ka_4 = 2.0256e-05 J4_kd_4 = 0.0001 J5_ka_5 = 2.9344e-05 J5_kd_5 = 0.0001 J6_ka_6 = 3.3056e-05 J6_kd_6 = 0.0001 J7_ka_7 = 3.0944e-05 J7_kd_7 = 0.0001 J8_ka_8 = 5.6e-05 J9_ka_9 = 0.02352 J10_ka_10 = 5.6e-05 J11_ka_11 = 5.6e-05 J12_ka_12 = 5.6e-05 J13_ka_13 = 5.6e-05 J14_ka_14 = 5.6e-05 J15_ka_15 = 5.6e-05 J16_ka_16 = 5.6e-05 J17_ka_17 = 5.6e-05 J18_ka_18 = 0.00953471 J18_kd_18 = 6.60377e-05 J19_ka_19 = 0.00427827 J20_ka_20 = 0.0976562 J21_ka_21 = 0.001135 J22_ka_22 = 0.001135 J23_ka_23 = 0.0118534 J24_ka_24 = 0.1135 J25_ka_25 = 0.3125 J26_ka_26 = 0.3125 J27_ka_27 = 0.03125 J28_ka_28 = 0.03125 J29_ka_29 = 0.45 J30_ka_30 = 0.3125 J31_ka_31 = 0.3125 J32_ka_32 = 0.3 J33_ka_33 = 0.00976562 J34_ka_34 = 0.03125 J35_ka_35 = 6.4e-05 J35_kd_35 = 0.0001 J36_ka_36 = 1.6e-06 J36_kd_36 = 0.0001 J37_ka_37 = 2.24902e-06 J37_kd_37 = 0.0001 J38_ka_38 = 0.000772256 J38_kd_38 = 0.0001 J39_ka_39 = 9.6e-06 J39_kd_39 = 0.0001 J40_ka_40 = 0.0001 J41_ka_41 = 0.0001 J42_ka_42 = 0.0001 J43_ka_43 = 0.000394201 J44_ka_44 = 0.00154022 J45_ka_45 = 0.0001 J46_ka_46 = 0.0001 J47_ka_47 = 0.0115517 J48_ka_48 = 0.000470498 J49_ka_49 = 0.000104931 J50_ka_50 = 0.000165744 J51_ka_51 = 93.75 J52_ka_52 = 0.1 J53_ka_53 = 0.00625 J54_ka_54 = 1.25 J55_ka_55 = 0.104167 J56_ka_56 = 0.0125 J57_ka_57 = 3.0303e-05 J58_ka_58 = 0.0606061 J59_ka_59 = 0.005 J59_kd_59 = 0.00257576 J60_ka_60 = 1.4348 J61_ka_61 = 0.0151515 J62_ka_62 = 3.78788e-05 J63_ka_63 = 0.0151515 J64_ka_64 = 3.33333e-05 J65_ka_65 = 0.0506061 J66_ka_66 = 3.33333e-05 J67_ka_67 = 0.00687273 J68_ka_68 = 0.000197531 J68_kd_68 = 6.17284e-05 J69_ka_69 = 4.93827e-05 J69_kd_69 = 6.17284e-05 J70_ka_70 = 3.95062e-06 J70_kd_70 = 6.17284e-05 J71_ka_71 = 5.78704e-05 J72_ka_72 = 5.78704e-05 J73_ka_73 = 5.78704e-05 J74_ka_74 = 5.78704e-05 J75_ka_75 = 1.66603e-06 J75_kd_75 = 5.78704e-06 J76_ka_76 = 5.78704e-05 J77_ka_77 = 5.78704e-06 J77_kd_77 = 9.64506e-06 J78_ka_78 = 5.78704e-06 J79_ka_79 = 0.015625 J80_ka_80 = 0.009375 J81_ka_81 = 0.0015625 J82_ka_82 = 0.625 J82_kd_82 = 0.001 J83_ka_83 = 1.875 J84_ka_84 = 5e-05 J85_ka_85 = 0.15625 J86_ka_86 = 0.15625 J87_ka_87 = 0.1875 J88_ka_88 = 0.520833 J88_kd_88 = 0.001 cytoplasm = 3.2 extracellular = 1344.0 nucleus = 1.056 #initial values A20 = 0.104434 A20_mRNA = 5.56657e-05 BAR = 0.28789 BAR_Casp8 = 0.0 Casp3 = 0.0 Casp6 = 0.0 Casp8 = 0.0 FADD = 0.30944 FLIP = 0.0320472 FLIP_mRNA = 0.000139056 IKK = 0.64 IKKa = 0.0 IkBa = 0.00101518 IkBa_N = 0.0013839 IkBa_NFkB = 0.0151032 IkBa_NFkB_N = 9.00189e-05 IkBa_mRNA = 5.31517e-05 NFkB = 0.000115365 NFkB_N = 0.000691431 PARP = 1.66667 PIkBa = 0.0 RIP = 0.20256 TNFR = 0.00028 TNFRC1 = 0.0 TNFRC2 = 0.0 TNFRC2_FLIP = 0.0 TNFRC2_FLIP_FLIP = 0.0 TNFRC2_FLIP_pCasp8 = 0.0 TNFRC2_FLIP_pCasp8_RIP_TRAF2 = 0.0 TNFRC2_pCasp8 = 0.0 TNFRC2_pCasp8_pCasp8 = 0.0 TNFRCint1 = 0.0 TNFRCint2 = 0.0 TNFRCint3 = 0.0 TNFR_E = 0.005 TNF_E = 0.2688 TNF_TNFR_E = 0.0 TNF_TNFR_TRADD = 0.0 TRADD = 0.29344 TRAF2 = 0.33056 XIAP = 7.83371 XIAP_Casp3 = 0.0 XIAP_mRNA = 0.000219646 cPARP = 0.0 pCasp3 = 0.8 pCasp6 = 0.064 pCasp8 = 3.2 #assignment rules