// Created by libAntimony v2.8.0 model *Bakker2001_Glycolysis() // Compartments and Species: compartment tot_cell, glycosome, cytosol, extracellular; species GlcI in tot_cell, Pg in glycosome, Glc6P in glycosome, Fru6P in glycosome; species Fru16BP in glycosome, DHAP in tot_cell, GAP in glycosome, NAD in glycosome; species BPGA13 in glycosome, NADH in glycosome, Pyr in cytosol, Nb in tot_cell; species Pc in cytosol, $PyrE in extracellular, $Gly in glycosome, $GlcE in extracellular; species $Gly3P in tot_cell, $Gly3Pc in cytosol, $Gly3Pg in glycosome, $ATPc in cytosol; species $ADPc in cytosol, $ATPg in glycosome, $ADPg in glycosome, $DHAPg in glycosome; species $DHAPc in cytosol, $PGAg in glycosome, $PEPc in cytosol; // Assignment Rules: Gly3P := (Gly3Pc*cytosol + Gly3Pg*glycosome)/tot_cell; Gly3Pc := sumc5 - DHAPc; Gly3Pg := (Gly3Pc*DHAPg)/(Keq_anti*DHAPc); ATPc := (Pc*(1 - 4*KeqAK) - sumAc + ((sumAc - (1 - 4*KeqAK)*Pc)^2 + 4*(1 - 4*KeqAK)*KeqAK*Pc^2)^0.5)/(2*(1 - 4*KeqAK)); ADPc := Pc - 2*ATPc; ATPg := (Pg*(1 - 4*KeqAK) - sumAg + ((sumAg - (1 - 4*KeqAK)*Pg)^2 + 4*(1 - 4*KeqAK)*KeqAK*Pg^2)^0.5)/(2*(1 - 4*KeqAK)); ADPg := Pg - 2*ATPg; DHAPg := (DHAP*Vt - DHAPc*Vc)/Vg; DHAPc := (sumc5*(1 + Vc/Vg)*DHAP)/((sumc4 + (sumc5*Vc)/Vg) - (BPGA13 + 2*Fru16BP + Fru6P + GAP + Glc6P + Pg)); Vc := (cytosol*Vt)/tot_cell; Vg := (glycosome*Vt)/tot_cell; PGAg := (Nb*(1 + Vc/Vg))/(1 + ((1 + Keq_PGM + Keq_PGM*Keq_ENO)*Vc)/Vg); PEPc := Keq_ENO*Keq_PGM*PGAg; // Reactions: vGlcTr: $GlcE -> GlcI; (tot_cell/Vt*vGlcTr_Vm1*(GlcE - GlcI))/(vGlcTr_K1Glc + GlcE + GlcI + (vGlcTr_afac*GlcE*GlcI)/vGlcTr_K1Glc); vHK: Pg + GlcI => Glc6P; (tot_cell/Vt*vHK_Vm2*GlcI*ATPg)/(vHK_K2ATPg*vHK_K2GlcI*(1 + Glc6P/vHK_K2Glc6P + GlcI/vHK_K2GlcI)*(1 + ATPg/vHK_K2ATPg + ADPg/vHK_K2ADPg)); vPGI: Glc6P -> Fru6P; (tot_cell/Vt*vPGI_Vm3*(Glc6P/vPGI_K3Glc6P - Fru6P/vPGI_K3Fru6P))/(1 + Glc6P/vPGI_K3Glc6P + Fru6P/vPGI_K3Fru6P); vPFK: Pg + Fru6P => Fru16BP; (tot_cell/Vt*vPFK_K4i1Fru16BP*vPFK_Vm4*Fru6P*ATPg)/(vPFK_K4ATPg*vPFK_K4Fru6P*(vPFK_K4i1Fru16BP + Fru16BP)*(1 + Fru16BP/vPFK_K4i2Fru16BP + Fru6P/vPFK_K4Fru6P)*(1 + ATPg/vPFK_K4ATPg)); vALD: Fru16BP -> GAP + DHAP; (tot_cell/Vt*((vALD_Vm5f*Fru16BP)/(0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65)) - (vALD_Vm5r*GAP*DHAPg)/(vALD_K5DHAP*vALD_K5GAP)))/(1 + GAP/vALD_K5GAP + DHAPg/vALD_K5DHAP + (GAP*DHAPg)/(vALD_K5DHAP*vALD_K5GAP) + Fru16BP/(0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65)) + (Fru16BP*GAP)/(vALD_K5GAPi*0.009*(1 + ATPg/0.68 + ADPg/1.51 + (sumAg - (ATPg + ADPg))/3.65))); vTPI: DHAP -> GAP; (tot_cell/Vt*TPIact*vTPI_Vm6*(DHAPg/vTPI_K6DHAPg - (5.7*GAP)/vTPI_K6GAP))/(1 + GAP/vTPI_K6GAP + DHAPg/vTPI_K6DHAPg); vGAPdh: GAP + NAD -> NADH + BPGA13; tot_cell/Vt*vGAPdh_Vm7*((vGAPdh_Vm7f*(GAP*(NAD/vGAPdh_K7GAP/vGAPdh_K7NAD) - vGAPdh_Vm7r/vGAPdh_Vm7f*((BPGA13*NADH)/vGAPdh_K7BPGA13/vGAPdh_K7NADH)))/((1 + GAP/vGAPdh_K7GAP + BPGA13/vGAPdh_K7BPGA13)*(1 + NAD/vGAPdh_K7NAD + NADH/vGAPdh_K7NADH))); vGDH: DHAP + NADH -> NAD + $Gly3P; (tot_cell/Vt*vGDH_Vm8*vGDH_Vm8f*((NADH*DHAPg)/(vGDH_K8DHAPg*vGDH_K8NADH) - (vGDH_Vm8r*NAD*Gly3Pg)/(vGDH_K8Gly3Pg*vGDH_K8NAD*vGDH_Vm8f)))/((1 + NAD/vGDH_K8NAD + NADH/vGDH_K8NADH)*(1 + DHAPg/vGDH_K8DHAPg + Gly3Pg/vGDH_K8Gly3Pg)); vGPO: $Gly3P => DHAP; (tot_cell/Vt*vGPO_Vm9*Gly3Pc)/(vGPO_K9Gly3Pc*1 + Gly3Pc); vPyrTr: Pyr => $PyrE; (tot_cell/Vt*vPyrTr_Vm10*Pyr)/vPyrTr_K10Pyr/(1 + Pyr/vPyrTr_K10Pyr); vPGK: BPGA13 -> Nb + Pg; (tot_cell/Vt*vPGK_Vm11*vPGK_Vm11f*((-vPGK_Vm11r*PGAg*ATPg)/(vPGK_K11ATPg*vPGK_K11PGA3*vPGK_Vm11f) + (BPGA13*ADPg)/(vPGK_K11ADPg*vPGK_K11BPGA13)))/((1 + BPGA13/vPGK_K11BPGA13 + PGAg/vPGK_K11PGA3)*(1 + ATPg/vPGK_K11ATPg + ADPg/vPGK_K11ADPg)); vPK: Nb => Pc + Pyr; (tot_cell/Vt*vPK_Vm12*(PEPc/(0.34*(1 + ADPc/0.57 + ATPc/0.64)))^vPK_n12*ADPc)/vPK_K12ADP/((1 + (PEPc/(0.34*(1 + ADPc/0.57 + ATPc/0.64)))^vPK_n12)*(1 + ADPc/vPK_K12ADP)); vATPase: Pc => ; (tot_cell/Vt*vATPase_K13*ATPc)/ADPc; vGlyK: $Gly3P -> Pg + $Gly; (tot_cell/Vt*vGlyK_Vm14*((vGlyK_Vm14f*ADPg*Gly3Pg)/(vGlyK_K14ADPg*vGlyK_K14Gly3Pg) - (Gly*vGlyK_Vm14r*ATPg)/(vGlyK_K14ATPg*vGlyK_K14Gly)))/((1 + Gly/vGlyK_K14Gly + Gly3Pg/vGlyK_K14Gly3Pg)*(1 + ATPg/vGlyK_K14ATPg + ADPg/vGlyK_K14ADPg)); // Species initializations: GlcI = 0.0340009; Pg = 7.63936; Glc6P = 2.07199; Fru6P = 0.511773; Fru16BP = 16.5371; DHAP = 3.89921; GAP = 0.0399329; NAD = 3.95514; BPGA13 = 0.0326745; NADH = 0.0448639; Pyr = 4.77413; Nb = 1.59603; Pc = 6.51839; PyrE = 0; Gly = 0; GlcE = 5; // Compartment initializations: tot_cell = 5.7; glycosome = 0.2446; cytosol = 5.4554; extracellular = 1; // Variable initializations: KeqAK = 0.442; KeqAK has dimensionless; sumAc = 3.9; sumAc has mM; sumAg = 6; sumAg has mM; Vt = 5.7; Vt has microlitre_per_mg; Vc has microlitre_per_mg; Vg has microlitre_per_mg; sumc5 = 5; sumc5 has mM; sumc4 = 45; sumc4 has mM; Keq_anti = 1; Keq_anti has dimensionless; Keq_PGM = 0.187; Keq_PGM has dimensionless; Keq_ENO = 6.7; Keq_ENO has dimensionless; TPIact = 1; TPIact has dimensionless; vGlcTr_Vm1 = 106.2; vGlcTr_Vm1 has nanomole_per_min_per_mg; vGlcTr_K1Glc = 2; vGlcTr_K1Glc has mM; vGlcTr_afac = 0.75; vGlcTr_afac has dimensionless; vHK_Vm2 = 625; vHK_Vm2 has nanomole_per_min_per_mg; vHK_K2ATPg = 0.116; vHK_K2ATPg has mM; vHK_K2GlcI = 0.1; vHK_K2GlcI has mM; vHK_K2Glc6P = 12; vHK_K2Glc6P has mM; vHK_K2ADPg = 0.126; vHK_K2ADPg has mM; vPGI_Vm3 = 848; vPGI_Vm3 has nanomole_per_min_per_mg; vPGI_K3Glc6P = 0.4; vPGI_K3Glc6P has mM; vPGI_K3Fru6P = 0.12; vPGI_K3Fru6P has mM; vPFK_K4i1Fru16BP = 15.8; vPFK_K4i1Fru16BP has mM; vPFK_Vm4 = 780; vPFK_Vm4 has nanomole_per_min_per_mg; vPFK_K4ATPg = 0.026; vPFK_K4ATPg has mM; vPFK_K4Fru6P = 0.82; vPFK_K4Fru6P has mM; vPFK_K4i2Fru16BP = 10.7; vPFK_K4i2Fru16BP has mM; vALD_Vm5r = 219.555; vALD_Vm5r has nanomole_per_min_per_mg; vALD_K5DHAP = 0.015; vALD_K5DHAP has mM; vALD_K5GAP = 0.067; vALD_K5GAP has mM; vALD_Vm5f = 184.5; vALD_Vm5f has nanomole_per_min_per_mg; vALD_K5GAPi = 0.098; vALD_K5GAPi has mM; vTPI_Vm6 = 842; vTPI_Vm6 has nanomole_per_min_per_mg; vTPI_K6GAP = 0.25; vTPI_K6GAP has mM; vTPI_K6DHAPg = 1.2; vTPI_K6DHAPg has mM; vGAPdh_Vm7 = 1; vGAPdh_Vm7 has dimensionless; vGAPdh_Vm7f = 1470; vGAPdh_Vm7f has nanomole_per_min_per_mg; vGAPdh_K7GAP = 0.15; vGAPdh_K7GAP has mM; vGAPdh_K7NAD = 0.45; vGAPdh_K7NAD has mM; vGAPdh_Vm7r = 984.9; vGAPdh_Vm7r has nanomole_per_min_per_mg; vGAPdh_K7BPGA13 = 0.1; vGAPdh_K7BPGA13 has mM; vGAPdh_K7NADH = 0.02; vGAPdh_K7NADH has mM; vGDH_Vm8 = 1; vGDH_Vm8 has dimensionless; vGDH_Vm8f = 533; vGDH_Vm8f has nanomole_per_min_per_mg; vGDH_K8DHAPg = 0.1; vGDH_K8DHAPg has mM; vGDH_K8NADH = 0.01; vGDH_K8NADH has mM; vGDH_Vm8r = 149.24; vGDH_Vm8r has nanomole_per_min_per_mg; vGDH_K8Gly3Pg = 2; vGDH_K8Gly3Pg has mM; vGDH_K8NAD = 0.4; vGDH_K8NAD has mM; vGPO_Vm9 = 368; vGPO_Vm9 has nanomole_per_min_per_mg; vGPO_K9Gly3Pc = 1.7; vGPO_K9Gly3Pc has mM; vPyrTr_Vm10 = 200; vPyrTr_Vm10 has nanomole_per_min_per_mg; vPyrTr_K10Pyr = 1.96; vPyrTr_K10Pyr has mM; vPGK_Vm11 = 1; vPGK_Vm11 has dimensionless; vPGK_Vm11f = 640; vPGK_Vm11f has nanomole_per_min_per_mg; vPGK_Vm11r = 18.56; vPGK_Vm11r has nanomole_per_min_per_mg; vPGK_K11ATPg = 0.29; vPGK_K11ATPg has mM; vPGK_K11PGA3 = 1.62; vPGK_K11PGA3 has mM; vPGK_K11ADPg = 0.1; vPGK_K11ADPg has dimensionless; vPGK_K11BPGA13 = 0.05; vPGK_K11BPGA13 has dimensionless; vPK_n12 = 2.5; vPK_n12 has dimensionless; vPK_Vm12 = 2600; vPK_Vm12 has nanomole_per_min_per_mg; vPK_K12ADP = 0.114; vPK_K12ADP has mM; vATPase_K13 = 50; vATPase_K13 has nanomole_per_min_per_mg; vGlyK_Vm14 = 1; vGlyK_Vm14 has dimensionless; vGlyK_Vm14r = 33400; vGlyK_Vm14r has nanomole_per_min_per_mg; vGlyK_K14ATPg = 0.19; vGlyK_K14ATPg has mM; vGlyK_K14Gly = 0.12; vGlyK_K14Gly has mM; vGlyK_Vm14f = 200; vGlyK_Vm14f has nanomole_per_min_per_mg; vGlyK_K14ADPg = 0.12; vGlyK_K14ADPg has mM; vGlyK_K14Gly3Pg = 5.1; vGlyK_K14Gly3Pg has mM; // Other declarations: var Vc, Vg; const tot_cell, glycosome, cytosol, extracellular, KeqAK, sumAc, sumAg; const Vt, sumc5, sumc4, Keq_anti, Keq_PGM, Keq_ENO, TPIact; // Unit definitions: unit substance = 1e-9 mole; unit volume = 1e-6 litre; unit microlitre_per_mg = 1e-6 litre / 1e-3 gram; unit nanomole_per_min_per_mg = 1e-9 mole / (60 second * 1e-3 gram); unit time_unit = 60 second; unit mM = 1e-9 mole / 1e-6 litre; // Display Names: substance is "nanomole"; volume is "microlitre"; time_unit is "minute"; tot_cell is "total cell"; GlcI is "Glucose"; Pg is "Phosphates in Glycosome"; Glc6P is "Glucose 6-phosphate"; Fru6P is "Fructose 6-phosphate"; Fru16BP is "Fructose 1,6-bisphosphate"; DHAP is "Dihydroxyacetone phosphate"; GAP is "Glyceraldehyde 3-phosphate"; BPGA13 is "1,3-bisphosphoglycerate"; Pyr is "Pyruvate"; Nb is "3-PGA 2-PGA PEP"; Pc is "Phosphates cytosol"; PyrE is "Pyruvate external"; Gly is "Glycerol"; GlcE is "Glucose external"; Gly3P is "Glycerol 3-phosphate"; Gly3Pc is "Gy3P c."; Gly3Pg is "Gy3P g."; ATPc is "ATP cyt."; ADPc is "ADP cyt."; ATPg is "ATP gly."; ADPg is "ADP gly."; DHAPg is "DHAP gly."; Vt is "tot volume per mg protein"; DHAPc is "DHAP cyt."; PGAg is "3-PGA g."; PEPc is "PEP c."; vGlcTr is "Glucose transport"; vHK is "Hexokinase"; vPGI is "Glucose-phosphate isomerase"; vPFK is "Phosphofructokinase"; vALD is "Aldolase"; vTPI is "Triosephosphate isomerase"; vGAPdh is "Glyceraldehyde 3-phosphate dehydrogenase"; vGDH is "Glycerol 3-phosphate dehydrogenase"; vGPO is "Glycerol 3-phosphate oxidase"; vPyrTr is "Pyruvate transport"; vPGK is "Phosphoglycerate kinase"; vPK is "Pyruvate kinase"; vATPase is "ATPase"; vGlyK is "Glycerol kinase"; end