// Created by libAntimony v2.8.0 model *Proctor2010_UCHL1_ProteinAggregation() // Compartments and Species: compartment cytosol; substanceOnly species NatP in cytosol, MisP in cytosol, Ub in cytosol, E1 in cytosol; substanceOnly species E2 in cytosol, E3 in cytosol, E3_MisP in cytosol; substanceOnly species DUB in cytosol, Proteasome in cytosol, ROS in cytosol; substanceOnly species E1_Ub in cytosol, E2_Ub in cytosol, E3_MisP_Ub in cytosol; substanceOnly species E3_MisP_Ub2 in cytosol, E3_MisP_Ub3 in cytosol, E3_MisP_Ub4 in cytosol; substanceOnly species E3_MisP_Ub5 in cytosol, E3_MisP_Ub6 in cytosol, E3_MisP_Ub7 in cytosol; substanceOnly species E3_MisP_Ub8 in cytosol, MisP_Ub4_Proteasome in cytosol; substanceOnly species MisP_Ub5_Proteasome in cytosol, MisP_Ub6_Proteasome in cytosol; substanceOnly species MisP_Ub7_Proteasome in cytosol, MisP_Ub8_Proteasome in cytosol; substanceOnly species E3_MisP_Ub_DUB in cytosol, E3_MisP_Ub2_DUB in cytosol; substanceOnly species E3_MisP_Ub3_DUB in cytosol, E3_MisP_Ub4_DUB in cytosol; substanceOnly species E3_MisP_Ub5_DUB in cytosol, E3_MisP_Ub6_DUB in cytosol; substanceOnly species E3_MisP_Ub7_DUB in cytosol, E3_MisP_Ub8_DUB in cytosol; substanceOnly species AggP1 in cytosol, AggP2 in cytosol, AggP3 in cytosol; substanceOnly species AggP4 in cytosol, AggP5 in cytosol, SeqAggP in cytosol; substanceOnly species AggP_Proteasome in cytosol, $ATP in cytosol, $ADP in cytosol; substanceOnly species $AMP in cytosol, UCHL1 in cytosol, UCHL1_Proteasome in cytosol; substanceOnly species UCHL1_damaged_Proteasome in cytosol, Lysosome in cytosol; substanceOnly species UCHL1_damaged in cytosol, Lamp2a in cytosol, Lamp2a_UCHL1_damaged in cytosol; substanceOnly species Ub_UCHL1 in cytosol, SUB in cytosol, SUB_misfolded in cytosol; substanceOnly species E3SUB in cytosol, E3SUB_SUB_misfolded in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub in cytosol, E3SUB_SUB_misfolded_Ub2 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub3 in cytosol, E3SUB_SUB_misfolded_Ub4 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub5 in cytosol, E3SUB_SUB_misfolded_Ub6 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub7 in cytosol, E3SUB_SUB_misfolded_Ub8 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub_UCHL1 in cytosol, E3SUB_SUB_misfolded_Ub2_UCHL1 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub3_UCHL1 in cytosol, E3SUB_SUB_misfolded_Ub4_UCHL1 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub5_UCHL1 in cytosol, E3SUB_SUB_misfolded_Ub6_UCHL1 in cytosol; substanceOnly species E3SUB_SUB_misfolded_Ub7_UCHL1 in cytosol, E3SUB_SUB_misfolded_Ub8_UCHL1 in cytosol; substanceOnly species SUB_misfolded_Ub4_Proteasome in cytosol, SUB_misfolded_Ub5_Proteasome in cytosol; substanceOnly species SUB_misfolded_Ub6_Proteasome in cytosol, SUB_misfolded_Ub7_Proteasome in cytosol; substanceOnly species SUB_misfolded_Ub8_Proteasome in cytosol, asyn in cytosol; substanceOnly species asyn_Proteasome in cytosol, asyn_Lamp2a in cytosol; substanceOnly species asyn_dam in cytosol, Parkin in cytosol, Parkin_asyn_dam in cytosol; substanceOnly species Parkin_asyn_dam_Ub in cytosol, Parkin_asyn_dam_Ub2 in cytosol; substanceOnly species Parkin_asyn_dam_Ub3 in cytosol, Parkin_asyn_dam_Ub4 in cytosol; substanceOnly species Parkin_asyn_dam_Ub5 in cytosol, Parkin_asyn_dam_Ub6 in cytosol; substanceOnly species Parkin_asyn_dam_Ub7 in cytosol, Parkin_asyn_dam_Ub8 in cytosol; substanceOnly species Parkin_asyn_dam_Ub_DUB in cytosol, Parkin_asyn_dam_Ub2_DUB in cytosol; substanceOnly species Parkin_asyn_dam_Ub3_DUB in cytosol, Parkin_asyn_dam_Ub4_DUB in cytosol; substanceOnly species Parkin_asyn_dam_Ub5_DUB in cytosol, Parkin_asyn_dam_Ub6_DUB in cytosol; substanceOnly species Parkin_asyn_dam_Ub7_DUB in cytosol, Parkin_asyn_dam_Ub8_DUB in cytosol; substanceOnly species asyn_dam_Ub4_Proteasome in cytosol, asyn_dam_Ub5_Proteasome in cytosol; substanceOnly species asyn_dam_Ub6_Proteasome in cytosol, asyn_dam_Ub7_Proteasome in cytosol; substanceOnly species asyn_dam_Ub8_Proteasome in cytosol, AggA1 in cytosol; substanceOnly species AggA2 in cytosol, AggA3 in cytosol, AggA4 in cytosol; substanceOnly species AggA5 in cytosol, AggD1 in cytosol, AggD2 in cytosol; substanceOnly species AggD3 in cytosol, AggD4 in cytosol, AggD5 in cytosol; substanceOnly species AggU1 in cytosol, AggU2 in cytosol, AggU3 in cytosol; substanceOnly species AggU4 in cytosol, AggU5 in cytosol, AggS1 in cytosol; substanceOnly species AggS2 in cytosol, AggS3 in cytosol, AggS4 in cytosol; substanceOnly species AggS5 in cytosol, $Source in cytosol, $Sink in cytosol; substanceOnly species aggasyn in cytosol, aggasyndam in cytosol, aggParkin in cytosol; substanceOnly species aggUb in cytosol, aggE3 in cytosol, aggDUB in cytosol; substanceOnly species aggMisP in cytosol, aggUchl1 in cytosol, aggUchl1dam in cytosol; substanceOnly species aggSUB in cytosol, upregUb in cytosol; // Assignment Rules: Tot_MisP := E3_MisP + E3_MisP_Ub + E3_MisP_Ub_DUB + E3_MisP_Ub2 + E3_MisP_Ub2_DUB + E3_MisP_Ub3 + E3_MisP_Ub3_DUB + E3_MisP_Ub4 + E3_MisP_Ub4_DUB + E3_MisP_Ub5 + E3_MisP_Ub5_DUB + E3_MisP_Ub6 + E3_MisP_Ub6_DUB + E3_MisP_Ub7 + E3_MisP_Ub7_DUB + E3_MisP_Ub8 + E3_MisP_Ub8_DUB + MisP + MisP_Ub4_Proteasome + MisP_Ub5_Proteasome + MisP_Ub6_Proteasome + MisP_Ub7_Proteasome + MisP_Ub8_Proteasome; Tot_Protein := Tot_MisP + NatP; Ub_Conjugates := aggUb + 4*asyn_dam_Ub4_Proteasome + 5*asyn_dam_Ub5_Proteasome + 6*asyn_dam_Ub6_Proteasome + 7*asyn_dam_Ub7_Proteasome + 8*asyn_dam_Ub8_Proteasome + E1_Ub + E2_Ub + E3_MisP_Ub + E3_MisP_Ub_DUB + 2*E3_MisP_Ub2 + 2*E3_MisP_Ub2_DUB + 3*E3_MisP_Ub3 + 3*E3_MisP_Ub3_DUB + 4*E3_MisP_Ub4 + 4*E3_MisP_Ub4_DUB + 5*E3_MisP_Ub5 + 5*E3_MisP_Ub5_DUB + 6*E3_MisP_Ub6 + 6*E3_MisP_Ub6_DUB + 7*E3_MisP_Ub7 + 7*E3_MisP_Ub7_DUB + 8*E3_MisP_Ub8 + 8*E3_MisP_Ub8_DUB + E3SUB_SUB_misfolded_Ub + E3SUB_SUB_misfolded_Ub_UCHL1 + 2*E3SUB_SUB_misfolded_Ub2 + 2*E3SUB_SUB_misfolded_Ub2_UCHL1 + 3*E3SUB_SUB_misfolded_Ub3 + 3*E3SUB_SUB_misfolded_Ub3_UCHL1 + 4*E3SUB_SUB_misfolded_Ub4 + 4*E3SUB_SUB_misfolded_Ub4_UCHL1 + 5*E3SUB_SUB_misfolded_Ub5 + 5*E3SUB_SUB_misfolded_Ub5_UCHL1 + 6*E3SUB_SUB_misfolded_Ub6 + 6*E3SUB_SUB_misfolded_Ub6_UCHL1 + 7*E3SUB_SUB_misfolded_Ub7 + 7*E3SUB_SUB_misfolded_Ub7_UCHL1 + 8*E3SUB_SUB_misfolded_Ub8 + 8*E3SUB_SUB_misfolded_Ub8_UCHL1 + E3SUB_SUB_misfolded_Ub_UCHL1 + 4*MisP_Ub4_Proteasome + 5*MisP_Ub5_Proteasome + 6*MisP_Ub6_Proteasome + 7*MisP_Ub7_Proteasome + 8*MisP_Ub8_Proteasome + Parkin_asyn_dam_Ub + Parkin_asyn_dam_Ub_DUB + 2*Parkin_asyn_dam_Ub2 + 2*Parkin_asyn_dam_Ub2_DUB + 3*Parkin_asyn_dam_Ub3 + 3*Parkin_asyn_dam_Ub3_DUB + 4*Parkin_asyn_dam_Ub4 + 4*Parkin_asyn_dam_Ub4_DUB + 5*Parkin_asyn_dam_Ub5 + 5*Parkin_asyn_dam_Ub5_DUB + 6*Parkin_asyn_dam_Ub6 + 6*Parkin_asyn_dam_Ub6_DUB + 7*Parkin_asyn_dam_Ub7 + 7*Parkin_asyn_dam_Ub7_DUB + 8*Parkin_asyn_dam_Ub8 + 8*Parkin_asyn_dam_Ub8_DUB + 4*SUB_misfolded_Ub4_Proteasome + 5*SUB_misfolded_Ub5_Proteasome + 6*SUB_misfolded_Ub6_Proteasome + 7*SUB_misfolded_Ub7_Proteasome + 8*SUB_misfolded_Ub8_Proteasome + Ub_UCHL1 + upregUb; Tot_Ub := Ub_Conjugates + Ub; AggP := AggA1 + AggA2 + AggA3 + AggA4 + AggA5 + aggasyn + aggasyndam + AggD1 + AggD2 + AggD3 + AggD4 + AggD5 + aggDUB + aggE3 + aggMisP + AggP1 + AggP2 + AggP3 + AggP4 + AggP5 + aggParkin + AggS1 + AggS2 + AggS3 + AggS4 + AggS5 + aggSUB + AggU1 + AggU2 + AggU3 + AggU4 + AggU5 + aggUb + aggUchl1 + aggUchl1dam; Tot_asyn_dam := asyn_dam + asyn_dam_Ub4_Proteasome + asyn_dam_Ub5_Proteasome + asyn_dam_Ub6_Proteasome + asyn_dam_Ub7_Proteasome + asyn_dam_Ub8_Proteasome + asyn_dam_Ub4_Proteasome + Parkin_asyn_dam + Parkin_asyn_dam_Ub + Parkin_asyn_dam_Ub_DUB + Parkin_asyn_dam_Ub2 + Parkin_asyn_dam_Ub2_DUB + Parkin_asyn_dam_Ub3 + Parkin_asyn_dam_Ub3_DUB + Parkin_asyn_dam_Ub4 + Parkin_asyn_dam_Ub4_DUB + Parkin_asyn_dam_Ub5 + Parkin_asyn_dam_Ub5_DUB + Parkin_asyn_dam_Ub6 + Parkin_asyn_dam_Ub6_DUB + Parkin_asyn_dam_Ub7 + Parkin_asyn_dam_Ub7_DUB + Parkin_asyn_dam_Ub8 + Parkin_asyn_dam_Ub8_DUB; Tot_asyn := asyn + asyn_Lamp2a + asyn_Proteasome; Tot_UCHL1 := UCHL1 + UCHL1_substrate; UCHL1_substrate := E3SUB_SUB_misfolded_Ub_UCHL1 + E3SUB_SUB_misfolded_Ub2_UCHL1 + E3SUB_SUB_misfolded_Ub3_UCHL1 + E3SUB_SUB_misfolded_Ub4_UCHL1 + E3SUB_SUB_misfolded_Ub5_UCHL1 + E3SUB_SUB_misfolded_Ub6_UCHL1 + E3SUB_SUB_misfolded_Ub7_UCHL1 + E3SUB_SUB_misfolded_Ub8_UCHL1 + Lamp2a_UCHL1_damaged + Ub_UCHL1 + UCHL1_damaged + UCHL1_damaged_Proteasome + UCHL1_Proteasome; // Reactions: UbSynthesis: $Source => Ub; kubs*Source; UbDegradation: Ub + Proteasome => Proteasome; kubd*Proteasome*Ub*kproteff; UbUpregulation: MisP => MisP + 3Ub + 3upregUb; kubss*(MisP^6/(1500^6 + MisP^6)); ProteinSynthesis: $Source => NatP; ksynNatP*Source; Misfolding: NatP + ROS => MisP + ROS; kmisfold*NatP*ROS; Refolding: MisP => NatP; krefold*MisP; MisPE3Binding: MisP + E3 => E3_MisP; kbinMisPE3*MisP*E3; MisPE3Release: E3_MisP => MisP + E3; krelMisPE3*E3_MisP; E1UbBinding: E1 + Ub + $ATP => E1_Ub + $AMP; (kbinE1Ub*E1*Ub*ATP)/(5000 + ATP); E2UbBinding: E2 + E1_Ub => E2_Ub + E1; kbinE2Ub*E2*E1_Ub; Monoubiquitination: E2_Ub + E3_MisP => E3_MisP_Ub + E2; kmonoUb*E2_Ub*E3_MisP; Polyubiquitination1: E3_MisP_Ub + E2_Ub => E3_MisP_Ub2 + E2; kpolyUb*E3_MisP_Ub*E2_Ub; Polyubiquitination2: E3_MisP_Ub2 + E2_Ub => E3_MisP_Ub3 + E2; kpolyUb*E3_MisP_Ub2*E2_Ub; Polyubiquitination3: E3_MisP_Ub3 + E2_Ub => E3_MisP_Ub4 + E2; kpolyUb*E3_MisP_Ub3*E2_Ub; Polyubiquitination4: E3_MisP_Ub4 + E2_Ub => E3_MisP_Ub5 + E2; kpolyUb*E3_MisP_Ub4*E2_Ub; Polyubiquitination5: E3_MisP_Ub5 + E2_Ub => E3_MisP_Ub6 + E2; kpolyUb*E3_MisP_Ub5*E2_Ub; Polyubiquitination6: E3_MisP_Ub6 + E2_Ub => E3_MisP_Ub7 + E2; kpolyUb*E3_MisP_Ub6*E2_Ub; Polyubiquitination7: E3_MisP_Ub7 + E2_Ub => E3_MisP_Ub8 + E2; kpolyUb*E3_MisP_Ub7*E2_Ub; MisPDUBbinding1: E3_MisP_Ub + DUB => E3_MisP_Ub_DUB; kbinMisPDUB*E3_MisP_Ub*DUB; MisPDUBbinding2: E3_MisP_Ub2 + DUB => E3_MisP_Ub2_DUB; kbinMisPDUB*E3_MisP_Ub2*DUB; MisPDUBbinding3: E3_MisP_Ub3 + DUB => E3_MisP_Ub3_DUB; kbinMisPDUB*E3_MisP_Ub3*DUB; MisPDUBbinding4: E3_MisP_Ub4 + DUB => E3_MisP_Ub4_DUB; kbinMisPDUB*E3_MisP_Ub4*DUB; MisPDUBbinding5: E3_MisP_Ub5 + DUB => E3_MisP_Ub5_DUB; kbinMisPDUB*E3_MisP_Ub5*DUB; MisPDUBbinding6: E3_MisP_Ub6 + DUB => E3_MisP_Ub6_DUB; kbinMisPDUB*E3_MisP_Ub6*DUB; MisPDUBbinding7: E3_MisP_Ub7 + DUB => E3_MisP_Ub7_DUB; kbinMisPDUB*E3_MisP_Ub7*DUB; MisPDUBbinding8: E3_MisP_Ub8 + DUB => E3_MisP_Ub8_DUB; kbinMisPDUB*E3_MisP_Ub8*DUB; Deubiquitination8: E3_MisP_Ub8_DUB => E3_MisP_Ub7_DUB + Ub; kactDUB*E3_MisP_Ub8_DUB; Deubiquitination7: E3_MisP_Ub7_DUB => E3_MisP_Ub6_DUB + Ub; kactDUB*E3_MisP_Ub7_DUB; Deubiquitination6: E3_MisP_Ub6_DUB => E3_MisP_Ub5_DUB + Ub; kactDUB*E3_MisP_Ub6_DUB; Deubiquitination5: E3_MisP_Ub5_DUB => E3_MisP_Ub4_DUB + Ub; kactDUB*E3_MisP_Ub5_DUB; Deubiquitination4: E3_MisP_Ub4_DUB => E3_MisP_Ub3_DUB + Ub; kactDUB*E3_MisP_Ub4_DUB; Deubiquitination3: E3_MisP_Ub3_DUB => E3_MisP_Ub2_DUB + Ub; kactDUB*E3_MisP_Ub3_DUB; Deubiquitination2: E3_MisP_Ub2_DUB => E3_MisP_Ub_DUB + Ub; kactDUB*E3_MisP_Ub2_DUB; Deubiquitination1: E3_MisP_Ub_DUB => E3_MisP + DUB + Ub; kactDUB*E3_MisP_Ub_DUB; ProteasomeBindingUb4: E3_MisP_Ub4 + Proteasome => E3 + MisP_Ub4_Proteasome; kbinProt*E3_MisP_Ub4*Proteasome; ProteasomeBindingUb5: E3_MisP_Ub5 + Proteasome => E3 + MisP_Ub5_Proteasome; kbinProt*E3_MisP_Ub5*Proteasome; ProteasomeBindingUb6: E3_MisP_Ub6 + Proteasome => E3 + MisP_Ub6_Proteasome; kbinProt*E3_MisP_Ub6*Proteasome; ProteasomeBindingUb7: E3_MisP_Ub7 + Proteasome => E3 + MisP_Ub7_Proteasome; kbinProt*E3_MisP_Ub7*Proteasome; ProteasomeBindingUb8: E3_MisP_Ub8 + Proteasome => E3 + MisP_Ub8_Proteasome; kbinProt*E3_MisP_Ub8*Proteasome; DeubiquitinationBoundMisP5: MisP_Ub8_Proteasome + DUB => MisP_Ub7_Proteasome + Ub + DUB; kactDUBProt*MisP_Ub8_Proteasome*DUB; DeubiquitinationBoundMisP4: MisP_Ub7_Proteasome + DUB => MisP_Ub6_Proteasome + Ub + DUB; kactDUBProt*MisP_Ub7_Proteasome*DUB; DeubiquitinationBoundMisP3: MisP_Ub6_Proteasome + DUB => MisP_Ub5_Proteasome + Ub + DUB; kactDUBProt*MisP_Ub6_Proteasome*DUB; DeubiquitinationBoundMisP2: MisP_Ub5_Proteasome + DUB => MisP_Ub4_Proteasome + Ub + DUB; kactDUBProt*MisP_Ub5_Proteasome*DUB; DeubiquitinationBoundMisP1: MisP_Ub4_Proteasome + DUB => MisP + Proteasome + 4Ub + DUB; kactDUBProt*MisP_Ub4_Proteasome*DUB; ProteasomeActivity1: MisP_Ub4_Proteasome + $ATP => 4Ub + Proteasome + $ADP; (kactProt*kproteff*MisP_Ub4_Proteasome*ATP)/(5000 + ATP); ProteasomeActivity2: MisP_Ub5_Proteasome + $ATP => 5Ub + Proteasome + $ADP; (kactProt*kproteff*MisP_Ub5_Proteasome*ATP)/(5000 + ATP); ProteasomeActivity3: MisP_Ub6_Proteasome + $ATP => 6Ub + Proteasome + $ADP; (kactProt*kproteff*MisP_Ub6_Proteasome*ATP)/(5000 + ATP); ProteasomeActivity4: MisP_Ub7_Proteasome + $ATP => 7Ub + Proteasome + $ADP; (kactProt*kproteff*MisP_Ub7_Proteasome*ATP)/(5000 + ATP); ProteasomeActivity5: MisP_Ub8_Proteasome + $ATP => 8Ub + Proteasome + $ADP; (kactProt*kproteff*MisP_Ub8_Proteasome*ATP)/(5000 + ATP); Aggregation1: 2MisP => AggP1; kagg1*MisP*(MisP - 1)*0.5; Aggregation2: MisP + AggP1 => AggP2; kagg2*MisP*AggP1; Aggregation3: MisP + AggP2 => AggP3; kagg2*MisP*AggP2; Aggregation4: MisP + AggP3 => AggP4; kagg2*MisP*AggP3; Aggregation5: MisP + AggP4 => AggP5; kagg2*MisP*AggP4; Disaggregation1: AggP5 => AggP4 + MisP; kdisagg5*AggP5; Disaggregation2: AggP4 => AggP3 + MisP; kdisagg4*AggP4; Disaggregation3: AggP3 => AggP2 + MisP; kdisagg3*AggP3; Disaggregation4: AggP2 => AggP1 + MisP; kdisagg2*AggP2; Disaggregation5: AggP1 => 2MisP; kdisagg1*AggP1; InclusionFormation: MisP + AggP5 => SeqAggP + 7aggMisP; kagg2*MisP*AggP5; InclusionGrowth1: MisP + SeqAggP => 2SeqAggP + aggMisP; kigrowth1*MisP*SeqAggP; InclusionGrowth2: E3_MisP + SeqAggP => 2SeqAggP + aggMisP + aggE3; kigrowth2*E3_MisP*SeqAggP; InclusionGrowth3: E3_MisP_Ub + SeqAggP => 2SeqAggP + aggMisP + aggUb + aggE3; kigrowth2*E3_MisP_Ub*SeqAggP; InclusionGrowth4: E3_MisP_Ub2 + SeqAggP => 2SeqAggP + aggMisP + 2aggUb + aggE3; kigrowth2*E3_MisP_Ub2*SeqAggP; InclusionGrowth5: E3_MisP_Ub3 + SeqAggP => 2SeqAggP + aggMisP + 3aggUb + aggE3; kigrowth2*E3_MisP_Ub3*SeqAggP; InclusionGrowth6: E3_MisP_Ub4 + SeqAggP => 2SeqAggP + aggMisP + 4aggUb + aggE3; kigrowth2*E3_MisP_Ub4*SeqAggP; InclusionGrowth7: E3_MisP_Ub5 + SeqAggP => 2SeqAggP + aggMisP + 5aggUb + aggE3; kigrowth2*E3_MisP_Ub5*SeqAggP; InclusionGrowth8: E3_MisP_Ub6 + SeqAggP => 2SeqAggP + aggMisP + 6aggUb + aggE3; kigrowth2*E3_MisP_Ub6*SeqAggP; InclusionGrowth9: E3_MisP_Ub7 + SeqAggP => 2SeqAggP + aggMisP + 7aggUb + aggE3; kigrowth2*E3_MisP_Ub7*SeqAggP; InclusionGrowth10: E3_MisP_Ub8 + SeqAggP => 2SeqAggP + 8aggUb + aggE3; kigrowth2*E3_MisP_Ub8*SeqAggP; InclusionGrowth11: E3_MisP_Ub_DUB + SeqAggP => 2SeqAggP + aggMisP + aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub_DUB*SeqAggP; InclusionGrowth12: E3_MisP_Ub2_DUB + SeqAggP => 2SeqAggP + aggMisP + 2aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub2_DUB*SeqAggP; InclusionGrowth13: E3_MisP_Ub3_DUB + SeqAggP => 2SeqAggP + aggMisP + 3aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub3_DUB*SeqAggP; InclusionGrowth14: E3_MisP_Ub4_DUB + SeqAggP => 2SeqAggP + aggMisP + 4aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub4_DUB*SeqAggP; InclusionGrowth15: E3_MisP_Ub5_DUB + SeqAggP => 2SeqAggP + aggMisP + 5aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub5_DUB*SeqAggP; InclusionGrowth16: E3_MisP_Ub6_DUB + SeqAggP => 2SeqAggP + aggMisP + 6aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub6_DUB*SeqAggP; InclusionGrowth17: E3_MisP_Ub7_DUB + SeqAggP => 2SeqAggP + aggMisP + 7aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub7_DUB*SeqAggP; InclusionGrowth18: E3_MisP_Ub8_DUB + SeqAggP => 2SeqAggP + aggMisP + 8aggUb + aggE3 + aggDUB; kigrowth2*E3_MisP_Ub8_DUB*SeqAggP; ProteasomeInhibition1: AggP1 + Proteasome => AggP_Proteasome; kbinAggProt*AggP1*Proteasome; ProteasomeInhibition2: AggP2 + Proteasome => AggP_Proteasome; kbinAggProt*AggP2*Proteasome; ProteasomeInhibition3: AggP3 + Proteasome => AggP_Proteasome; kbinAggProt*AggP3*Proteasome; ProteasomeInhibition4: AggP4 + Proteasome => AggP_Proteasome; kbinAggProt*AggP4*Proteasome; ProteasomeInhibition5: AggP5 + Proteasome => AggP_Proteasome; kbinAggProt*AggP5*Proteasome; ROSgenerationSmallAggP1: AggP1 => AggP1 + ROS; kgenROSAggP*AggP1; ROSgenerationSmallAggP2: AggP2 => AggP2 + ROS; kgenROSAggP*AggP2; ROSgenerationSmallAggP3: AggP3 => AggP3 + ROS; kgenROSAggP*AggP3; ROSgenerationSmallAggP4: AggP4 => AggP4 + ROS; kgenROSAggP*AggP4; ROSgenerationSmallAggP5: AggP5 => AggP5 + ROS; kgenROSAggP*AggP5; UCHL1Synthesis: $Source => UCHL1; ksynUCHL1*Source; UCHL1ProteasomeBinding: UCHL1 + Proteasome => UCHL1_Proteasome; kbinUCHL1Prot*UCHL1*Proteasome; UCHL1ProteasomeDegradation: UCHL1_Proteasome => Proteasome; kdegProtUCHL1*UCHL1_Proteasome*kproteff; UCHL1LysosomalDegradation: UCHL1 + Lysosome => Lysosome; kdegLysUCHL1*UCHL1*Lysosome; UCHL1damage: UCHL1 + ROS => UCHL1_damaged + ROS; kdamUCHL1*UCHL1*ROS; UCHL1DamgedProteasomeBinding: UCHL1_damaged + Proteasome => UCHL1_damaged_Proteasome; kbinUCHL1Prot*UCHL1_damaged*Proteasome; UCHL1DamagedProteasomeDegradation: UCHL1_damaged_Proteasome => Proteasome; kdegProtUCHL1*UCHL1_damaged_Proteasome*kproteff; UCHL1DamagedLysosomalDegradation: UCHL1_damaged + Lysosome => Lysosome; kdegLysUCHL1dam*UCHL1_damaged*Lysosome; UCHL1Lamp2abinding: UCHL1_damaged + Lamp2a => Lamp2a_UCHL1_damaged; kbinLamp2aUCHL1dam*UCHL1_damaged*Lamp2a; UCHL1Lamp2aRelease: Lamp2a_UCHL1_damaged => UCHL1_damaged + Lamp2a; krelLamp2aUCHL1dam*Lamp2a_UCHL1_damaged; UbUCHL1binding: Ub + UCHL1 => Ub_UCHL1; kbinUbUCHL1*Ub*UCHL1; UbUCHL1release: Ub_UCHL1 => Ub + UCHL1; krelUbUCHL1*Ub_UCHL1; SUBsynthesis: $Source => SUB; ksynSUB*Source; SUBmisfolding: SUB + ROS => SUB_misfolded + ROS; kmisfoldSUB*SUB*ROS; SUBRefolding: SUB_misfolded => SUB; krefoldSUB*SUB_misfolded; E3SUBBinding: SUB_misfolded + E3SUB => E3SUB_SUB_misfolded; kbinE3SUB*SUB_misfolded*E3SUB; E3SUBRelease: E3SUB_SUB_misfolded => SUB_misfolded + E3SUB; krelE3SUB*E3SUB_SUB_misfolded; SUBMonoubiquitination: E2_Ub + E3SUB_SUB_misfolded => E3SUB_SUB_misfolded_Ub + E2; kmonoUb*E2_Ub*E3SUB_SUB_misfolded; SUBPolyubiquitination1: E3SUB_SUB_misfolded_Ub + E2_Ub => E3SUB_SUB_misfolded_Ub2 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub*E2_Ub; SUBPolyubiquitination2: E3SUB_SUB_misfolded_Ub2 + E2_Ub => E3SUB_SUB_misfolded_Ub3 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub2*E2_Ub; SUBPolyubiquitination3: E3SUB_SUB_misfolded_Ub3 + E2_Ub => E3SUB_SUB_misfolded_Ub4 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub3*E2_Ub; SUBPolyubiquitination4: E3SUB_SUB_misfolded_Ub4 + E2_Ub => E3SUB_SUB_misfolded_Ub5 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub4*E2_Ub; SUBPolyubiquitination5: E3SUB_SUB_misfolded_Ub5 + E2_Ub => E3SUB_SUB_misfolded_Ub6 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub5*E2_Ub; SUBPolyubiquitination6: E3SUB_SUB_misfolded_Ub6 + E2_Ub => E3SUB_SUB_misfolded_Ub7 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub6*E2_Ub; SUBPolyubiquitination7: E3SUB_SUB_misfolded_Ub7 + E2_Ub => E3SUB_SUB_misfolded_Ub8 + E2; kpolyUb*E3SUB_SUB_misfolded_Ub7*E2_Ub; SUBUCHL1binding1: E3SUB_SUB_misfolded_Ub + UCHL1 => E3SUB_SUB_misfolded_Ub_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub*UCHL1; SUBUCHL1binding2: E3SUB_SUB_misfolded_Ub2 + UCHL1 => E3SUB_SUB_misfolded_Ub2_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub2*UCHL1; SUBUCHL1binding3: E3SUB_SUB_misfolded_Ub3 + UCHL1 => E3SUB_SUB_misfolded_Ub3_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub3*UCHL1; SUBUCHL1binding4: E3SUB_SUB_misfolded_Ub4 + UCHL1 => E3SUB_SUB_misfolded_Ub4_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub4*UCHL1; SUBUCHL1binding5Ub_UCHL1: E3SUB_SUB_misfolded_Ub5 + UCHL1 => E3SUB_SUB_misfolded_Ub5_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub5*UCHL1; SUBUCHL1binding6: E3SUB_SUB_misfolded_Ub6 + UCHL1 => E3SUB_SUB_misfolded_Ub6_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub6*UCHL1; SUBUCHL1binding7: E3SUB_SUB_misfolded_Ub7 + UCHL1 => E3SUB_SUB_misfolded_Ub7_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub7*UCHL1; SUBUCHL1binding8: E3SUB_SUB_misfolded_Ub8 + UCHL1 => E3SUB_SUB_misfolded_Ub8_UCHL1; kbinSUBUCHL1*E3SUB_SUB_misfolded_Ub8*UCHL1; SUBDeubiquitination8: E3SUB_SUB_misfolded_Ub8_UCHL1 => E3SUB_SUB_misfolded_Ub7_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub8_UCHL1; SUBDeubiquitination7: E3SUB_SUB_misfolded_Ub7_UCHL1 => E3SUB_SUB_misfolded_Ub6_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub7_UCHL1; SUBDeubiquitination6: E3SUB_SUB_misfolded_Ub6_UCHL1 => E3SUB_SUB_misfolded_Ub5_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub6_UCHL1; SUBDeubiquitination5: E3SUB_SUB_misfolded_Ub5_UCHL1 => E3SUB_SUB_misfolded_Ub4_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub5_UCHL1; SUBDeubiquitination4: E3SUB_SUB_misfolded_Ub4_UCHL1 => E3SUB_SUB_misfolded_Ub3_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub4_UCHL1; SUBDeubiquitination3: E3SUB_SUB_misfolded_Ub3_UCHL1 => E3SUB_SUB_misfolded_Ub2_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub3_UCHL1; SUBDeubiquitination2: E3SUB_SUB_misfolded_Ub2_UCHL1 => E3SUB_SUB_misfolded_Ub_UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub2_UCHL1; SUBDeubiquitination1: E3SUB_SUB_misfolded_Ub_UCHL1 => E3SUB_SUB_misfolded + UCHL1 + Ub; kactUchl1*E3SUB_SUB_misfolded_Ub_UCHL1; SUBProteasomeBindingUb4: E3SUB_SUB_misfolded_Ub4 + Proteasome => SUB_misfolded_Ub4_Proteasome + E3SUB; kbinProt*E3SUB_SUB_misfolded_Ub4*Proteasome; SUBProteasomeBindingUb5: E3SUB_SUB_misfolded_Ub5 + Proteasome => SUB_misfolded_Ub5_Proteasome + E3SUB; kbinProt*E3SUB_SUB_misfolded_Ub5*Proteasome; SUBProteasomeBindingUb6: E3SUB_SUB_misfolded_Ub6 + Proteasome => SUB_misfolded_Ub6_Proteasome + E3SUB; kbinProt*E3SUB_SUB_misfolded_Ub6*Proteasome; SUBProteasomeBindingUb7: E3SUB_SUB_misfolded_Ub7 + Proteasome => SUB_misfolded_Ub7_Proteasome + E3SUB; kbinProt*E3SUB_SUB_misfolded_Ub7*Proteasome; SUBProteasomeBindingUb8: E3SUB_SUB_misfolded_Ub8 + Proteasome => SUB_misfolded_Ub8_Proteasome + E3SUB; kbinProt*E3SUB_SUB_misfolded_Ub8*Proteasome; DeubiquitinationBoundSUB8: SUB_misfolded_Ub8_Proteasome + DUB => SUB_misfolded_Ub7_Proteasome + Ub + DUB; kactDUBProt*SUB_misfolded_Ub8_Proteasome*DUB; DeubiquitinationBoundSUB7: SUB_misfolded_Ub7_Proteasome + DUB => SUB_misfolded_Ub6_Proteasome + Ub + DUB; kactDUBProt*SUB_misfolded_Ub7_Proteasome*DUB; DeubiquitinationBoundSUB6: SUB_misfolded_Ub6_Proteasome + DUB => SUB_misfolded_Ub5_Proteasome + Ub + DUB; kactDUBProt*SUB_misfolded_Ub6_Proteasome*DUB; DeubiquitinationBoundSUB5: SUB_misfolded_Ub5_Proteasome + DUB => SUB_misfolded_Ub4_Proteasome + Ub + DUB; kactDUBProt*SUB_misfolded_Ub5_Proteasome*DUB; DeubiquitinationBoundSUB4: SUB_misfolded_Ub4_Proteasome + DUB => SUB_misfolded + Proteasome + 4Ub + DUB; kactDUBProt*SUB_misfolded_Ub4_Proteasome*DUB; SUBDegradationUb4: SUB_misfolded_Ub4_Proteasome + $ATP => 4Ub + Proteasome + $ADP; (kactProt*SUB_misfolded_Ub4_Proteasome*kproteff*ATP)/(5000 + ATP); SUBDegradationUb5: SUB_misfolded_Ub5_Proteasome + $ATP => 5Ub + Proteasome + $ADP; (kactProt*SUB_misfolded_Ub5_Proteasome*kproteff*ATP)/(5000 + ATP); SUBDegradationUb6: SUB_misfolded_Ub6_Proteasome + $ATP => 6Ub + Proteasome + $ADP; (kactProt*SUB_misfolded_Ub6_Proteasome*kproteff*ATP)/(5000 + ATP); SUBDegradationUb7: SUB_misfolded_Ub7_Proteasome + $ATP => 7Ub + Proteasome + $ADP; (kactProt*SUB_misfolded_Ub7_Proteasome*kproteff*ATP)/(5000 + ATP); SUBDegradationUb8: SUB_misfolded_Ub8_Proteasome + $ATP => 8Ub + Proteasome + $ADP; (kactProt*SUB_misfolded_Ub8_Proteasome*kproteff*ATP)/(5000 + ATP); asynSynthesis1: $Source => asyn; ksynasyn*Source; asynProt20Sbinding: asyn + Proteasome => asyn_Proteasome; kbinasynProt*asyn*Proteasome; asynProt20Sdegradation: asyn_Proteasome => Proteasome; kdegasynProt*kproteff*asyn_Proteasome; asynLamp2aBinding: asyn + Lamp2a => asyn_Lamp2a; kbinasynLamp2a*asyn*Lamp2a; asynCMAdegradation: asyn_Lamp2a => Lamp2a; kCMAasyn*asyn_Lamp2a; asynDamage: asyn + ROS => asyn_dam + ROS; kdamasyn*ROS*asyn; asyn_damParkinBinding: asyn_dam + Parkin => Parkin_asyn_dam; kbinasynParkin*asyn_dam*Parkin; asyn_damParkinRelease: Parkin_asyn_dam => asyn_dam + Parkin; krelasynParkin*Parkin_asyn_dam; AsynMonoubiquitination: E2_Ub + Parkin_asyn_dam => Parkin_asyn_dam_Ub + E2; kmonoUb*E2_Ub*Parkin_asyn_dam; AsynPolyubiquitination1: Parkin_asyn_dam_Ub + E2_Ub => Parkin_asyn_dam_Ub2 + E2; kpolyUb*Parkin_asyn_dam_Ub*E2_Ub; AsynPolyubiquitination2: Parkin_asyn_dam_Ub2 + E2_Ub => Parkin_asyn_dam_Ub3 + E2; kpolyUb*Parkin_asyn_dam_Ub2*E2_Ub; AsynPolyubiquitination3: Parkin_asyn_dam_Ub3 + E2_Ub => Parkin_asyn_dam_Ub4 + E2; kpolyUb*Parkin_asyn_dam_Ub3*E2_Ub; AsynPolyubiquitination4: Parkin_asyn_dam_Ub4 + E2_Ub => Parkin_asyn_dam_Ub5 + E2; kpolyUb*Parkin_asyn_dam_Ub4*E2_Ub; AsynPolyubiquitination5: Parkin_asyn_dam_Ub5 + E2_Ub => Parkin_asyn_dam_Ub6 + E2; kpolyUb*Parkin_asyn_dam_Ub5*E2_Ub; AsynPolyubiquitination6: Parkin_asyn_dam_Ub6 + E2_Ub => Parkin_asyn_dam_Ub7 + E2; kpolyUb*Parkin_asyn_dam_Ub6*E2_Ub; AsynPolyubiquitination7: Parkin_asyn_dam_Ub7 + E2_Ub => Parkin_asyn_dam_Ub8 + E2; kpolyUb*Parkin_asyn_dam_Ub7*E2_Ub; AsynDUBbindingUb8: Parkin_asyn_dam_Ub8 + DUB => Parkin_asyn_dam_Ub8_DUB; kbinasynDUB*Parkin_asyn_dam_Ub8*DUB; AsynDUBbindingUb7: Parkin_asyn_dam_Ub7 + DUB => Parkin_asyn_dam_Ub7_DUB; kbinasynDUB*Parkin_asyn_dam_Ub7*DUB; AsynDUBbindingUb6: Parkin_asyn_dam_Ub6 + DUB => Parkin_asyn_dam_Ub6_DUB; kbinasynDUB*Parkin_asyn_dam_Ub6*DUB; AsynDUBbindingUb5: Parkin_asyn_dam_Ub5 + DUB => Parkin_asyn_dam_Ub5_DUB; kbinasynDUB*Parkin_asyn_dam_Ub5*DUB; AsynDUBbindingUb4: Parkin_asyn_dam_Ub4 + DUB => Parkin_asyn_dam_Ub4_DUB; kbinasynDUB*Parkin_asyn_dam_Ub4*DUB; AsynDUBbindingUb3: Parkin_asyn_dam_Ub3 + DUB => Parkin_asyn_dam_Ub3_DUB; kbinasynDUB*Parkin_asyn_dam_Ub3*DUB; AsynDUBbindingUb2: Parkin_asyn_dam_Ub2 + DUB => Parkin_asyn_dam_Ub2_DUB; kbinasynDUB*Parkin_asyn_dam_Ub2*DUB; AsynDUBbindingUb1: Parkin_asyn_dam_Ub + DUB => Parkin_asyn_dam_Ub_DUB; kbinasynDUB*Parkin_asyn_dam_Ub*DUB; AsynDeubiquitinationUb8: Parkin_asyn_dam_Ub8_DUB => Parkin_asyn_dam_Ub7_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub8_DUB; AsynDeubiquitinationUb7: Parkin_asyn_dam_Ub7_DUB => Parkin_asyn_dam_Ub6_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub7_DUB; AsynDeubiquitinationUb6: Parkin_asyn_dam_Ub6_DUB => Parkin_asyn_dam_Ub5_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub6_DUB; AsynDeubiquitinationUb5: Parkin_asyn_dam_Ub5_DUB => Parkin_asyn_dam_Ub4_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub5_DUB; AsynDeubiquitinationUb4: Parkin_asyn_dam_Ub4_DUB => Parkin_asyn_dam_Ub3_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub4_DUB; AsynDeubiquitinationUb3: Parkin_asyn_dam_Ub3_DUB => Parkin_asyn_dam_Ub2_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub3_DUB; AsynDeubiquitinationUb2: Parkin_asyn_dam_Ub2_DUB => Parkin_asyn_dam_Ub_DUB + Ub; kactDUB*Parkin_asyn_dam_Ub2_DUB; AsynDeubiquitinationUb1: Parkin_asyn_dam_Ub_DUB => Parkin_asyn_dam + DUB + Ub; kactDUB*Parkin_asyn_dam_Ub_DUB; AsynProteasomeBindingUb4: Parkin_asyn_dam_Ub4 + Proteasome => asyn_dam_Ub4_Proteasome + Parkin; kbinProt*Parkin_asyn_dam_Ub4*Proteasome; AsynProteasomeBindingUb5: Parkin_asyn_dam_Ub5 + Proteasome => asyn_dam_Ub5_Proteasome + Parkin; kbinProt*Parkin_asyn_dam_Ub5*Proteasome; AsynProteasomeBindingUb6: Parkin_asyn_dam_Ub6 + Proteasome => asyn_dam_Ub6_Proteasome + Parkin; kbinProt*Parkin_asyn_dam_Ub6*Proteasome; AsynProteasomeBindingUb7: Parkin_asyn_dam_Ub7 + Proteasome => asyn_dam_Ub7_Proteasome + Parkin; kbinProt*Parkin_asyn_dam_Ub7*Proteasome; AsynProteasomeBindingUb8: Parkin_asyn_dam_Ub8 + Proteasome => asyn_dam_Ub8_Proteasome + Parkin; kbinProt*Parkin_asyn_dam_Ub8*Proteasome; DeubiquitinationBoundasyn_damUb8: asyn_dam_Ub8_Proteasome + DUB => asyn_dam_Ub7_Proteasome + Ub + DUB; kactDUBProt*asyn_dam_Ub8_Proteasome*DUB; DeubiquitinationBoundasynDamUb7: asyn_dam_Ub7_Proteasome + DUB => asyn_dam_Ub6_Proteasome + Ub + DUB; kactDUBProt*asyn_dam_Ub7_Proteasome*DUB; DeubiquitinationBoundasynDamUb6: asyn_dam_Ub6_Proteasome + DUB => asyn_dam_Ub5_Proteasome + Ub + DUB; kactDUBProt*asyn_dam_Ub6_Proteasome*DUB; DeubiquitinationBoundasynDamUb5: asyn_dam_Ub5_Proteasome + DUB => asyn_dam_Ub4_Proteasome + Ub + DUB; kactDUBProt*asyn_dam_Ub5_Proteasome*DUB; DeubiquitinationBoundasynDamUb4: asyn_dam_Ub4_Proteasome + DUB => asyn_dam + Proteasome + 4Ub + DUB; kactDUBProt*asyn_dam_Ub4_Proteasome*DUB; AsynProteasomeActivityUb4: asyn_dam_Ub4_Proteasome + $ATP => 4Ub + Proteasome + $ADP; (kactProt*kproteff*asyn_dam_Ub4_Proteasome*ATP)/(5000 + ATP); AsynDegradationUb5: asyn_dam_Ub5_Proteasome + $ATP => 5Ub + Proteasome + $ADP; (kactProt*kproteff*asyn_dam_Ub5_Proteasome*ATP)/(5000 + ATP); AsynDegradationUb6: asyn_dam_Ub6_Proteasome + $ATP => 6Ub + Proteasome + $ADP; (kactProt*kproteff*asyn_dam_Ub6_Proteasome*ATP)/(5000 + ATP); AsynDegradationUb7: asyn_dam_Ub7_Proteasome + $ATP => 7Ub + Proteasome + $ADP; (kactProt*kproteff*asyn_dam_Ub7_Proteasome*ATP)/(5000 + ATP); AsynDegradationUb8: asyn_dam_Ub8_Proteasome + $ATP => 8Ub + Proteasome + $ADP; (kactProt*kproteff*asyn_dam_Ub8_Proteasome*ATP)/(5000 + ATP); Aggregationasyn1: 2asyn => AggA1; kaggasyn1*asyn*(asyn - 1)*0.5; Aggregationasyn2: asyn + AggA1 => AggA2; kaggasyn2*asyn*AggA1; Aggregationasyn3: asyn + AggA2 => AggA3; kaggasyn2*asyn*AggA2; Aggregationasyn4: asyn + AggA3 => AggA4; kaggasyn2*asyn*AggA3; Aggregationasyn5: asyn + AggA4 => AggA5; kaggasyn2*asyn*AggA4; DisAggregationasyn1: AggA5 => AggA4 + asyn; kdisaggasyn5*AggA5; DisAggregationasyn2: AggA4 => AggA3 + asyn; kdisaggasyn4*AggA4; DisAggregationasyn3: AggA3 => AggA2 + asyn; kdisaggasyn3*AggA3; DisAggregationasyn4: AggA2 => AggA1 + asyn; kdisaggasyn2*AggA2; DisAggregationasyn5: AggA1 => 2asyn; kdisaggasyn1*AggA1; AggA1ProteasomeInhibition: AggA1 + Proteasome => AggP_Proteasome; kbinAggProt*AggA1*Proteasome; AggA2ProteasomeInhibition: AggA2 + Proteasome => AggP_Proteasome; kbinAggProt*AggA2*Proteasome; AggA3ProteasomeInhibition: AggA3 + Proteasome => AggP_Proteasome; kbinAggProt*AggA3*Proteasome; AggA4ProteasomeInhibition: AggA4 + Proteasome => AggP_Proteasome; kbinAggProt*AggA4*Proteasome; AggA5ProteasomeInhibition: AggA5 + Proteasome => AggP_Proteasome; kbinAggProt*AggA5*Proteasome; AsynInclusionFormation: asyn + AggA5 => SeqAggP + 7aggasyn; kaggasyn2*asyn*AggA5; AsynInclusionGrowth: SeqAggP + asyn => 2SeqAggP + aggasyn; kigrowth1*SeqAggP*asyn; ROSgenerationSmallAggA1: AggA1 => AggA1 + ROS; kgenROSAggP*AggA1; ROSgenerationSmallAggA2: AggA2 => AggA2 + ROS; kgenROSAggP*AggA2; ROSgenerationSmallAggA3: AggA3 => AggA3 + ROS; kgenROSAggP*AggA3; ROSgenerationSmallAggA4: AggA4 => AggA4 + ROS; kgenROSAggP*AggA4; ROSgenerationSmallAggA5: AggA5 => AggA5 + ROS; kgenROSAggP*AggA5; AggregationAsynDam1: 2asyn_dam => AggD1; kagg1dam*asyn_dam*(asyn_dam - 1)*0.5; AggregationAsynDam2: asyn_dam + AggD1 => AggD2; kagg2dam*asyn_dam*AggD1; AggregationAsynDam3: asyn_dam + AggD2 => AggD3; kagg2dam*asyn_dam*AggD2; AggregationAsynDam4: asyn_dam + AggD3 => AggD4; kagg2dam*asyn_dam*AggD3; AggregationAsynDam5: asyn_dam + AggD4 => AggD5; kagg2dam*asyn_dam*AggD4; DisaggregationAsynDam1: AggD5 => AggD4 + asyn_dam; kdisaggasyndam5*AggD5; DisaggregationAsynDam2: AggD4 => AggD3 + asyn_dam; kdisaggasyndam4*AggD4; DisaggregationAsynDam3: AggD3 => AggD2 + asyn_dam; kdisaggasyndam3*AggD3; DisaggregationAsynDam4: AggD2 => AggD1 + asyn_dam; kdisaggasyndam2*AggD2; DisaggregationAsynDam5: AggD1 => 2asyn_dam; kdisaggasyndam1*AggD1; AggD1ProteasomeInhibition: AggD1 + Proteasome => AggP_Proteasome; kbinAggProt*AggD1*Proteasome; AggD2ProteasomeInhibition: AggD2 + Proteasome => AggP_Proteasome; kbinAggProt*AggD2*Proteasome; AggD3ProteasomeInhibition: AggD3 + Proteasome => AggP_Proteasome; kbinAggProt*AggD3*Proteasome; AggD4ProteasomeInhibition: AggD4 + Proteasome => AggP_Proteasome; kbinAggProt*AggD4*Proteasome; AggD5ProteasomeInhibition: AggD5 + Proteasome => AggP_Proteasome; kbinAggProt*AggD5*Proteasome; AsynDamInclusionFormation: asyn_dam + AggD5 => SeqAggP + 7aggasyndam; kagg2dam*asyn_dam*AggD5; AsynDamInclusionGrowth1: SeqAggP + asyn_dam => 2SeqAggP + aggasyndam; kigrowth1*SeqAggP*asyn_dam; AsynDamInclusionGrowth2: SeqAggP + Parkin_asyn_dam => 2SeqAggP + aggasyndam + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam; AsynDamInclusionGrowth3: SeqAggP + Parkin_asyn_dam_Ub => 2SeqAggP + aggasyndam + aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub; AsynDamInclusionGrowth4: SeqAggP + Parkin_asyn_dam_Ub2 => 2SeqAggP + aggasyndam + 2aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub2; AsynDamInclusionGrowth5: SeqAggP + Parkin_asyn_dam_Ub3 => 2SeqAggP + aggasyndam + 3aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub3; AsynDamInclusionGrowth6: SeqAggP + Parkin_asyn_dam_Ub4 => 2SeqAggP + aggasyndam + 4aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub4; AsynDamInclusionGrowth7: SeqAggP + Parkin_asyn_dam_Ub5 => 2SeqAggP + aggasyndam + 5aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub5; AsynDamInclusionGrowth8: SeqAggP + Parkin_asyn_dam_Ub6 => 2SeqAggP + aggasyndam + 6aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub6; AsynDamInclusionGrowth9: SeqAggP + Parkin_asyn_dam_Ub7 => 2SeqAggP + aggasyndam + 7aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub7; AsynDamInclusionGrowth10: SeqAggP + Parkin_asyn_dam_Ub8 => 2SeqAggP + aggasyndam + 8aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub8; AsynDamInclusionGrowth11: SeqAggP + Parkin_asyn_dam_Ub_DUB => 2SeqAggP + aggasyndam + aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub_DUB; AsynDamInclusionGrowth12: SeqAggP + Parkin_asyn_dam_Ub2_DUB => 2SeqAggP + aggasyndam + 2aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub2_DUB; AsynDamInclusionGrowth13: SeqAggP + Parkin_asyn_dam_Ub3_DUB => 2SeqAggP + aggasyndam + 3aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub3_DUB; AsynDamInclusionGrowth14: SeqAggP + Parkin_asyn_dam_Ub4_DUB => 2SeqAggP + aggasyndam + 4aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub4_DUB; AsynDamInclusionGrowth15: SeqAggP + Parkin_asyn_dam_Ub5_DUB => 2SeqAggP + aggasyndam + 5aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub5_DUB; AsynDamInclusionGrowth16: SeqAggP + Parkin_asyn_dam_Ub6_DUB => 2SeqAggP + aggasyndam + 6aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub6_DUB; AsynDamInclusionGrowth17: SeqAggP + Parkin_asyn_dam_Ub7_DUB => 2SeqAggP + aggasyndam + 7aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub7_DUB; AsynDamInclusionGrowth18: SeqAggP + Parkin_asyn_dam_Ub8_DUB => 2SeqAggP + aggasyndam + 8aggUb + aggParkin; kigrowth2*SeqAggP*Parkin_asyn_dam_Ub8_DUB; ROSgenerationSmallAggD1: AggD1 => AggD1 + ROS; kgenROSAggP*AggD1; ROSgenerationSmallAggD2: AggD2 => AggD2 + ROS; kgenROSAggP*AggD2; ROSgenerationSmallAggD3: AggD3 => AggD3 + ROS; kgenROSAggP*AggD3; ROSgenerationSmallAggD4: AggD4 => AggD4 + ROS; kgenROSAggP*AggD4; ROSgenerationSmallAggD5: AggD5 => AggD5 + ROS; kgenROSAggP*AggD5; AggregationUCHL1Dam1: 2UCHL1_damaged => AggU1; kagg1dam*UCHL1_damaged*(UCHL1_damaged - 1)*0.5; AggregationUCHL1Dam2: UCHL1_damaged + AggU1 => AggU2; kagg2dam*UCHL1_damaged*AggU1; AggregationUCHL1Dam3: UCHL1_damaged + AggU2 => AggU3; kagg2dam*UCHL1_damaged*AggU2; AggregationUCHL1Dam4: UCHL1_damaged + AggU3 => AggU4; kagg2dam*UCHL1_damaged*AggU3; AggregationUCHL1Dam5: UCHL1_damaged + AggU4 => AggU5; kagg2dam*UCHL1_damaged*AggU4; DisaggregationUCHL1Dam1: AggU5 => AggU4 + UCHL1_damaged; kdisagguchl1dam5*AggU5; DisaggregationUCHL1Dam2: AggU4 => AggU3 + UCHL1_damaged; kdisagguchl1dam4*AggU4; DisaggregationUCHL1Dam3: AggU3 => AggU2 + UCHL1_damaged; kdisagguchl1dam3*AggU3; DisaggregationUCHL1Dam4: AggU2 => AggU1 + UCHL1_damaged; kdisagguchl1dam2*AggU2; DisaggregationUCHL1Dam5: AggU1 => 2UCHL1_damaged; kdisagguchl1dam1*AggU1; AggU1ProteasomeInhibition: AggU1 + Proteasome => AggP_Proteasome; kbinAggProt*AggU1*Proteasome; AggU2ProteasomeInhibition: AggU2 + Proteasome => AggP_Proteasome; kbinAggProt*AggU2*Proteasome; AggU3ProteasomeInhibition: AggU3 + Proteasome => AggP_Proteasome; kbinAggProt*AggU3*Proteasome; AggU4ProteasomeInhibition: AggU4 + Proteasome => AggP_Proteasome; kbinAggProt*AggU4*Proteasome; AggU5ProteasomeInhibition: AggU5 + Proteasome => AggP_Proteasome; kbinAggProt*AggU5*Proteasome; UCHL1DamInclusionFormation: UCHL1_damaged + AggU5 => SeqAggP + 7aggUchl1dam; kagg2dam*UCHL1_damaged*AggU5; UCHL1DamagedSequestering: SeqAggP + UCHL1_damaged => 2SeqAggP + aggUchl1dam; kigrowth1*SeqAggP*UCHL1_damaged; UCHL1DamagedLamp2aSequestering: SeqAggP + Lamp2a_UCHL1_damaged => 2SeqAggP + aggUchl1dam; kigrowth1*SeqAggP*Lamp2a_UCHL1_damaged; ROSgenerationSmallAggU1: AggU1 => AggU1 + ROS; kgenROSAggP*AggU1; ROSgenerationSmallAggU2: AggU2 => AggU2 + ROS; kgenROSAggP*AggU2; ROSgenerationSmallAggU3: AggU3 => AggU3 + ROS; kgenROSAggP*AggU3; ROSgenerationSmallAggU4: AggU4 => AggU4 + ROS; kgenROSAggP*AggU4; ROSgenerationSmallAggU5: AggU5 => AggU5 + ROS; kgenROSAggP*AggU5; SUBAggregation1: 2SUB_misfolded => AggS1; kaggSUB1*SUB_misfolded*(SUB_misfolded - 1)*0.5; SUBAggregation2: SUB_misfolded + AggS1 => AggS2; kaggSUB2*SUB_misfolded*AggS1; SUBAggregation3: SUB_misfolded + AggS2 => AggS3; kaggSUB2*SUB_misfolded*AggS2; SUBAggregation4: SUB_misfolded + AggS3 => AggS4; kaggSUB2*SUB_misfolded*AggS3; SUBAggregation5: SUB_misfolded + AggS4 => AggS5; kaggSUB2*SUB_misfolded*AggS4; SUBDisaggregation1: AggS5 => AggS4 + SUB_misfolded; kdisaggSUB5*AggS5; SUBDisaggregation2: AggS4 => AggS3 + SUB_misfolded; kdisaggSUB4*AggS4; SUBDisaggregation3: AggS3 => AggS2 + SUB_misfolded; kdisaggSUB3*AggS3; SUBDisaggregation4: AggS2 => AggS1 + SUB_misfolded; kdisaggSUB2*AggS2; SUBDisaggregation5: AggS1 => 2SUB_misfolded; kdisaggSUB1*AggS1; AggS1ProteasomeInhibition: AggS1 + Proteasome => AggP_Proteasome; kbinAggProt*AggS1*Proteasome; AggS2ProteasomeInhibition: AggS2 + Proteasome => AggP_Proteasome; kbinAggProt*AggS2*Proteasome; AggS3ProteasomeInhibition: AggS3 + Proteasome => AggP_Proteasome; kbinAggProt*AggS3*Proteasome; AggS4ProteasomeInhibition: AggS4 + Proteasome => AggP_Proteasome; kbinAggProt*AggS4*Proteasome; AggS5ProteasomeInhibition: AggS5 + Proteasome => AggP_Proteasome; kbinAggProt*AggS5*Proteasome; SUBInclusionFormation: AggS5 + SUB_misfolded => SeqAggP + 7aggSUB; kaggSUB2*AggS5*SUB_misfolded; SUBInclusionGrowth0: SeqAggP + SUB_misfolded => 2SeqAggP + aggSUB; kigrowth1*SeqAggP*SUB_misfolded; SUBInclusionGrowth1: E3SUB_SUB_misfolded + SeqAggP => 2SeqAggP + aggSUB; kigrowth2*E3SUB_SUB_misfolded*SeqAggP; SUBInclusionGrowth2: E3SUB_SUB_misfolded_Ub + SeqAggP => 2SeqAggP + aggSUB + aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub*SeqAggP; SUBInclusionGrowth3: E3SUB_SUB_misfolded_Ub2 + SeqAggP => 2SeqAggP + aggSUB + 2aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub2*SeqAggP; SUBInclusionGrowth4: E3SUB_SUB_misfolded_Ub3 + SeqAggP => 2SeqAggP + aggSUB + 3aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub3*SeqAggP; SUBInclusionGrowth5: E3SUB_SUB_misfolded_Ub4 + SeqAggP => 2SeqAggP + aggSUB + 4aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub4*SeqAggP; SUBInclusionGrowth6: E3SUB_SUB_misfolded_Ub5 + SeqAggP => 2SeqAggP + aggSUB + 5aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub5*SeqAggP; SUBInclusionGrowth7: E3SUB_SUB_misfolded_Ub6 + SeqAggP => 2SeqAggP + aggSUB + 6aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub6*SeqAggP; SUBInclusionGrowth8: E3SUB_SUB_misfolded_Ub7 + SeqAggP => 2SeqAggP + aggSUB + 7aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub7*SeqAggP; SUBInclusionGrowth9: E3SUB_SUB_misfolded_Ub8 + SeqAggP => 2SeqAggP + aggSUB + 8aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub8*SeqAggP; SUBInclusionGrowth10: E3SUB_SUB_misfolded_Ub_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub_UCHL1*SeqAggP; SUBInclusionGrowth11: E3SUB_SUB_misfolded_Ub2_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 2aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub2_UCHL1*SeqAggP; SUBInclusionGrowth12: E3SUB_SUB_misfolded_Ub3_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 3aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub3_UCHL1*SeqAggP; SUBInclusionGrowth13: E3SUB_SUB_misfolded_Ub4_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 4aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub4_UCHL1*SeqAggP; SUBInclusionGrowth14: E3SUB_SUB_misfolded_Ub5_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 5aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub5_UCHL1*SeqAggP; SUBInclusionGrowth15: E3SUB_SUB_misfolded_Ub6_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 6aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub6_UCHL1*SeqAggP; SUBInclusionGrowth16: E3SUB_SUB_misfolded_Ub7_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 7aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub7_UCHL1*SeqAggP; SUBInclusionGrowth17: E3SUB_SUB_misfolded_Ub8_UCHL1 + SeqAggP => 2SeqAggP + aggSUB + aggUchl1 + 8aggUb; kigrowth2*E3SUB_SUB_misfolded_Ub8_UCHL1*SeqAggP; ROSgenerationSmallAggS1: AggS1 => AggS1 + ROS; kgenROSAggP*AggS1; ROSgenerationSmallAggS2: AggS2 => AggS2 + ROS; kgenROSAggP*AggS2; ROSgenerationSmallAggS3: AggS3 => AggS3 + ROS; kgenROSAggP*AggS3; ROSgenerationSmallAggS4: AggS4 => AggS4 + ROS; kgenROSAggP*AggS4; ROSgenerationSmallAggS5: AggS5 => AggS5 + ROS; kgenROSAggP*AggS5; radicalFormation: $Source => ROS; kgenROS*Source; radicalScavenging: ROS => $Sink; kremROS*ROS; // Species initializations: NatP = 6000/cytosol; MisP = 80/cytosol; Ub = 1500/cytosol; E1 = 105/cytosol; E2 = 50/cytosol; E3 = 300/cytosol; E3_MisP = 2/cytosol; DUB = 160/cytosol; Proteasome = 1500/cytosol; ROS = 10/cytosol; E1_Ub = 795/cytosol; E2_Ub = 950/cytosol; E3_MisP_Ub = 0; E3_MisP_Ub2 = 0; E3_MisP_Ub3 = 0; E3_MisP_Ub4 = 0; E3_MisP_Ub5 = 0; E3_MisP_Ub6 = 0; E3_MisP_Ub7 = 0; E3_MisP_Ub8 = 300/cytosol; MisP_Ub4_Proteasome = 0; MisP_Ub5_Proteasome = 1/cytosol; MisP_Ub6_Proteasome = 2/cytosol; MisP_Ub7_Proteasome = 10/cytosol; MisP_Ub8_Proteasome = 350/cytosol; E3_MisP_Ub_DUB = 100/cytosol; E3_MisP_Ub2_DUB = 100/cytosol; E3_MisP_Ub3_DUB = 100/cytosol; E3_MisP_Ub4_DUB = 100/cytosol; E3_MisP_Ub5_DUB = 100/cytosol; E3_MisP_Ub6_DUB = 100/cytosol; E3_MisP_Ub7_DUB = 100/cytosol; E3_MisP_Ub8_DUB = 100/cytosol; AggP1 = 0; AggP2 = 0; AggP3 = 0; AggP4 = 0; AggP5 = 0; SeqAggP = 0; AggP_Proteasome = 0; ATP = 10000/cytosol; ADP = 1000/cytosol; AMP = 1000/cytosol; UCHL1 = 5785/cytosol; UCHL1_Proteasome = 10/cytosol; UCHL1_damaged_Proteasome = 0; Lysosome = 1200/cytosol; UCHL1_damaged = 0; Lamp2a = 200/cytosol; Lamp2a_UCHL1_damaged = 0; Ub_UCHL1 = 500/cytosol; SUB = 815/cytosol; SUB_misfolded = 5/cytosol; E3SUB = 160/cytosol; E3SUB_SUB_misfolded = 5/cytosol; E3SUB_SUB_misfolded_Ub = 0; E3SUB_SUB_misfolded_Ub2 = 0; E3SUB_SUB_misfolded_Ub3 = 0; E3SUB_SUB_misfolded_Ub4 = 0; E3SUB_SUB_misfolded_Ub5 = 0; E3SUB_SUB_misfolded_Ub6 = 0; E3SUB_SUB_misfolded_Ub7 = 0; E3SUB_SUB_misfolded_Ub8 = 15/cytosol; E3SUB_SUB_misfolded_Ub_UCHL1 = 20/cytosol; E3SUB_SUB_misfolded_Ub2_UCHL1 = 20/cytosol; E3SUB_SUB_misfolded_Ub3_UCHL1 = 25/cytosol; E3SUB_SUB_misfolded_Ub4_UCHL1 = 25/cytosol; E3SUB_SUB_misfolded_Ub5_UCHL1 = 30/cytosol; E3SUB_SUB_misfolded_Ub6_UCHL1 = 30/cytosol; E3SUB_SUB_misfolded_Ub7_UCHL1 = 40/cytosol; E3SUB_SUB_misfolded_Ub8_UCHL1 = 40/cytosol; SUB_misfolded_Ub4_Proteasome = 0; SUB_misfolded_Ub5_Proteasome = 0; SUB_misfolded_Ub6_Proteasome = 0; SUB_misfolded_Ub7_Proteasome = 5/cytosol; SUB_misfolded_Ub8_Proteasome = 20/cytosol; asyn = 3000/cytosol; asyn_Proteasome = 0; asyn_Lamp2a = 0; asyn_dam = 0; Parkin = 4800/cytosol; Parkin_asyn_dam = 0; Parkin_asyn_dam_Ub = 0; Parkin_asyn_dam_Ub2 = 0; Parkin_asyn_dam_Ub3 = 0; Parkin_asyn_dam_Ub4 = 0; Parkin_asyn_dam_Ub5 = 0; Parkin_asyn_dam_Ub6 = 0; Parkin_asyn_dam_Ub7 = 0; Parkin_asyn_dam_Ub8 = 0; Parkin_asyn_dam_Ub_DUB = 0; Parkin_asyn_dam_Ub2_DUB = 0; Parkin_asyn_dam_Ub3_DUB = 0; Parkin_asyn_dam_Ub4_DUB = 0; Parkin_asyn_dam_Ub5_DUB = 0; Parkin_asyn_dam_Ub6_DUB = 0; Parkin_asyn_dam_Ub7_DUB = 0; Parkin_asyn_dam_Ub8_DUB = 0; asyn_dam_Ub4_Proteasome = 0; asyn_dam_Ub5_Proteasome = 0; asyn_dam_Ub6_Proteasome = 0; asyn_dam_Ub7_Proteasome = 0; asyn_dam_Ub8_Proteasome = 0; AggA1 = 0; AggA2 = 0; AggA3 = 0; AggA4 = 0; AggA5 = 0; AggD1 = 0; AggD2 = 0; AggD3 = 0; AggD4 = 0; AggD5 = 0; AggU1 = 0; AggU2 = 0; AggU3 = 0; AggU4 = 0; AggU5 = 0; AggS1 = 0; AggS2 = 0; AggS3 = 0; AggS4 = 0; AggS5 = 0; Source = 1/cytosol; Sink = 1/cytosol; aggasyn = 0; aggasyndam = 0; aggParkin = 0; aggUb = 0; aggE3 = 0; aggDUB = 0; aggMisP = 0; aggUchl1 = 0; aggUchl1dam = 0; aggSUB = 0; upregUb = 0; // Compartment initializations: cytosol = 1; // Variable initializations: ksynNatP = 2.4; kmisfold = 4e-005; krefold = 8e-005; kbinMisPE3 = 0.0001; krelMisPE3 = 0.0002; kbinE1Ub = 0.0002; kbinE2Ub = 0.001; kmonoUb = 0.001; kpolyUb = 0.01; kactDUB = 0.0001; kbinProt = 5e-006; kactDUBProt = 1e-006; kactProt = 0.01; kagg1 = 1e-012; kagg2 = 1e-010; kdisagg1 = 1e-008; kdisagg2 = 8e-009; kdisagg3 = 6e-009; kdisagg4 = 4e-009; kdisagg5 = 2e-009; kigrowth1 = 5e-009; kigrowth2 = 5e-009; kbinAggProt = 5e-009; kbinMisPDUB = 2e-007; kgenROS = 0.01; kremROS = 0.001; kubs = 0.009; kubd = 4.4e-009; kubss = 0.1; ksynUCHL1 = 0.022; kbinUCHL1Prot = 4e-010; kdegProtUCHL1 = 0.01; kdegLysUCHL1 = 2.7e-009; kdamUCHL1 = 1e-008; kbinLamp2aUCHL1dam = 1e-005; krelLamp2aUCHL1dam = 5e-005; kdegLysUCHL1dam = 2.7e-009; kbinUbUCHL1 = 3e-006; krelUbUCHL1 = 0.05; kactUchl1 = 0.0001; kbinSUBUCHL1 = 4e-008; ksynSUB = 0.13; kmisfoldSUB = 2e-005; krefoldSUB = 5e-005; kbinE3SUB = 0.0005; krelE3SUB = 0.0002; ksynasyn = 0.028; kbinasynProt = 1.7e-009; kdegasynProt = 0.01; kbinasynLamp2a = 4e-008; kCMAasyn = 0.001; kdamasyn = 5e-008; kbinasynDUB = 2e-007; kbinasynParkin = 0.0001; krelasynParkin = 0.0002; kaggasyn1 = 5e-012; kaggasyn2 = 5e-010; kdisaggasyn1 = 1e-008; kdisaggasyn2 = 8e-009; kdisaggasyn3 = 6e-009; kdisaggasyn4 = 4e-009; kdisaggasyn5 = 2e-009; kgenROSAggP = 2e-005; kagg1dam = 1e-005; kagg2dam = 0.005; kdisaggasyndam1 = 1e-008; kdisaggasyndam2 = 8e-009; kdisaggasyndam3 = 6e-009; kdisaggasyndam4 = 4e-009; kdisaggasyndam5 = 2e-009; kdisagguchl1dam1 = 1e-008; kdisagguchl1dam2 = 8e-009; kdisagguchl1dam3 = 6e-009; kdisagguchl1dam4 = 4e-009; kdisagguchl1dam5 = 2e-009; kaggSUB1 = 1e-012; kaggSUB2 = 1e-010; kdisaggSUB1 = 1e-008; kdisaggSUB2 = 8e-009; kdisaggSUB3 = 6e-009; kdisaggSUB4 = 4e-009; kdisaggSUB5 = 2e-009; kproteff = 1; // Other declarations: var kproteff, Tot_MisP, Tot_Protein, Ub_Conjugates, Tot_Ub, AggP, Tot_asyn_dam; var Tot_asyn, Tot_UCHL1, UCHL1_substrate; const cytosol, ksynNatP, kmisfold, krefold, kbinMisPE3, krelMisPE3, kbinE1Ub; const kbinE2Ub, kmonoUb, kpolyUb, kactDUB, kbinProt, kactDUBProt, kactProt; const kagg1, kagg2, kdisagg1, kdisagg2, kdisagg3, kdisagg4, kdisagg5, kigrowth1; const kigrowth2, kbinAggProt, kbinMisPDUB, kgenROS, kremROS, kubs, kubd; const kubss, ksynUCHL1, kbinUCHL1Prot, kdegProtUCHL1, kdegLysUCHL1, kdamUCHL1; const kbinLamp2aUCHL1dam, krelLamp2aUCHL1dam, kdegLysUCHL1dam, kbinUbUCHL1; const krelUbUCHL1, kactUchl1, kbinSUBUCHL1, ksynSUB, kmisfoldSUB, krefoldSUB; const kbinE3SUB, krelE3SUB, ksynasyn, kbinasynProt, kdegasynProt, kbinasynLamp2a; const kCMAasyn, kdamasyn, kbinasynDUB, kbinasynParkin, krelasynParkin, kaggasyn1; const kaggasyn2, kdisaggasyn1, kdisaggasyn2, kdisaggasyn3, kdisaggasyn4; const kdisaggasyn5, kgenROSAggP, kagg1dam, kagg2dam, kdisaggasyndam1, kdisaggasyndam2; const kdisaggasyndam3, kdisaggasyndam4, kdisaggasyndam5, kdisagguchl1dam1; const kdisagguchl1dam2, kdisagguchl1dam3, kdisagguchl1dam4, kdisagguchl1dam5; const kaggSUB1, kaggSUB2, kdisaggSUB1, kdisaggSUB2, kdisaggSUB3, kdisaggSUB4; const kdisaggSUB5; // Unit definitions: unit substance = item; end