#tang1

FIX: Sink Source

#reactions
AggP_ProteasomeSequestering:
 {1.0}AggP_Proteasome + {1.0}SeqAggP = {2.0}SeqAggP
  kseqAggPProt * AggP_Proteasome * SeqAggP * kalive
MisPInclusionGrowth:
 {1.0}MisP + {1.0}SeqAggP = {2.0}SeqAggP
  kseqMisP * MisP * SeqAggP * kalive
MisP_Aggregation1:
 {2.0}MisP = {1.0}AggP1
  kaggMisP * MisP * (MisP - 1) * 0.5 * kalive
MisP_Aggregation2:
 {1.0}MisP + {1.0}AggP1 = {1.0}AggP2
  kagg2MisP * MisP * AggP1 * kalive
MisP_Aggregation3:
 {1.0}MisP + {1.0}AggP2 = {1.0}AggP3
  kagg2MisP * MisP * AggP2 * kalive
MisP_Aggregation4:
 {1.0}MisP + {1.0}AggP3 = {1.0}AggP4
  kagg2MisP * MisP * AggP3 * kalive
MisP_Aggregation5:
 {1.0}MisP + {1.0}AggP4 = {1.0}AggP5
  kagg2MisP * MisP * AggP4 * kalive
MisP_Degradation:
 {1.0}MisP_Proteasome = {1.0}Proteasome
  kdegMisP * MisP_Proteasome * kalive * kproteff
MisP_Disaggregation1:
 {1.0}AggP1 = {2.0}MisP
  kdisaggMisP1 * AggP1 * kalive
MisP_Disaggregation2:
 {1.0}AggP2 = {1.0}MisP + {1.0}AggP1
  kdisaggMisP2 * AggP2 * kalive
MisP_Disaggregation3:
 {1.0}AggP3 = {1.0}MisP + {1.0}AggP2
  kdisaggMisP3 * AggP3 * kalive
MisP_Disaggregation4:
 {1.0}AggP4 = {1.0}MisP + {1.0}AggP3
  kdisaggMisP4 * AggP4 * kalive
MisP_Disaggregation5:
 {1.0}AggP5 = {1.0}MisP + {1.0}AggP4
  kdisaggMisP5 * AggP5 * kalive
MisP_InclusionFormation:
 {1.0}MisP + {1.0}AggP5 = {7.0}SeqAggP
  kagg2MisP * MisP * AggP5 * kalive
MisP_ProteasomeBinding:
 {1.0}MisP + {1.0}Proteasome = {1.0}MisP_Proteasome
  kbinMisPProt * MisP * Proteasome * kalive
MisP_ProteasomeRelease:
 {1.0}MisP_Proteasome = {1.0}MisP + {1.0}Proteasome
  krelMisPProt * MisP_Proteasome * kalive
MisP_ProteasomeSequestering:
 {1.0}MisP_Proteasome + {1.0}SeqAggP = {2.0}SeqAggP
  kseqMisPProt * MisP_Proteasome * SeqAggP * kalive
Misfolding:
 {1.0}NatP + {1.0}ROS = {1.0}MisP + {1.0}ROS
  kmisfold * NatP * ROS * kalive
P38DeathPathway:
 {1.0}p38_P = {1.0}p38_P + {1.0}p38death
  kp38death * p38_P * kalive * kp38act
PIDeathPathway:
 {1.0}AggP_Proteasome = {1.0}AggP_Proteasome + {1.0}PIdeath
  kPIdeath * AggP_Proteasome * kalive
PolyQAggregation1:
 {2.0}PolyQ + {1.0}ROS = {1.0}AggPolyQ1 + {1.0}ROS
  kaggPolyQ * PolyQ * (PolyQ - 1) * 0.5 * (pow(ROS, 2) / (pow(10, 2) + pow(ROS, 2))) * kalive
PolyQAggregation2:
 {1.0}PolyQ + {1.0}AggPolyQ1 + {1.0}ROS = {1.0}AggPolyQ2 + {1.0}ROS
  kaggPolyQ * PolyQ * AggPolyQ1 * (pow(ROS, 2) / (pow(10, 2) + pow(ROS, 2))) * kalive
PolyQAggregation3:
 {1.0}PolyQ + {1.0}AggPolyQ2 + {1.0}ROS = {1.0}AggPolyQ3 + {1.0}ROS
  kaggPolyQ * PolyQ * AggPolyQ2 * (pow(ROS, 2) / (pow(10, 2) + pow(ROS, 2))) * kalive
PolyQAggregation4:
 {1.0}PolyQ + {1.0}AggPolyQ3 + {1.0}ROS = {1.0}AggPolyQ4 + {1.0}ROS
  kaggPolyQ * PolyQ * AggPolyQ3 * (pow(ROS, 2) / (pow(10, 2) + pow(ROS, 2))) * kalive
PolyQAggregation5:
 {1.0}PolyQ + {1.0}AggPolyQ4 + {1.0}ROS = {1.0}AggPolyQ5 + {1.0}ROS
  kaggPolyQ * PolyQ * AggPolyQ4 * (pow(ROS, 2) / (pow(10, 2) + pow(ROS, 2))) * kalive
PolyQDegradation:
 {1.0}PolyQ_Proteasome = {1.0}Proteasome
  kdegPolyQ * PolyQ_Proteasome * kalive * kproteff
PolyQDisaggregation1:
 {1.0}AggPolyQ1 = {2.0}PolyQ
  kdisaggPolyQ1 * AggPolyQ1 * kalive
PolyQDisaggregation2:
 {1.0}AggPolyQ2 = {1.0}PolyQ + {1.0}AggPolyQ1
  kdisaggPolyQ2 * AggPolyQ2 * kalive
PolyQDisaggregation3:
 {1.0}AggPolyQ3 = {1.0}PolyQ + {1.0}AggPolyQ2
  kdisaggPolyQ3 * AggPolyQ3 * kalive
PolyQDisaggregation4:
 {1.0}AggPolyQ4 = {1.0}PolyQ + {1.0}AggPolyQ3
  kdisaggPolyQ4 * AggPolyQ4 * kalive
PolyQDisaggregation5:
 {1.0}AggPolyQ5 = {1.0}PolyQ + {1.0}AggPolyQ4
  kdisaggPolyQ5 * AggPolyQ5 * kalive
PolyQInclusionFormation:
 {1.0}PolyQ + {1.0}AggPolyQ5 = {7.0}SeqAggP
  kaggPolyQ * PolyQ * AggPolyQ5 * kalive
PolyQInclusionGrowth:
 {1.0}PolyQ + {1.0}SeqAggP = {2.0}SeqAggP
  kseqPolyQ * PolyQ * SeqAggP * kalive
PolyQ_ProteasomeSequestering:
 {1.0}PolyQ_Proteasome + {1.0}SeqAggP = {2.0}SeqAggP
  kseqPolyQProt * PolyQ_Proteasome * SeqAggP * kalive
ProteasomeInhibition1:
 {1.0}AggPolyQ1 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggPolyQ1 * Proteasome * kalive
ProteasomeInhibition2:
 {1.0}AggPolyQ2 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggPolyQ2 * Proteasome * kalive
ProteasomeInhibition3:
 {1.0}AggPolyQ3 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggPolyQ3 * Proteasome * kalive
ProteasomeInhibition4:
 {1.0}AggPolyQ4 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggPolyQ4 * Proteasome * kalive
ProteasomeInhibition5:
 {1.0}AggPolyQ5 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggPolyQ5 * Proteasome * kalive
ProteasomeInhibitionAggP1:
 {1.0}AggP1 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggP1 * Proteasome * kalive
ProteasomeInhibitionAggP2:
 {1.0}AggP2 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggP2 * Proteasome * kalive
ProteasomeInhibitionAggP3:
 {1.0}AggP3 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggP3 * Proteasome * kalive
ProteasomeInhibitionAggP4:
 {1.0}AggP4 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggP4 * Proteasome * kalive
ProteasomeInhibitionAggP5:
 {1.0}AggP5 + {1.0}Proteasome = {1.0}AggP_Proteasome
  kinhprot * AggP5 * Proteasome * kalive
ProteinSynthesis:
 {1.0}Source = {1.0}NatP
  ksynNatP * Source * kalive
ROSgenerationAggPProteasome:
 {1.0}AggP_Proteasome = {1.0}AggP_Proteasome + {1.0}ROS
  kgenROSAggP * AggP_Proteasome * kalive
ROSgenerationBasal:
 {1.0}Source = {1.0}ROS
  kgenROS * Source * kalive
ROSgenerationSeqAggP:
 {1.0}SeqAggP = {1.0}SeqAggP + {1.0}ROS
  kgenROSSeqAggP * SeqAggP * kalive
ROSgenerationSmallAggP1:
 {1.0}AggP1 = {1.0}AggP1 + {1.0}ROS
  kgenROSAggP * AggP1 * kalive
ROSgenerationSmallAggP2:
 {1.0}AggP2 = {1.0}AggP2 + {1.0}ROS
  kgenROSAggP * AggP2 * kalive
ROSgenerationSmallAggP3:
 {1.0}AggP3 = {1.0}AggP3 + {1.0}ROS
  kgenROSAggP * AggP3 * kalive
ROSgenerationSmallAggP4:
 {1.0}AggP4 = {1.0}AggP4 + {1.0}ROS
  kgenROSAggP * AggP4 * kalive
ROSgenerationSmallAggP5:
 {1.0}AggP5 = {1.0}AggP5 + {1.0}ROS
  kgenROSAggP * AggP5 * kalive
ROSgenerationSmallAggPolyQ1:
 {1.0}AggPolyQ1 = {1.0}AggPolyQ1 + {1.0}ROS
  kgenROSAggP * AggPolyQ1 * kalive
ROSgenerationSmallAggPolyQ2:
 {1.0}AggPolyQ2 = {1.0}AggPolyQ2 + {1.0}ROS
  kgenROSAggP * AggPolyQ2 * kalive
ROSgenerationSmallAggPolyQ3:
 {1.0}AggPolyQ3 = {1.0}AggPolyQ3 + {1.0}ROS
  kgenROSAggP * AggPolyQ3 * kalive
ROSgenerationSmallAggPolyQ4:
 {1.0}AggPolyQ4 = {1.0}AggPolyQ4 + {1.0}ROS
  kgenROSAggP * AggPolyQ4 * kalive
ROSgenerationSmallAggPolyQ5:
 {1.0}AggPolyQ5 = {1.0}AggPolyQ5 + {1.0}ROS
  kgenROSAggP * AggPolyQ5 * kalive
ROSremoval:
 {1.0}ROS = {1.0}Sink
  kremROS * ROS * kalive
Refolding:
 {1.0}MisP = {1.0}NatP
  krefold * MisP * kalive
mRFPuDegradation:
 {1.0}mRFPu_Proteasome = {1.0}Proteasome
  kdegmRFPu * mRFPu_Proteasome * kalive * kproteff
mRFPuProteasomeBinding:
 {1.0}mRFPu + {1.0}Proteasome = {1.0}mRFPu_Proteasome
  kbinmRFPu * mRFPu * Proteasome * kalive
mRFPuProteasomeRelease:
 {1.0}mRFPu_Proteasome = {1.0}mRFPu + {1.0}Proteasome
  krelmRFPu * mRFPu_Proteasome * kalive
mRFPuProteasomeSequestering:
 {1.0}mRFPu_Proteasome + {1.0}SeqAggP = {2.0}SeqAggP
  kseqmRFPuProt * mRFPu_Proteasome * SeqAggP * kalive
mRFPuSequestering:
 {1.0}mRFPu + {1.0}SeqAggP = {2.0}SeqAggP
  kseqmRFPu * mRFPu * SeqAggP * kalive
mRFPuSynthesis:
 {1.0}Source = {1.0}mRFPu
  ksynmRFPu * Source * kalive
p38_P_ROS_Generation:
 {1.0}p38_P = {1.0}p38_P + {1.0}ROS
  kgenROSp38 * p38_P * kp38act * kalive
p38activation:
 {1.0}ROS + {1.0}p38 = {1.0}ROS + {1.0}p38_P
  kactp38 * ROS * p38 * kalive
p38inactivation:
 {1.0}p38_P = {1.0}p38
  kinactp38 * p38_P * kalive
polyQSynthesis:
 {1.0}Source = {1.0}PolyQ
  ksynPolyQ * Source * kalive
polyqProteasomeBinding:
 {1.0}PolyQ + {1.0}Proteasome = {1.0}PolyQ_Proteasome
  kbinPolyQ * PolyQ * Proteasome * kalive
polyqProteasomeRelease:
 {1.0}PolyQ_Proteasome = {1.0}PolyQ + {1.0}Proteasome
  krelPolyQ * PolyQ_Proteasome * kalive


#parameters
kPIdeath = 2.5e-08
kactp38 = 5e-06
kagg2MisP = 1e-10
kaggMisP = 1e-11
kaggPolyQ = 5e-08
kalive = 1.0
kbinMisPProt = 5e-08
kbinPolyQ = 5e-08
kbinmRFPu = 5e-07
kdegMisP = 0.01
kdegPolyQ = 0.0025
kdegmRFPu = 0.005
kdisaggMisP1 = 5e-07
kdisaggMisP2 = 4e-07
kdisaggMisP3 = 3e-07
kdisaggMisP4 = 2e-07
kdisaggMisP5 = 1e-07
kdisaggPolyQ1 = 5e-07
kdisaggPolyQ2 = 4e-07
kdisaggPolyQ3 = 3e-07
kdisaggPolyQ4 = 2e-07
kdisaggPolyQ5 = 1e-07
kgenROS = 0.0017
kgenROSAggP = 5e-06
kgenROSSeqAggP = 1e-07
kgenROSp38 = 0.0007
kinactp38 = 0.002
kinhprot = 5e-09
kmisfold = 2e-06
kp38act = 1.0
kp38death = 9e-08
kproteff = 1.0
krefold = 8e-05
krelMisPProt = 1e-08
krelPolyQ = 1e-09
krelmRFPu = 1e-08
kremROS = 0.0002
kseqAggPProt = 5e-07
kseqMisP = 1e-09
kseqMisPProt = 5e-07
kseqPolyQ = 8e-07
kseqPolyQProt = 5e-07
kseqmRFPu = 1e-10
kseqmRFPuProt = 5e-07
ksynNatP = 2.4
ksynPolyQ = 0.007
ksynmRFPu = 0.138
Sink = 1.0
Source = 1.0
cytosol = 1.0


#initial values
AggP1 = 0.0
AggP2 = 0.0
AggP3 = 0.0
AggP4 = 0.0
AggP5 = 0.0
AggP_Proteasome = 0.0
AggPolyQ1 = 0.0
AggPolyQ2 = 0.0
AggPolyQ3 = 0.0
AggPolyQ4 = 0.0
AggPolyQ5 = 0.0
MisP = 0.0
MisP_Proteasome = 0.0
NatP = 19500.0
PIdeath = 0.0
PolyQ = 1000.0
PolyQ_Proteasome = 0.0
Proteasome = 1000.0
ROS = 10.0
SeqAggP = 0.0
mRFPu = 300.0
mRFPu_Proteasome = 0.0
p38 = 100.0
p38_P = 0.0
p38death = 0.0


#assignment rules
!F oligomers = AggPolyQ1 + AggPolyQ2 + AggPolyQ3 + AggPolyQ4 + AggPolyQ5