diff --git a/SI/Gi_parameters.csv b/SI/Gi_parameters.csv new file mode 100644 index 0000000000000000000000000000000000000000..c0602dd098255f6c097b82fb32fed62836cda660 --- /dev/null +++ b/SI/Gi_parameters.csv @@ -0,0 +1,68 @@ +Parameter,Value,Unit +time_in,0,s +time_out,0,s +L_init,0.01,uM +R_init,2,uM +Gi_init,3,uM +AC5_init,0.7,uM +Ca_cytos_free,0.06,uM +ATP_init,5000,uM +PDE4_init,2,uM +PDE10_init,1,uM +PKA_init,1.2,uM +RL_kon,100.0,uM-1*s-1 +RL_koff,200,s-1 +RL_Gi_kon,6600.0,uM-1*s-1 +RL_Gi_koff,200,s-1 +RL_Gi_decay,60,s-1 +GaiGTP_decay,30,s-1 +Gi_formation,100,s-1 +AC5_ATP_kon,0.1,uM-1*s-1 +AC5_ATP_koff,1,s-1 +AC5_basal,1,uM-1*s-1 +AC5_reverse_basal,0.0004, +AC5_Ca_kon,1.0,uM-1*s-1 +AC5_Ca_koff,0.9,s-1 +AC5_Ca_ATP_kon,0.075,uM-1*s-1 +AC5_Ca_ATP_koff,1,s-1 +AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1 +AC5_Ca_ATP_to_cAMP_reverse,0.00015, +AC5_ATP_Ca_kon,1.0,uM-1*s-1 +AC5_ATP_Ca_koff,0.9,s-1 +AC5_GaiGTP_kon,50000,uM-1*s-1 +AC5_GaiGTP_koff,5,s-1 +AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1 +AC5_GaiGTP_ATP_koff,1,s-1 +AC5_ATP_GaiGTP_kon,50000,uM-1*s-1 +AC5_ATP_GaiGTP_koff,5,s-1 +AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1 +AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105, +AC5_GaiGTP_decay,30,s-1 +AC5_GaiGTP_decay_koff,30,s-1 +AC5_Ca_GaiGTP_kon,50000,uM-1*s-1 +AC5_Ca_GaiGTP_koff,5,s-1 +AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1 +AC5_Ca_GaiGTP_ATP_koff,1,s-1 +AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1 +AC5_Ca_ATP_GaiGTP_koff,5,s-1 +AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1 +AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1 +AC5_Ca_GaiGTP_decay,30,s-1 +AC5_Ca_GaiGTP_ATP_decay,30,s-1 +PDE4_cAMP_kon,10.0,uM-1*s-1 +PDE4_cAMP_koff,1,s-1 +PDE4_cAMP_to_AMP,2,s-1 +PDE10_2cAMP_kon,0.001,uM-1*s-1 +PDE10_2cAMP_koff,9,s-1 +PDE10_cAMP_kon,100.0,uM-1*s-1 +PDE10_cAMP_koff,2,s-1 +PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1 +PDE10_2cAMP_cAMP_koff,2,s-1 +PDE10_cAMP_decay,3,s-1 +PDE10_2cAMP_cAMP_decay,10,s-1 +PKA_cAMP2_kon,0.26,uM-1*s-1 +PKA_cAMP2_koff,1,s-1 +PKA_cAMP4_kon,0.346,uM-1*s-1 +PKA_cAMP4_koff,1,s-1 +PKA_activation,10000.0,uM-1*s-1 +PKA_activation_reverse,0.025,s-1 diff --git a/SI/Gi_pathway_parameters.md b/SI/Gi_pathway_parameters.md deleted file mode 100644 index 4f213af71e31bf5bb0de87b6904e2bdfd7cc8641..0000000000000000000000000000000000000000 --- a/SI/Gi_pathway_parameters.md +++ /dev/null @@ -1,39 +0,0 @@ -| Reaction number | Reaction | Foward parameters names | Reverse parameters names | Foward default values (1/(nM*s)) | Reverse default values (1/s) | -|:---------------:|:------------------------------------------:|:------------------------:|:---------------------------------:|:--------------------------------:|:----------------------------:| -| 1 | DA + D2R <-> D2RDA | RL_kon | RL_koff | 0.1 | 200 | -| 3 | D2RDA + Gi <-> D2RDAGi | RL_Gi_kon | RL_Gi_koff | 6.6 | 200 | -| 9 | D2RDAGi -> GaiGTP + D2RDA + Gbgi | | RL_Gi_decay | | 60 | -| 13 | GaolfGTP -> GaolfGDP | | GaiGTP_decay | | 30 | -| 14 | GaolfGDP + Gbgolf -> Golf | | Gi_formation | | 100 | -| 16 | AC5 + Ca <-> AC5Ca | AC5_Ca_kon | AC5_Ca_koff | 0.001 | 0.9 | -| 21 | AC5 + ATP <-> [AC5*ATP] | AC5_ATP_kon | AC5_ATP_koff | 0.0001 | 1 | -| 22 | [AC5*ATP] -> cAMP + AC5 | | AC5_basal | | 1 | -| 23 | cAMP + AC5 -> [AC5*ATP] | | AC5_reverse_basal | | 0.0004 | -| 24 | AC5Ca + ATP <-> [AC5Ca*ATP] | AC5_Ca_ATP_kon | AC5_Ca_ATP_koff | 7.50E-05 | 1 | -| 25 | [AC5Ca*ATP] -> cAMP + AC5Ca | | AC5_Ca_ATP_to_cAMP | | 0.5 | -| 26 | cAMP + AC5Ca -> [AC5Ca*ATP] | | AC5_Ca_ATP_to_cAMP_reverse | | 0.00015 | -| 30 | Ca + [AC5*ATP] <-> [AC5Ca*ATP] | AC5_ATP_Ca_kon | AC5_ATP_Ca_koff | 0.001 | 0.9 | -| 37 | GaiGTP + AC5 <-> AC5GaiGTP | AC5_GaiGTP_kon | AC5_GaiGTP_koff | 50 | 5 | -| 38 | ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP] | AC5_GaiGTP_ATP_kon | AC5_GaiGTP_ATP_koff | 6.25E-05 | 1 | -| 39 | [AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP] | AC5_ATP_GaiGTP_kon | AC5_ATP_GaiGTP_koff | 50 | 5 | -| 40 | [AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP | | AC5_GaiGTP_ATP_to_cAMP | | 0.25 | -| 41 | cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP] | | AC5_GaiGTP_ATP_to_cAMP_reverse | | 0.00105 | -| 42 | AC5GaiGTP -> AC5 + GaiGDP | | AC5_GaiGTP_decay | | 30 | -| 43 | [AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP | | AC5_GaiGTP_decay_koff | | 30 | -| 55 | GaiGTP + AC5Ca <-> AC5CaGaiGTP | AC5_Ca_GaiGTP_kon | AC5_Ca_GaiGTP_koff | 50 | 5 | -| 56 | AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_GaiGTP_ATP_kon | AC5_Ca_GaiGTP_ATP_koff | 5.63E-05 | 1 | -| 57 | [AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP] | AC5_Ca_ATP_GaiGTP_kon | AC5_Ca_ATP_GaiGTP_koff | 50 | 5 | -| 58 | [AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP | | AC5_Ca_GaiGTP_ATP_to_cAMP | | 0.125 | -| 59 | cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP] | | AC5_Ca_GaiGTP_ATP_to_cAMP_reverse | | 2.81E-05 | -| 60 | AC5CaGaiGTP -> AC5Ca + GaiGDP | | AC5_Ca_GaiGTP_decay | | 30 | -| 61 | [AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP | | AC5_Ca_GaiGTP_ATP_decay | | 30 | -| 73 | cAMP + PDE4 <-> [PDE4*cAMP] | PDE104_cAMP_kon | PDE4_cAMP_koff | 0.01 | 1 | -| 74 | PDE10 + 2 cAMP <-> PDE10c | PDE10_2cAMP_kon | PDE10_2cAMP_koff | 1.00E-06 | 9 | -| 75 | [PDE4*cAMP] -> PDE4 + AMP | | PDE4_cAMP_to_AMP | | 2 | -| 76 | cAMP + PDE10 <-> [PDE10*cAMP] | PDE10_cAMP_kon | PDE10_cAMP_koff | 0.1 | 2 | -| 77 | cAMP + PDE10c <-> [PDE10c*cAMP] | PDE10_2cAMP_cAMP_kon | PDE10_2cAMP_cAMP_koff | 0.13 | 2 | -| 78 | [PDE10*cAMP] -> PDE10 + AMP | | PDE10_cAMP_decay | | 3 | -| 79 | [PDE10c*cAMP] -> PDE10c + AMP | | PDE10_2cAMP_cAMP_decay | | 10 | -| 80 | cAMP + PKA <-> PKAcAMP2 | PKA_cAMP2_kon | PKA_cAMP2_koff | 0.00026 | 1 | -| 81 | cAMP + PKAcAMP2 <-> PKAcAMP4 | PKA_cAMP4_kon | PKA_cAMP4_koff | 0.000346 | 1 | -| 82 | PKAcAMP4 <-> PKAc + PKAreg | PKA_activation | PKA_activation_reverse | 10 | 0.025 | diff --git a/SI/Gi_pathway_parameters.csv b/SI/Gi_reactions.csv similarity index 63% rename from SI/Gi_pathway_parameters.csv rename to SI/Gi_reactions.csv index 373b03155ec3cd2b455a55d176879cca3193dae7..4e04782065601ebf582da736501e39727299f497 100644 --- a/SI/Gi_pathway_parameters.csv +++ b/SI/Gi_reactions.csv @@ -1,38 +1,38 @@ -Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s) -1,DA + D2R <-> D2RDA,RL_kon,RL_koff,0.1,200 -3,D2RDA + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200 -9,D2RDAGi -> GaiGTP + D2RDA + Gbgi,,RL_Gi_decay,,60 +Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s) +1,L + R <-> LR,RL_kon,RL_koff,100.0,200 +3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200 +9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60 13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30 14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100 -16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9 -21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 +16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9 +21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 -24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 +24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 -30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 -37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5 -38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1 -39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5 +30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9 +37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5 +38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1 +39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5 40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25 41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105 42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30 43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30 -55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5 -56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1 -57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5 +55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5 +56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1 +57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5 58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125 59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05 60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30 61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30 -73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1 -74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 +73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1 +74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9 75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 -76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 -77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 +76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2 +77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 -80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 -81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 -82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025 +80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1 +81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1 +82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025 diff --git a/SI/Gq_parameters.csv b/SI/Gq_parameters.csv new file mode 100644 index 0000000000000000000000000000000000000000..8f1b5a12cbc7018b497df4b95123a44e2fb35e4f --- /dev/null +++ b/SI/Gq_parameters.csv @@ -0,0 +1,40 @@ +Parameter,Value,Unit +time_in,0,s +time_out,0,s +Gq_a_GDP_init:0.0027739,uM +Gq_a_GDP_init:6.4172E-4,uM +Gq_bg_init:0.0037173,uM +RGS4_init:0.019994,uM +RGS4_Gq_a_GTP_init:6.4168E-6,uM +Ca_init:0.1,uM +PLCb_init:0.090022,uM +PLCb_Gq_a_GTP_init:1.4492E-4,uM +PLCb_Ca_init:0.0093825,uM +PLCb_Ca_Gq_a_GTP_init:1.5038E-4,uM +PIP2_init:2.6578,uM +IP3_init:0.21952,uM +DAG_init:0.055555,uM +R_Gq_trimer_init:0,uM +R_L_Gq_trimer_init:0,uM +Gq_trimer_init:0.61869,uM +RL_kon:1.00,uM-1*s-1 +RL_koff:0.0046,s-1 +Gqa_Gqbg_kon:6.0,uM-1*s-1 +Gqa_Gqbg_koff:0.0001,s-1 +RL_Gq_decay:0.04,s-1 +RGS4_Gq_a_GTP_kon:20.83,uM-1*s-1 +RGS4_Gq_a_GTP_koff:33.32,s-1 +RGS4_Gq_a_GTP_decay:8.33,s-1 +Gq_a_GTP_decay:0.01,s-1 +Gq_a_GTP_PLCb_kon:2.52,uM-1*s-1 +Gq_a_GTP_PLCb_off:1.00,s-1 +Gq_a_GTP_PLCb_Ca_kon:30.0,uM-1*s-1 +Gq_a_GTP_PLCb_Ca_koff:1.00,s-1 +Gq_a_GTP_PLCb_Ca_decay:0.013,s-1 +PLCb_Ca_kon:3.00,uM-1*s-1 +PLCb_Ca_koff:1.00,s-1 +PLCb_Ca_Gq_a_GTP_kon:25.2,uM-1*s-1 +PLCb_Ca_Gq_a_GTP_koff:1.00,s-1 +DAG_decay:0.15,s-1 + + diff --git a/SI/Gq_reactions.csv b/SI/Gq_reactions.csv new file mode 100644 index 0000000000000000000000000000000000000000..0f6d4a7e79fd62d2e2cfb2141918864d00ab922c --- /dev/null +++ b/SI/Gq_reactions.csv @@ -0,0 +1,2 @@ +Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s) + diff --git a/SI/Gs_parameters.csv b/SI/Gs_parameters.csv index fb28a2f375eb78a62c4c35308f99a0c4ec51e999..96069301a4956e0ebebab55cfe399c24c9f0b5bc 100644 --- a/SI/Gs_parameters.csv +++ b/SI/Gs_parameters.csv @@ -1,38 +1,68 @@ -Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)), Reverse default (1/s) -1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5 -3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5 -9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15 -10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30 -11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100 -15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1 -16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9 -17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1 -18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1 -19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20 -20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084 -21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 -22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 -23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 -24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 -25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 -26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 -27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1 -28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2 -29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2 -30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 -31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1 -32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1 -33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10 -34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022 -35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2 -36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2 -73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1 -74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 -75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 -76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 -77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 -78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 -79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 -80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 -81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 -82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01 +Parameter,Value,Unit +time_in,0,s +time_out,0,s +L_init,0.01,uM +R_init,2,uM +Golf_init,2,uM +AC5_init,0.7,uM +Ca_init,0.06,uM +ATP_init,5000,uM +PDE4_init,2,uM +PDE10_init,0.7,uM +PKA_init,1.2,uM +RL_kon,5.0,uM-1*s-1 +RL_koff,5,s-1 +RL_Golf_kon,3.0,uM-1*s-1 +RL_Golf_koff,5.0,s-1 +RL_Golf_decay,15,s-1 +GaolfGTP_decay,30,s-1 +Golf_formation,100,s-1 +AC5_ATP_kon,0.1,uM-1*s-1 +AC5_ATP_koff,1,uM-1*s-1 +AC5_basal,1,s-1 +AC5_reverse_basal,0.0004,s-1 +AC5_Ca_kon,1.0,uM-1*s-1 +AC5_Ca_koff,0.9,s-1 +AC5_Ca_ATP_kon,0.075,uM-1*s-1 +AC5_Ca_ATP_koff,1,s-1 +AC5_Ca_ATP_to_cAMP,0.5,s-1 +AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1 +AC5_ATP_Ca_kon,1.0,uM-1*s-1 +AC5_ATP_Ca_koff,0.9, +AC5_GaolfGTP_kon,200.0,uM-1*s-1 +AC5_GaolfGTP_koff,0.1, +AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1 +AC5_GaolfGTP_ATP_i_koff,1, +cAMP_formation,20,s-1 +cAMP_reverse,0.084,s-1 +AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1 +AC5_GaolfGTP_ATP_a_koff,0.1, +AC5_GaolfGTP_decay,0.2,s-1 +AC5_GaolfGTP_ATP_decay,0.2,s-1 +AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1 +AC5_Ca_GaolfGTP_koff,0.1,s-1 +AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1 +AC5_Ca_GaolfGTP_ATP_koff,1,s-1 +AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1 +AC5_CA_ATP_GaolfGTP_koff,0.1,s-1 +AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1 +AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1 +AC5_Ca_GaolfGTP_decay,0.2,s-1 +AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1 +PDE4_cAMP_kon,10.0,uM-1*s-1 +PDE4_cAMP_koff,1,s-1 +PDE4_cAMP_to_AMP,2,s-1 +PDE10_2cAMP_kon,0.001,uM-1*s-1 +PDE10_2cAMP_koff,9,s-1 +PDE10_cAMP_kon,100.0,uM-1*s-1 +PDE10_cAMP_koff,2,s-1 +PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1 +PDE10_2cAMP_cAMP_koff,2,s-1 +PDE10_cAMP_decay,3,s-1 +PDE10_2cAMP_cAMP_decay,10,s-1 +PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1 +PKA_cAMP2_koff,1,s-1 +PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1 +PKA_cAMP4_koff,1,s-1 +PKA_activation,10000.0,uM-1*s-1 +PKA_activation_reverse,0.01,s-1 diff --git a/SI/Gs_reactions.csv b/SI/Gs_reactions.csv new file mode 100644 index 0000000000000000000000000000000000000000..af9bc902c7782658b0f1d257adf64ed2603c770f --- /dev/null +++ b/SI/Gs_reactions.csv @@ -0,0 +1,38 @@ +Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s) +1,R + L <-> RL,RL_kon,RL_koff,5.0,5 +3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5 +9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15 +10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30 +11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100 +15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1 +16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9 +17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1 +18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1 +19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20 +20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084 +21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1 +22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 +23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 +24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1 +25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 +26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 +27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1 +28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2 +29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2 +30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9 +31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1 +32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1 +33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10 +34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022 +35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2 +36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2 +73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1 +74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 +75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9 +76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2 +77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2 +78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 +79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 +80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1 +81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1 +82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01 diff --git a/src/lib/pathways/Gi_parameters.csv b/src/lib/pathways/Gi_parameters.csv index fac775f35b122602a036c25664036c91ff583e61..c0602dd098255f6c097b82fb32fed62836cda660 100644 --- a/src/lib/pathways/Gi_parameters.csv +++ b/src/lib/pathways/Gi_parameters.csv @@ -10,59 +10,59 @@ ATP_init,5000,uM PDE4_init,2,uM PDE10_init,1,uM PKA_init,1.2,uM -RL_kon,0.1*1E3,uM-1*s-1 +RL_kon,100.0,uM-1*s-1 RL_koff,200,s-1 -RL_Gi_kon,6.6*1E3,uM-1*s-1 +RL_Gi_kon,6600.0,uM-1*s-1 RL_Gi_koff,200,s-1 RL_Gi_decay,60,s-1 GaiGTP_decay,30,s-1 Gi_formation,100,s-1 -AC5_ATP_kon,0.0001*1E3,uM-1*s-1 +AC5_ATP_kon,0.1,uM-1*s-1 AC5_ATP_koff,1,s-1 AC5_basal,1,uM-1*s-1 AC5_reverse_basal,0.0004, -AC5_Ca_kon,0.001*1E3,uM-1*s-1 +AC5_Ca_kon,1.0,uM-1*s-1 AC5_Ca_koff,0.9,s-1 -AC5_Ca_ATP_kon,7.50E-5*1E3,uM-1*s-1 +AC5_Ca_ATP_kon,0.075,uM-1*s-1 AC5_Ca_ATP_koff,1,s-1 AC5_Ca_ATP_to_cAMP,0.5,uM-1*s-1 AC5_Ca_ATP_to_cAMP_reverse,0.00015, -AC5_ATP_Ca_kon,0.001*1E3,uM-1*s-1 +AC5_ATP_Ca_kon,1.0,uM-1*s-1 AC5_ATP_Ca_koff,0.9,s-1 -AC5_GaiGTP_kon,50*1E3,uM-1*s-1 +AC5_GaiGTP_kon,50000,uM-1*s-1 AC5_GaiGTP_koff,5,s-1 -AC5_GaiGTP_ATP_kon,6.25E-5*1E3,uM-1*s-1 +AC5_GaiGTP_ATP_kon,0.0625,uM-1*s-1 AC5_GaiGTP_ATP_koff,1,s-1 -AC5_ATP_GaiGTP_kon,50*1E3,uM-1*s-1 +AC5_ATP_GaiGTP_kon,50000,uM-1*s-1 AC5_ATP_GaiGTP_koff,5,s-1 AC5_GaiGTP_ATP_to_cAMP,0.25,uM-1*s-1 AC5_GaiGTP_ATP_to_cAMP_reverse,0.00105, AC5_GaiGTP_decay,30,s-1 AC5_GaiGTP_decay_koff,30,s-1 -AC5_Ca_GaiGTP_kon,50*1E3,uM-1*s-1 +AC5_Ca_GaiGTP_kon,50000,uM-1*s-1 AC5_Ca_GaiGTP_koff,5,s-1 -AC5_Ca_GaiGTP_ATP_kon,5.63E-5*1E3,uM-1*s-1 +AC5_Ca_GaiGTP_ATP_kon,0.0563,uM-1*s-1 AC5_Ca_GaiGTP_ATP_koff,1,s-1 -AC5_Ca_ATP_GaiGTP_kon,50*1E3,uM-1*s-1 +AC5_Ca_ATP_GaiGTP_kon,50000,uM-1*s-1 AC5_Ca_ATP_GaiGTP_koff,5,s-1 AC5_Ca_GaiGTP_ATP_to_cAMP,0.125,uM-1*s-1 -AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5, +AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,2.81E-5,s-1 AC5_Ca_GaiGTP_decay,30,s-1 AC5_Ca_GaiGTP_ATP_decay,30,s-1 -PDE4_cAMP_kon,0.01*1E3,uM-1*s-1 +PDE4_cAMP_kon,10.0,uM-1*s-1 PDE4_cAMP_koff,1,s-1 PDE4_cAMP_to_AMP,2,s-1 -PDE10_2cAMP_kon,1.0E-6*1E3, +PDE10_2cAMP_kon,0.001,uM-1*s-1 PDE10_2cAMP_koff,9,s-1 -PDE10_cAMP_kon,0.1*1E3, +PDE10_cAMP_kon,100.0,uM-1*s-1 PDE10_cAMP_koff,2,s-1 -PDE10_2cAMP_cAMP_kon,0.13*1E3, +PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1 PDE10_2cAMP_cAMP_koff,2,s-1 PDE10_cAMP_decay,3,s-1 PDE10_2cAMP_cAMP_decay,10,s-1 -PKA_cAMP2_kon,0.00026*1E3,uM-1*s-1 +PKA_cAMP2_kon,0.26,uM-1*s-1 PKA_cAMP2_koff,1,s-1 -PKA_cAMP4_kon,0.000346*1E3,uM-1*s-1 +PKA_cAMP4_kon,0.346,uM-1*s-1 PKA_cAMP4_koff,1,s-1 -PKA_activation,10*1E3,uM-1*s-1 +PKA_activation,10000.0,uM-1*s-1 PKA_activation_reverse,0.025,s-1 diff --git a/src/lib/pathways/Gi_reactions.csv b/src/lib/pathways/Gi_reactions.csv index f7e994d22ab38e05cd0b18b2b899e2c9e6f9da81..4e04782065601ebf582da736501e39727299f497 100644 --- a/src/lib/pathways/Gi_reactions.csv +++ b/src/lib/pathways/Gi_reactions.csv @@ -1,38 +1,38 @@ -Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(nM*s)),Reverse default values (1/s) -1,L + R <-> LR,RL_kon,RL_koff,0.1,200 -3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6.6,200 +Reaction number,Reaction,Forward parameters names,Reverse parameters names,Forward default values (1/(uM*s)),Reverse default values (1/s) +1,L + R <-> LR,RL_kon,RL_koff,100.0,200 +3,LR + Gi <-> D2RDAGi,RL_Gi_kon,RL_Gi_koff,6600.0,200 9,LRGi -> GaiGTP + LR + Gbgi,,RL_Gi_decay,,60 13,GaolfGTP -> GaolfGDP,,GaiGTP_decay,,30 14,GaolfGDP + Gbgolf -> Golf,,Gi_formation,,100 -16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,0.001,0.9 -21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 +16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_Ca_koff,1.0,0.9 +21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 -24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 +24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 -30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 -37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,50,5 -38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,6.25E-05,1 -39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50,5 +30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9 +37,GaiGTP + AC5 <-> AC5GaiGTP,AC5_GaiGTP_kon,AC5_GaiGTP_koff,5000,5 +38,ATP + AC5GaiGTP <-> [AC5GaiGTP*ATP],AC5_GaiGTP_ATP_kon,AC5_GaiGTP_ATP_koff,0.0625,1 +39,[AC5*ATP] + GaiGTP <-> [AC5GaiGTP*ATP],AC5_ATP_GaiGTP_kon,AC5_ATP_GaiGTP_koff,50000,5 40,[AC5GaiGTP*ATP] -> cAMP + AC5GaiGTP,,AC5_GaiGTP_ATP_to_cAMP,,0.25 41,cAMP + AC5GaiGTP -> [AC5GaiGTP*ATP],,AC5_GaiGTP_ATP_to_cAMP_reverse,,0.00105 42,AC5GaiGTP -> AC5 + GaiGDP,,AC5_GaiGTP_decay,,30 43,[AC5GaiGTP*ATP] -> [AC5*ATP] + GaiGDP,,AC5_GaiGTP_decay_koff,,30 -55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50,5 -56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,5.63E-05,1 -57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50,5 +55,GaiGTP + AC5Ca <-> AC5CaGaiGTP,AC5_Ca_GaiGTP_kon,AC5_Ca_GaiGTP_koff,50000,5 +56,AC5CaGaiGTP + ATP <-> [AC5CaGaiGTP*ATP],AC5_Ca_GaiGTP_ATP_kon,AC5_Ca_GaiGTP_ATP_koff,0.0563,1 +57,[AC5Ca*ATP] + GaiGTP <-> [AC5CaGaiGTP*ATP],AC5_Ca_ATP_GaiGTP_kon,AC5_Ca_ATP_GaiGTP_koff,50000,5 58,[AC5CaGaiGTP*ATP] -> cAMP + AC5CaGaiGTP,,AC5_Ca_GaiGTP_ATP_to_cAMP,,0.125 59,cAMP + AC5CaGaiGTP -> [AC5CaGaiGTP*ATP],,AC5_Ca_GaiGTP_ATP_to_cAMP_reverse,,2.81E-05 60,AC5CaGaiGTP -> AC5Ca + GaiGDP,,AC5_Ca_GaiGTP_decay,,30 61,[AC5CaGaiGTP*ATP] -> [AC5Ca*ATP] + GaiGDP,,AC5_Ca_GaiGTP_ATP_decay,,30 -73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,0.01,1 -74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 +73,cAMP + PDE4 <-> [PDE4*cAMP],PDE104_cAMP_kon,PDE4_cAMP_koff,10.0,1 +74,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9 75,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 -76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 -77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 +76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2 +77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 -80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 -81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 -82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.025 +80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1 +81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1 +82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.025 diff --git a/src/lib/pathways/Gs_parameters.csv b/src/lib/pathways/Gs_parameters.csv index 67a6110dbe5f4ec10f3e8adf0725fbdb30c8302e..96069301a4956e0ebebab55cfe399c24c9f0b5bc 100644 --- a/src/lib/pathways/Gs_parameters.csv +++ b/src/lib/pathways/Gs_parameters.csv @@ -10,59 +10,59 @@ ATP_init,5000,uM PDE4_init,2,uM PDE10_init,0.7,uM PKA_init,1.2,uM -RL_kon,5.0,nM-1*s-1 +RL_kon,5.0,uM-1*s-1 RL_koff,5,s-1 -RL_Golf_kon,3.0,nM-1*s-1 +RL_Golf_kon,3.0,uM-1*s-1 RL_Golf_koff,5.0,s-1 RL_Golf_decay,15,s-1 GaolfGTP_decay,30,s-1 Golf_formation,100,s-1 -AC5_ATP_kon,0.1,nM-1*s-1 -AC5_ATP_koff,1,nM-1*s-1 +AC5_ATP_kon,0.1,uM-1*s-1 +AC5_ATP_koff,1,uM-1*s-1 AC5_basal,1,s-1 AC5_reverse_basal,0.0004,s-1 -AC5_Ca_kon,1.0,nM-1*s-1 +AC5_Ca_kon,1.0,uM-1*s-1 AC5_Ca_koff,0.9,s-1 -AC5_Ca_ATP_kon,0.075,nM-1*s-1 +AC5_Ca_ATP_kon,0.075,uM-1*s-1 AC5_Ca_ATP_koff,1,s-1 AC5_Ca_ATP_to_cAMP,0.5,s-1 AC5_Ca_ATP_to_cAMP_reverse,0.00015,s-1 -AC5_ATP_Ca_kon,1.0,nM-1*s-1 +AC5_ATP_Ca_kon,1.0,uM-1*s-1 AC5_ATP_Ca_koff,0.9, -AC5_GaolfGTP_kon,200.0,nM-1*s-1 +AC5_GaolfGTP_kon,200.0,uM-1*s-1 AC5_GaolfGTP_koff,0.1, -AC5_GaolfGTP_ATP_i_kon,1.05,nM-1*s-1 +AC5_GaolfGTP_ATP_i_kon,1.05,uM-1*s-1 AC5_GaolfGTP_ATP_i_koff,1, cAMP_formation,20,s-1 cAMP_reverse,0.084,s-1 -AC5_GaolfGTP_ATP_a_kon,200.0,nM-1*s-1 +AC5_GaolfGTP_ATP_a_kon,200.0,uM-1*s-1 AC5_GaolfGTP_ATP_a_koff,0.1, AC5_GaolfGTP_decay,0.2,s-1 AC5_GaolfGTP_ATP_decay,0.2,s-1 -AC5_Ca_GaolfGTP_kon,200.0,nM-1*s-1 +AC5_Ca_GaolfGTP_kon,200.0,uM-1*s-1 AC5_Ca_GaolfGTP_koff,0.1,s-1 -AC5_Ca_GaolfGTP_ATP_kon,0.55,nM-1*s-1 +AC5_Ca_GaolfGTP_ATP_kon,0.55,uM-1*s-1 AC5_Ca_GaolfGTP_ATP_koff,1,s-1 -AC5_CA_ATP_GaolfGTP_kon,200.0,nM-1*s-1 +AC5_CA_ATP_GaolfGTP_kon,200.0,uM-1*s-1 AC5_CA_ATP_GaolfGTP_koff,0.1,s-1 AC5_Ca_GaolfGTP_ATP_to_cAMP,10,s-1 AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,0.022,s-1 AC5_Ca_GaolfGTP_decay,0.2,s-1 AC5_Ca_GaolfGTP_ATP_decay,0.2,s-1 -PDE4_cAMP_kon,10.0,nM-1*s-1 +PDE4_cAMP_kon,10.0,uM-1*s-1 PDE4_cAMP_koff,1,s-1 PDE4_cAMP_to_AMP,2,s-1 -PDE10_2cAMP_kon,0.001,nM-1*s-1 +PDE10_2cAMP_kon,0.001,uM-1*s-1 PDE10_2cAMP_koff,9,s-1 -PDE10_cAMP_kon,100.0,nM-1*s-1 +PDE10_cAMP_kon,100.0,uM-1*s-1 PDE10_cAMP_koff,2,s-1 -PDE10_2cAMP_cAMP_kon,130.0,nM-1*s-1 +PDE10_2cAMP_cAMP_kon,130.0,uM-1*s-1 PDE10_2cAMP_cAMP_koff,2,s-1 PDE10_cAMP_decay,3,s-1 PDE10_2cAMP_cAMP_decay,10,s-1 -PKA_cAMP2_kon,0.25999999999999995,nM-1*s-1 +PKA_cAMP2_kon,0.25999999999999995,uM-1*s-1 PKA_cAMP2_koff,1,s-1 -PKA_cAMP4_kon,0.34600000000000003,nM-1*s-1 +PKA_cAMP4_kon,0.34600000000000003,uM-1*s-1 PKA_cAMP4_koff,1,s-1 -PKA_activation,10000.0,nM-1*s-1 +PKA_activation,10000.0,uM-1*s-1 PKA_activation_reverse,0.01,s-1 diff --git a/src/lib/pathways/Gs_reactions.csv b/src/lib/pathways/Gs_reactions.csv index ba93913b6b6fda17a709c5e03b6758414a4a380f..af9bc902c7782658b0f1d257adf64ed2603c770f 100644 --- a/src/lib/pathways/Gs_reactions.csv +++ b/src/lib/pathways/Gs_reactions.csv @@ -1,38 +1,38 @@ -Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(nM*s)),Reverse default (1/s) -1,D1R + DA <-> D1RDA,RL_kon,RL_koff,0.005,5 -3,D1RDA + Golf <-> D1RDAGolf,RL_Golf_kon,RL_Golf_koff,0.003,5 -9,D1RDAGolf -> Gbgolf + D1RDA + GaolfGTP,,RL_Golf_decay,,15 +Reaction number,Reaction,Forward parameters names,Reverse parameter names,Forward default (1/(uM*s)),Reverse default (1/s) +1,R + L <-> RL,RL_kon,RL_koff,5.0,5 +3,RL + Golf <-> RLGolf,RL_Golf_kon,RL_Golf_koff,3.0,5 +9,RLGolf -> Gbgolf + RL + GaolfGTP,,RL_Golf_decay,,15 10,GaolfGTP -> GaolfGDP,,GaolfGTP_decay,,30 11,GaolfGDP + Gbgolf -> Golf,,Golf_formation,,100 -15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,0.2,0.1 -16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,0.001,0.9 -17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,0.2,0.1 -18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,0.00105,1 +15,AC5 + GaolfGTP <-> AC5GaolfGTP,AC5_GaolfGTP_kon,AC5_GaolfGTP_koff,200.0,0.1 +16,AC5 + Ca <-> AC5Ca,AC5_Ca_kon,AC5_GaolfGTP_koff,1.0,0.9 +17,AC5Ca + GaolfGTP <-> AC5CaGaolfGTP,AC5_Ca_GaolfGTP_kon,AC5_Ca_GaolfGTP_koff,200.0,0.1 +18,AC5GaolfGTP + ATP <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_i_koff,AC5_GaolfGTP_ATP_i_koff,1.05,1 19,[AC5GaolfGTP*ATP] -> cAMP + AC5GaolfGTP,,cAMP_formation,,20 20,cAMP + AC5GaolfGTP -> [AC5GaolfGTP*ATP],,cAMP_reverse,,0.084 -21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.0001,1 +21,AC5 + ATP <-> [AC5*ATP],AC5_ATP_kon,AC5_ATP_koff,0.1,1 22,[AC5*ATP] -> cAMP + AC5,,AC5_basal,,1 23,cAMP + AC5 -> [AC5*ATP],,AC5_reverse_basal,,0.0004 -24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,7.50E-05,1 +24,AC5Ca + ATP <-> [AC5Ca*ATP],AC5_Ca_ATP_kon,AC5_Ca_ATP_koff,0.075,1 25,[AC5Ca*ATP] -> cAMP + AC5Ca,,AC5_Ca_ATP_to_cAMP,,0.5 26,cAMP + AC5Ca -> [AC5Ca*ATP],,AC5_Ca_ATP_to_cAMP_reverse,,0.00015 -27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_koff,AC5_GaolfGTP_ATP_a_koff,0.2,0.1 +27,GaolfGTP + [AC5*ATP] <-> [AC5GaolfGTP*ATP],AC5_GaolfGTP_ATP_a_kon,AC5_GaolfGTP_ATP_a_koff,200.0,0.1 28,AC5GaolfGTP -> AC5 + GaolfGDP,,AC5_GaolfGTP_decay,,0.2 29,[AC5GaolfGTP*ATP] -> [AC5*ATP] + GaolfGDP,,AC5_GaolfGTP_ATP_decay,,0.2 -30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,0.001,0.9 -31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.00055,1 -32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,0.2,0.1 +30,Ca + [AC5*ATP] <-> [AC5Ca*ATP],AC5_ATP_Ca_kon,AC5_ATP_Ca_koff,1.0,0.9 +31,AC5CaGaolfGTP + ATP <-> [AC5CaGaolfGTP*ATP],AC5_Ca_GaolfGTP_ATP_kon,AC5_Ca_GaolfGTP_ATP_koff,0.55,1 +32,GaolfGTP + [AC5Ca*ATP] <-> [AC5CaGaolfGTP*ATP],AC5_CA_ATP_GaolfGTP_kon,AC5_CA_ATP_GaolfGTP_koff,200.0,0.1 33,[AC5CaGaolfGTP*ATP] -> cAMP + AC5CaGaolfGTP,,AC5_Ca_GaolfGTP_ATP_to_cAMP,,10 34,cAMP + AC5CaGaolfGTP -> [AC5CaGaolfGTP*ATP],,AC5_Ca_GaolfGTP_ATP_to_cAMP_reverse,,0.022 35,AC5CaGaolfGTP -> AC5Ca + GaolfGDP,,AC5_Ca_GaolfGTP_decay,,0.2 36,[AC5CaGaolfGTP*ATP] -> [AC5Ca*ATP] + GaolfGDP,,AC5_Ca_GaolfGTP_ATP_decay,,0.2 -73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,0.01,1 +73,cAMP + PDE4 <-> [PDE4*cAMP],PDE4_cAMP_kon,PDE4_cAMP_koff,10.0,1 74,[PDE4*cAMP] -> PDE4 + AMP,,PDE4_cAMP_to_AMP,,2 -75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,1.00E-06,9 -76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,0.1,2 -77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,0.13,2 +75,PDE10 + 2 cAMP <-> PDE10c,PDE10_2cAMP_kon,PDE10_2cAMP_koff,0.001,9 +76,cAMP + PDE10 <-> [PDE10*cAMP],PDE10_cAMP_kon,PDE10_cAMP_koff,100.0,2 +77,cAMP + PDE10c <-> [PDE10c*cAMP],PDE10_2cAMP_cAMP_kon,PDE10_2cAMP_cAMP_koff,130.0,2 78,[PDE10*cAMP] -> PDE10 + AMP,,PDE10_cAMP_decay,,3 79,[PDE10c*cAMP] -> PDE10c + AMP,,PDE10_2cAMP_cAMP_decay,,10 -80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.00026,1 -81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.000346,1 -82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10,0.01 +80,cAMP + PKA <-> PKAcAMP2,PKA_cAMP2_kon,PKA_cAMP2_koff,0.26,1 +81,cAMP + PKAcAMP2 <-> PKAcAMP4,PKA_cAMP4_kon,PKA_cAMP4_koff,0.346,1 +82,PKAcAMP4 <-> PKAc + PKAreg,PKA_activation,PKA_activation_reverse,10000.0,0.01