Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| Fura4F_C+Ca_CCa_Fura4F_C |
Cabind_Fura4F
C
|
MassAction | Fura4F_C+Ca_CCa_Fura4F_C |
|
|
|
reaction rate (J): (((Kf * Fura4F_C) * Ca_C) - (Kr * Ca_Fura4F_C))[uM.s-1]
forward rate constant (Kf): speed_Ca_Fura4F[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Fura4F * kd_Fura4F)[s-1] user defined (speed_Ca_Fura4F): 10.0[uM-1.s-1] user defined (kd_Fura4F): 0.77[uM] |
|
| IP3_C+LIBRAvIII_CIP3_LIBRAvIII_C |
IP3_LibraVIII
C
|
MassAction | IP3_C+LIBRAvIII_CIP3_LIBRAvIII_C |
|
|
|
reaction rate (J): (((Kf * IP3_C) * LIBRAvIII_C) - (Kr * IP3_LIBRAvIII_C))[uM.s-1]
forward rate constant (Kf): speed_LibraVIII[s-1.uM-1] reverse rate constant (Kr): (speed_LibraVIII * KD_LibraVIII)[s-1] user defined (speed_LibraVIII): 1.0[uM-1.s-1] user defined (KD_LibraVIII): 0.5[uM] |
|
| PI4P_MDAG_M |
PLC_on_PI4P
M
|
GeneralKinetics | PI4P_MDAG_M |
|
|
|
reaction rate (J): (PI4P_M * (GaGTP_PLC_M * K_plc))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] |
|
| RG_GDP_MGaGTP_M+RGbeta_M |
NE_RG
M
|
MassAction | RG_GDP_MGaGTP_M+RGbeta_M |
|
|
|
reaction rate (J): ((Kf * RG_GDP_M) - ((Kr * GaGTP_M) * RGbeta_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.5E-5[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1] |
|
| R_M+oxoM_EXRL_M |
L1
M
|
MassAction | R_M+oxoM_EXRL_M |
|
|
|
reaction rate (J): (((Kf * R_M) * oxoM_EX) - (Kr * RL_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL1[s-1.uM-1] reverse rate constant (Kr): KrL1[s-1] |
|
| noninactiveIP3RinactiveIP3R |
h_reaction_IP3Rinactivation
ERM
|
GeneralKinetics | noninactiveIP3RinactiveIP3R |
|
|
|
reaction rate (J): - ((KD_inh_Ca_IP3R - ((Ca_C + KD_inh_Ca_IP3R) * h)) * Kon_Ca_IP3R)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (KD_inh_Ca_IP3R): 0.2[uM] user defined (Kon_Ca_IP3R): 2.7[molecules.um-2.uM-1.s-1] |
|
| PI4P_MPIP2_M |
PIP5K_5Pase
M
|
MassAction | PI4P_MPIP2_M |
|
|
|
reaction rate (J): ((Kf * PI4P_M) - (Kr * PIP2_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (foldPIP2 * (((t < start) * k5K_rest) + ((t >= start) * (t <= end) * k5k_Oxo)))[s-1] reverse rate constant (Kr): ((0.014 * foldPIP2) * (1.0 + (D_P * (exp(((start + 15.0 - t) / tau_d)) - 1.0) * ((start + 15.0) <= t) * (t < end))))[s-1] user defined (k5K_rest): 0.02[s-1] user defined (k5k_Oxo): (k5K_rest + ((stim_5k - k5K_rest + k5k_base) * scale5K * (1.0 - exp(((start - t) / tau_stim_5K_onset)))))[s-1] user defined (scale5K): 1.0[1] |
|
| G_GDP_MGaGTP_M+Gbeta_M |
NE_G
M
|
MassAction | G_GDP_MGaGTP_M+Gbeta_M |
|
|
|
reaction rate (J): ((Kf * G_GDP_M) - ((Kr * GaGTP_M) * Gbeta_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.5E-5[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1] |
|
| GaGTP_MGa_GDP_M |
GTPase_Ga
M
|
GeneralKinetics | GaGTP_MGa_GDP_M |
|
|
|
reaction rate (J): (Kf * GaGTP_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 0.026[s-1] |
|
| IP3_C |
IP3deg_Palk
C
|
MassAction | IP3_C |
|
|
|
reaction rate (J): (Kf * IP3_C)[uM.s-1]
forward rate constant (Kf): (r_Palk_IP3ase * (k5P + (k3K * Ca_C * Ca_C / ((Ca_C * Ca_C) + (kdeg * kdeg)))))[s-1] reverse rate constant (Kr): 0.0[uM.s-1] user defined (k3K): 40.0[s-1] user defined (r_Palk_IP3ase): 0.0[1] user defined (k5P): 0.005[s-1] user defined (kdeg): 0.4[uM] |
|
| Palk_C1Palk_C2 |
r12
C
|
MassAction | Palk_C1Palk_C2 |
|
|
|
reaction rate (J): ((Kf * Palk_C1) - (Kr * Palk_C2))[uM.s-1]
forward rate constant (Kf): (q12 * perms2pers)[s-1] reverse rate constant (Kr): (q21 * perms2pers)[s-1] user defined (q12): 0.74[1] user defined (q21): ((VP21 / (1.0 + (kp21 * (IP3_nM ^ 3.0)))) + bp21)[1] user defined (VP21): 0.0949[1] user defined (IP3_nM): (IP3_C * uM2nM)[1] user defined (bp21): 0.11[1] user defined (kp21): 5.0E-10[1] |
|
| Palk_C2Palk_C3 |
r23
C
|
MassAction | Palk_C2Palk_C3 |
|
|
|
reaction rate (J): ((Kf * Palk_C2) - (Kr * Palk_C3))[uM.s-1]
forward rate constant (Kf): (q23 * perms2pers)[s-1] reverse rate constant (Kr): (q32 * perms2pers)[s-1] user defined (q23): (alpha23 * p23 * P23)[1] user defined (q32): (alpha32 * p32 * P32)[1] user defined (p32): (((V32 / ((k32 ^ 3.0) + (Ca_nM ^ 3.0))) + b32) * ((Vm32 * (Ca_nM ^ 7.0) / ((km32 ^ 7.0) + (Ca_nM ^ 7.0))) + bm32))[1] user defined (P32): ((VP32 * (IP3_nM ^ 3.0) / (1.0 + (kp32 * (IP3_nM ^ 3.0)))) + bp32)[1] user defined (alpha32): 50.0[1] user defined (VP32): 3.0E-12[1] user defined (IP3_nM): (ip3_Palk_scale_factor * IP3_C * uM2nM)[1] user defined (bp32): 0.0[1] user defined (kp32): 1.5E-10[1] user defined (b32): 0.005[1] user defined (km32): 150.0[1] user defined (V32): 7000000.0[1] user defined (bm32): 0.03[1] user defined (k32): 520.0[1] user defined (Ca_nM): (Ca_C * uM2nM)[1] user defined (Vm32): 1.06[1] user defined (p23): (a23 - (((V23 / ((k23 ^ 2.0) + (Ca_nM ^ 2.0))) + b23) * ((Vm23 * (Ca_nM ^ 5.0) / ((km23 ^ 5.0) + (Ca_nM ^ 5.0))) + bm23)))[1] user defined (P23): ((VP23 / (1.0 + (kp23 * (IP3_nM ^ 3.0)))) + bp23)[1] user defined (alpha23): 1000.0[1] user defined (bp23): 0.001[1] user defined (VP23): 0.162[1] user defined (kp23): 5.0E-9[1] user defined (Vm23): 0.3545[1] user defined (km23): 72.0[1] user defined (b23): 2.2[1] user defined (bm23): 0.042[1] user defined (a23): 0.9775171065493647[1] user defined (V23): 1.08E-6[1] user defined (k23): 2000.0[1] user defined (ip3_Palk_scale_factor): 1.0[1] |
|
| Palk_C2Palk_O4 |
r24
C
|
MassAction | Palk_C2Palk_O4 |
|
|
|
reaction rate (J): ((Kf * Palk_C2) - (Kr * Palk_O4))[uM.s-1]
forward rate constant (Kf): q24[s-1] reverse rate constant (Kr): q42[s-1] user defined (q24): (7.84 * perms2pers)[s-1] user defined (q42): (3.6 * perms2pers)[s-1] |
|
| PIP2_MboundPIP2_M |
PIP2_buffering
M
|
MassAction | PIP2_MboundPIP2_M |
|
|
|
reaction rate (J): ((Kf * PIP2_M) - (Kr * boundPIP2_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (( - 1.0 + foldPIP2) * speed_buffering)[s-1] reverse rate constant (Kr): speed_buffering[s-1] user defined (speed_buffering): 1.0[s-1] |
|
| RGbeta_M+oxoM_EXRLGbeta_M |
L2beta
M
|
MassAction | RGbeta_M+oxoM_EXRLGbeta_M |
|
|
|
reaction rate (J): (((Kf * RGbeta_M) * oxoM_EX) - (Kr * RLGbeta_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1] |
|
| RLG_GDP_MRLGbeta_M+GaGTP_M |
NE_RLG
M
|
GeneralKinetics | RLG_GDP_MRLGbeta_M+GaGTP_M |
|
|
|
reaction rate (J): (Kf * RLG_GDP_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 0.65[s-1] |
|
| GaGDP_PLC_MGaGTP_PLC_M |
NE_GaP
M
|
GeneralKinetics | GaGDP_PLC_MGaGTP_PLC_M |
|
|
|
reaction rate (J): (4.7 * GaGDP_PLC_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] |
|
| PIP2_M+PH_YFP_CPH_YFP_PIP2_M |
PH_YFP_PIP2
M
|
MassAction | PIP2_M+PH_YFP_CPH_YFP_PIP2_M |
|
|
|
reaction rate (J): (((Kf * PIP2_M) * PH_YFP_C) - (Kr * PH_YFP_PIP2_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): speed_PH_PIP2[s-1.uM-1] reverse rate constant (Kr): (KD_PH_PIP2 * speed_PH_PIP2)[s-1] |
|
| PIP2_MPI4P_M |
VSP
M
|
MassAction | PIP2_MPI4P_M |
|
|
|
reaction rate (J): ((Kf * PIP2_M) - (Kr * PI4P_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kVSP * foldPIP2)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (kVSP): (VSPmax / (1.0 + exp((1.5 * qKT * (V - Vhalf)))))[s-1] user defined (Vhalf): 0.1[V] user defined (V): (Vhold + (( - Vhold + Vstep) * (t > VSP_start) * (t < VSP_end)))[V] user defined (VSPmax): 0.0[s-1] user defined (qKT): -40.5898[A.s3.kg-1.m-2] user defined (VSP_end): 150.0[s] user defined (Vstep): 0.1[V] user defined (Vhold): -0.06[V] user defined (VSP_start): 50.0[s] |
|
| R_M+Gbeta_MRGbeta_M |
G1beta
M
|
MassAction | R_M+Gbeta_MRGbeta_M |
|
|
|
reaction rate (J): (((Kf * R_M) * Gbeta_M) - (Kr * RGbeta_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG1[um2.s-1.molecules-1] reverse rate constant (Kr): KrG1[s-1] |
|
| DAG_MPA_2AG_M |
DAGPase
M
|
GeneralKinetics | DAG_MPA_2AG_M |
|
|
|
reaction rate (J): (Kf * DAG_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 5.0[s-1] |
|
| PI_MPI4P_M |
PI4K_4Pase
M
|
MassAction | PI_MPI4P_M |
|
|
|
reaction rate (J): ((Kf * PI_M) - (Kr * PI4P_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (foldPIP2 * ((K4_recover * (t > end)) + (K4_rest * (t < start)) + (K4_Oxo * (t >= start) * (t <= end))))[s-1] reverse rate constant (Kr): (0.03 * (1.0 + (D_P * (exp(((start + 15.0 - t) / tau_d)) - 1.0) * ((start + 15.0) <= t) * (t < end))))[s-1] user defined (K4_Oxo): (K4_rest + ((stim_4k - K4_rest + K4_base) * scale4K * (1.0 - exp(((start - t) / tau_stim_4K_onset)))))[s-1] user defined (K4_rest): 2.6E-4[s-1] user defined (K4_recover): ((exp(((end - t) / tau_stim_recovery)) * scale4K * (stim_4k - K4_rest + K4_base)) + K4_rest)[s-1] user defined (scale4K): 0.75[1] user defined (K4_base): 2.3534E-4[s-1] user defined (foldPIP2): 3.0[1] user defined (tau_stim_recovery): 5.0[s] |
|
| PH_YFP_C+IP3_CIP3_PH_YFP_C |
PH_YFP_IP3
C
|
MassAction | PH_YFP_C+IP3_CIP3_PH_YFP_C |
|
|
|
reaction rate (J): (((Kf * PH_YFP_C) * IP3_C) - (Kr * IP3_PH_YFP_C))[uM.s-1]
forward rate constant (Kf): speed_PH_IP3[s-1.uM-1] reverse rate constant (Kr): (KD_PH_IP3 * speed_PH_IP3)[s-1] |
|
| IP3_C |
IP3Pase_FDH
C
|
GeneralKinetics | IP3_C |
|
|
|
reaction rate (J): (K_IP3ase * IP3_C)[uM.s-1]
user defined (K_IP3ase): (0.08 * r_FDH_IP3ase)[s-1] user defined (r_FDH_IP3ase): 50.0[s-1] |
|
| RL_M+Gbeta_MRLGbeta_M |
G2beta
M
|
MassAction | RL_M+Gbeta_MRLGbeta_M |
|
|
|
reaction rate (J): (((Kf * RL_M) * Gbeta_M) - (Kr * RLGbeta_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG2[um2.s-1.molecules-1] reverse rate constant (Kr): KrG2[s-1] |
|
| GaGDP_PLC_MGa_GDP_M+PLC_M |
PLCdiss
M
|
MassAction | GaGDP_PLC_MGa_GDP_M+PLC_M |
|
|
|
reaction rate (J): ((Kf * GaGDP_PLC_M) - ((Kr * Ga_GDP_M) * PLC_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 0.71[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1] |
|
| RG_GDP_M+oxoM_EXRLG_GDP_M |
L2
M
|
MassAction | RG_GDP_M+oxoM_EXRLG_GDP_M |
|
|
|
reaction rate (J): (((Kf * RG_GDP_M) * oxoM_EX) - (Kr * RLG_GDP_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1] |
|
| PLC_M+GaGTP_MGaGTP_PLC_M |
PLCassoc
M
|
MassAction | PLC_M+GaGTP_MGaGTP_PLC_M |
|
|
|
reaction rate (J): (((Kf * PLC_M) * GaGTP_M) - (Kr * GaGTP_PLC_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.0[um2.s-1.molecules-1] reverse rate constant (Kr): 0.0[s-1] |
|
| G_GDP_M+R_MRG_GDP_M |
G1
M
|
MassAction | G_GDP_M+R_MRG_GDP_M |
|
|
|
reaction rate (J): (((Kf * G_GDP_M) * R_M) - (Kr * RG_GDP_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG1[um2.s-1.molecules-1] reverse rate constant (Kr): KrG1[s-1] |
|
| KCNQ_M+PIP2_MKCNQ_PIP2_M |
PIP2bindKCNQ
M
|
GeneralKinetics | KCNQ_M+PIP2_MKCNQ_PIP2_M |
|
|
|
reaction rate (J): ((Kf * PIP2_M * KCNQ_M) - (Kr * KCNQ_PIP2_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kr): (KD_PIP2_KCNQ * Kf)[s-1] user defined (Kf): speed_PIP2_KCNQ[um2.molecules-1.s-1] user defined (KD_PIP2_KCNQ): KA_PIP2_KCNQ[molecules.um-2] user defined (KA_PIP2_KCNQ): 2000.0[molecules.um-2] user defined (speed_PIP2_KCNQ): 0.05[um2.molecules-1.s-1] |
|
| PIP2_MIP3_C+DAG_M |
PIP2hydr
M
|
GeneralKinetics | PIP2_MIP3_C+DAG_M |
|
|
|
reaction rate (J): (PIP2_M * (K_plc * foldPIP2 * GaGTP_PLC_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] |
|
| IP3_pipetteIP3_C |
IP3_dialysis
M
|
MassAction | IP3_pipetteIP3_C |
|
|
|
reaction rate (J): ((Kf * IP3_pipette) - (Kr * IP3_C))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (0.015 * (t > start) * k_pipette)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): (0.015 * (t > start) * k_pipette)[molecules.um-2.s-1.uM-1] user defined (k_pipette): 0.0[s-1] |
|
| GaGTP_PLC_MGaGDP_PLC_M |
GTPase_GaP
M
|
GeneralKinetics | GaGTP_PLC_MGaGDP_PLC_M |
|
|
|
reaction rate (J): (15.0 * GaGTP_PLC_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] |
|
| OxoM_conc_EXoxoM_EX |
Oxo_appl
EX
|
MassAction | OxoM_conc_EXoxoM_EX |
|
|
|
reaction rate (J): ((Kf * OxoM_conc_EX) - (Kr * oxoM_EX))[uM.s-1]
forward rate constant (Kf): (50.0 * (t > start) * (t < end))[s-1] reverse rate constant (Kr): (50.0 * (t > end))[s-1] |
|
| RL_M+G_GDP_MRLG_GDP_M |
G2
M
|
MassAction | RL_M+G_GDP_MRLG_GDP_M |
|
|
|
reaction rate (J): (((Kf * RL_M) * G_GDP_M) - (Kr * RLG_GDP_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): KfG2[um2.s-1.molecules-1] reverse rate constant (Kr): KrG2[s-1] |
|
| Gbeta_M+Ga_GDP_MG_GDP_M |
reconstitution
M
|
GeneralKinetics | Gbeta_M+Ga_GDP_MG_GDP_M |
|
|
|
reaction rate (J): (Kf * Gbeta_M * Ga_GDP_M)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Kf): 1.0[um2.molecules-1.s-1] |
|
| C1_dom_C+DAG_MC1_DAG_M |
C1bindDAG
M
|
MassAction | C1_dom_C+DAG_MC1_DAG_M |
|
|
|
reaction rate (J): (((Kf * C1_dom_C) * DAG_M) - (Kr * C1_DAG_M))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): speed_DAG_C1[s-1.uM-1] reverse rate constant (Kr): (KD_DAG_C1 * speed_DAG_C1)[s-1] |
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| EX |
Compartment
(+) (-)
|
|
|
|
| Ca_store |
Compartment
(+) (-)
|
|
|
|
| C |
Compartment
(+) (-)
|
|
|
|
| M |
Membrane
N/A
|
|
|
|
| ERM |
Membrane
N/A
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| IP3_pipette | EX | |
|
|
|
|
| PI4P_M | M | |
|
|
|
|
| PH_YFP_PIP2_M | M | |
|
|
|
|
| KCNQ_M | M | |
|
|
|
|
| inactiveIP3R | ERM | |
|
|
|
|
| IP3_PH_YFP_C | C | |
|
|
|
|
| PI_M | M | |
|
|
|
|
| RLG_GDP_M | M | |
|
|
|
|
| RL_M | M | |
|
|
|
|
| GaGTP_PLC_M | M | |
|
|
|
|
| GaGTP_M | M | |
|
|
|
|
| RLGbeta_M | M | |
|
|
|
|
| Gbeta_M | M | |
|
|
|
|
| C1_dom_C | C | |
|
|
|
|
| K_C | C | |
|
|
|
|
| Ca_C | C | |
|
|
|
|
| RGbeta_M | M | |
|
|
|
|
| R_M | M | |
|
|
|
|
| noninactiveIP3R | ERM | |
|
|
|
|
| boundPIP2_M | M | |
|
|
|
|
| IP3_LIBRAvIII_C | C | |
|
|
|
|
| LIBRAvIII_C | C | |
|
|
|
|
| G_GDP_M | M | |
|
|
|
|
| RG_GDP_M | M | |
|
|
|
|
| Ga_GDP_M | M | |
|
|
|
|
| DAG_M | M | |
|
|
|
|
| oxoM_EX | EX | |
|
|
|
|
| PA_2AG_M | M | |
|
|
|
|
| PLC_M | M | |
|
|
|
|
| PH_YFP_C | C | |
|
|
|
|
| PIP2_M | M | |
|
|
|
|
| OxoM_conc_EX | EX | |
|
|
|
|
| Ca_Fura4F_C | C | |
|
|
|
|
| Ca_Ca_store | Ca_store | |
|
|
|
|
| Fura4F_C | C | |
|
|
|
|
| IP3_C | C | |
|
|
|
|
| Palk_C1 | C | |
|
|
|
|
| Palk_C2 | C | |
|
|
|
|
| Palk_C3 | C | |
|
|
|
|
| Palk_O4 | C | |
|
|
|
|
| C1_DAG_M | M | |
|
|
|
|
| GaGDP_PLC_M | M | |
|
|
|
|
| K_EX | EX | |
|
|
|
|
| KCNQ_PIP2_M | M | |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| modeling PI cycle | Deterministic (ODE) Compartmental | cloned from 'modeling PI cycle' owned by user cherubim0521 cloned from 'modelinOct2010' owned by user hillelab cloned from 'modelinOct2010' owned by user bfalken (copied from PBio519 talk) (copied from M1R activation, manuscript 1) (copied from M1R activation) (copied from PipDecay) cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab |
Application - modeling PI cycle
| Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IP3_pipette | 0.0 [uM] | 0.0
[um2/s] | oxoM_EX |
0.0
[uM]
|
0.0
[um2/s] | OxoM_conc_EX |
10.0
[uM]
|
0.0
[um2/s] | K_EX |
0.0
[uM]
|
0.0
[um2/s] | Ca_Ca_store |
400.0
[uM]
|
0.0
[um2/s] | IP3_PH_YFP_C |
0.0
[uM]
|
0.0
[um2/s] | C1_dom_C |
0.0
[uM]
|
0.0
[um2/s] | K_C |
100000.0
[uM]
|
0.0
[um2/s] | Ca_C |
0.13
[uM]
|
0.0
[um2/s] | IP3_LIBRAvIII_C |
0.0
[uM]
|
0.0
[um2/s] | LIBRAvIII_C |
0.0
[uM]
|
0.0
[um2/s] | PH_YFP_C |
0.0
[uM]
|
0.0
[um2/s] | Ca_Fura4F_C |
0.0
[uM]
|
0.0
[um2/s] | Fura4F_C |
0.0
[uM]
|
0.0
[um2/s] | IP3_C |
1.0E-6
[uM]
|
0.0
[um2/s] | Palk_C1 |
1.0
[uM]
|
0.0
[um2/s] | Palk_C2 |
0.0
[uM]
|
0.0
[um2/s] | Palk_C3 |
0.0
[uM]
|
0.0
[um2/s] | Palk_O4 |
0.0
[uM]
|
0.0
[um2/s] | PI4P_M |
4000.0
[uM]
|
0.0
[um2/s] | PH_YFP_PIP2_M |
0.0
[uM]
|
0.0
[um2/s] | KCNQ_M |
4.0
[uM]
|
0.0
[um2/s] | PI_M |
140000.0
[uM]
|
0.0
[um2/s] | RLG_GDP_M |
0.0
[uM]
|
0.0
[um2/s] | RL_M |
0.0
[uM]
|
0.0
[um2/s] | GaGTP_PLC_M |
0.0
[uM]
|
0.0
[um2/s] | GaGTP_M |
0.0
[uM]
|
0.0
[um2/s] | RLGbeta_M |
0.0
[uM]
|
0.0
[um2/s] | Gbeta_M |
0.0
[uM]
|
0.0
[um2/s] | RGbeta_M |
0.0
[uM]
|
0.0
[um2/s] | R_M |
500.0
[uM]
|
0.0
[um2/s] | boundPIP2_M |
(( - 1.0 + foldPIP2) * PIP2_M)
[uM]
|
0.0
[um2/s] | G_GDP_M |
40.0
[uM]
|
0.0
[um2/s] | RG_GDP_M |
0.0
[uM]
|
0.0
[um2/s] | Ga_GDP_M |
0.0
[uM]
|
0.0
[um2/s] | DAG_M |
2.0
[uM]
|
0.0
[um2/s] | PA_2AG_M |
0.0
[uM]
|
0.0
[um2/s] | PLC_M |
10.0
[uM]
|
0.0
[um2/s] | PIP2_M |
5000.0
[uM]
|
0.0
[um2/s] | C1_DAG_M |
0.0
[uM]
|
0.0
[um2/s] | GaGDP_PLC_M |
0.0
[uM]
|
0.0
[um2/s] | KCNQ_PIP2_M |
0.0
[uM]
|
0.0
[um2/s] | inactiveIP3R |
0.0
[uM]
|
0.0
[um2/s] | noninactiveIP3R |
1.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| Cabind_Fura4F | included |
| IP3_LibraVIII | included |
| PLC_on_PI4P | included |
| NE_RG | included |
| L1 | included |
| h_reaction_IP3Rinactivation | included |
| PIP5K_5Pase | included |
| NE_G | included |
| GTPase_Ga | included |
| IP3deg_Palk | excluded |
| r12 | excluded |
| r23 | excluded |
| r24 | excluded |
| PIP2_buffering | included |
| L2beta | included |
| NE_RLG | included |
| NE_GaP | included |
| PH_YFP_PIP2 | included |
| VSP | included |
| G1beta | included |
| DAGPase | included |
| PI4K_4Pase | included |
| PH_YFP_IP3 | included |
| IP3Pase_FDH | included |
| G2beta | included |
| PLCdiss | included |
| L2 | included |
| PLCassoc | included |
| G1 | included |
| PIP2bindKCNQ | included |
| PIP2hydr | included |
| IP3_dialysis | included |
| GTPase_GaP | included |
| Oxo_appl | included |
| G2 | included |
| reconstitution | included |
| C1bindDAG | included |
| RyR_Palk | excluded |
| leak_Palk | excluded |
| SERCA_Palk | excluded |
| KCNQ2/3 | included |
| ER_leak_flux_FDH | included |
| IP3R_flux_FDH | included |
| SERCA_flux_FDH | included |
| IP3R_Palk | excluded |
| Name | End Time | Output Options |
|---|---|---|
| 4K acceleration backbone | 720.0 [s] |
OutputTimeStep 1.0 |
| 4K acceleration InsP3_LIBRA | 720.0 [s] |
OutputTimeStep 1.0 |
| 5K acceleration backbone | 720.0 [s] |
OutputTimeStep 1.0 |
| 4K acceleration DAG_C1A | 720.0 [s] |
OutputTimeStep 1.0 |
| 5K acceleration InsP3_LIBRA | 720.0 [s] |
OutputTimeStep 1.0 |
| 5K acceleration DAG_C1A | 720.0 [s] |
OutputTimeStep 1.0 |
| PLC decrease backbone | 720.0 [s] |
OutputTimeStep 1.0 |
| PLC decrease InsP3_LIBRA | 720.0 [s] |
OutputTimeStep 1.0 |
| PLC decrease DAG_C1A | 720.0 [s] |
OutputTimeStep 1.0 |
| 4P and 5P decrease backbone | 720.0 [s] |
OutputTimeStep 1.0 |
| 4P and 5P decrease InsP3_LIBRA | 720.0 [s] |
OutputTimeStep 1.0 |
| 4P and 5P decrease DAG_C1A | 720.0 [s] |
OutputTimeStep 1.0 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | ERM |
Global Parameters
| Name | Expression |
|---|---|
| KfL1 | (KrL1 / KL1)[uM-1.s-1] |
|
|
|
| KrL1 | 5.555555555555555[s-1] |
|
|
|
| KfG1 | (0.1 * KfG2)[um2.molecules-1.s-1] |
|
|
|
| KfG2 | 0.0026666[um2.molecules-1.s-1] |
|
|
|
| KrG2 | 0.68[s-1] |
|
|
|
| KfL2 | KfL1[uM-1.s-1] |
|
|
|
| KrL2 | (KL2 * KfL2) [s-1] |
|
|
|
| allRL | (RL_M + RLG_GDP_M + RLGbeta_M)[molecules.um-2] |
|
|
|
| KrG1 | (KfG1 * KG1) [s-1] |
|
|
|
| alpha | 100.0 [1] |
|
|
|
| KL1 | 2.0 [uM] |
|
|
|
| KL2 | (KL1 / alpha) [uM] |
|
|
|
| KG1 | (KG2 * alpha) [molecules.um-2] |
|
|
|
| KG2 | (KrG2 / KfG2) [molecules.um-2] |
|
|
|
| allRGbeta | (RG_GDP_M + RLG_GDP_M + RLGbeta_M + RGbeta_M)[molecules.um-2] |
|
|
|
| allGabg | (G_GDP_M + RG_GDP_M + RLG_GDP_M)[molecules.um-2] |
|
|
|
| allGaPLC | (GaGTP_PLC_M + GaGDP_PLC_M)[molecules.um-2] |
|
|
|
| allPIP2M | (PIP2_M + KCNQ_PIP2_M + PH_YFP_PIP2_M + boundPIP2_M)[molecules.um-2] |
|
|
|
| allPH_cytoplasm | (PH_YFP_C + IP3_PH_YFP_C)[uM] |
|
|
|
| speed_PH_PIP2 | 1.0[uM-1.s-1] |
|
|
|
| KD_PH_PIP2 | 2.0[uM] |
|
|
|
| speed_PH_IP3 | 10.0[uM-1.s-1] |
|
|
|
| KD_PH_IP3 | 0.1[uM] |
|
|
|
| K_plc | (0.2 * decrease)[um2.molecules-1.s-1] |
|
|
|
| PLC_basal | 0.0[s-1] |
|
|
|
| start | 120.0[s] |
|
|
|
| end | 720.0[s] |
|
|
|
| foldPIP2 | 3.0 [1] |
|
|
|
| KD_act_Ca_IP3R | 0.2[uM] |
|
|
|
| KD_IP3_IP3R | 0.1[uM] |
|
|
|
| IP3R | pow((h * IP3_C * Ca_C / (IP3_C + KD_IP3_IP3R) / (Ca_C + KD_act_Ca_IP3R)),3.0)[1] |
|
|
|
| KD_DAG_C1 | 0.1[uM] |
|
|
|
| speed_DAG_C1 | 0.2[uM-1.s-1] |
|
|
|
| activePKC | (DAG_M * PIP2_M / ((DAG_M + (1000.0 * KD_DAG_C1)) * (PIP2_M + (1000.0 * KD_PH_PIP2))))[1] |
|
|
|
| h | (noninactiveIP3R / (noninactiveIP3R + inactiveIP3R))[1] |
|
|
|
| stim_4k | ((stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * (1.0 + (stim_4K_delay * (1.0 - exp(((start + time_4K_delay - t) / tau_4K_delay))) * ((start + time_4K_delay) < t) * (t <= end)))) [s-1] |
|
|
|
| stim_4k_max | 0.0023647 [s-1] |
|
|
|
| stim_5K_max | 0.1819 [s-1] |
|
|
|
| stim_5k | ((stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * (1.0 + (stim_5K_delay * (1.0 - exp(((start + time_5K_delay - t) / tau_5k_delay))) * ((start + time_5K_delay) < t) * (t <= end)))) [s-1] |
|
|
|
| tau_stim_4K_onset | 1.0[s] |
|
|
|
| tau_stim_recovery | 5.0[s] |
|
|
|
| k5k_base | 0.0181[s-1] |
|
|
|
| OxoMforKinases | 0.0 [uM] |
|
|
|
| all_IP3 | (IP3_C + IP3_LIBRAvIII_C + IP3_PH_YFP_C)[uM] |
|
|
|
| r_FDH | 1.0[1] |
|
|
|
| r_Palk | 0.0[1] |
|
|
|
| perms2pers | 1000.0[s-1] |
|
|
|
| uM2nM | 1000.0[uM-1] |
|
|
|
| removeuM | 1.0[uM-1] |
|
|
|
| stim_4K_delay | 0.0[tbd] |
|
|
|
| time_4K_delay | 20.0[tbd] |
|
|
|
| tau_4K_delay | 300.0[tbd] |
|
|
|
| stim_5K_delay | 0.0[tbd] |
|
|
|
| time_5K_delay | 20.0[tbd] |
|
|
|
| tau_stim_5K_onset | 1.0[tbd] |
|
|
|
| tau_5k_delay | 300.0[tbd] |
|
|
|
| tau_Ga_PLC | 1.0[s] |
|
|
|
| tau_PIP2_PLC | 1.0[s] |
|
|
|
| tau_d | 130.0[s] |
|
|
|
| decrease | (1.0 + (D_I * (exp(((start + 15.0 - t) / tau_d)) - 1.0) * ((start + 15.0) <= t) * (t <= end)))[tbd] |
|
|
|
| D_I | 0.0[1] |
|
|
|
| D_P | 0.0[s-1] |
|
|
|