Dashboard
Name - hillelab: KruseVivasTraynorKaplanHille_PI-metabolism_SCG_2015
BioModel ID - 98296160
Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
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): 1000.0[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] |
|
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] |
|
oxoM_EX+RGbeta_MRLGbeta_M |
L2beta
M
|
MassAction | oxoM_EX+RGbeta_MRLGbeta_M |
|
|
reaction rate (J): (((Kf * oxoM_EX) * RGbeta_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): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1] |
|
IP3_C+IP3R_IRBITIP3R_IP3 |
IP3R_IP3_binding
C
|
MassAction | IP3_C+IP3R_IRBITIP3R_IP3 |
|
|
reaction rate (J): (((Kf * IP3_C) * IP3R_IRBIT) - (Kr * IP3R_IP3))[uM.s-1]
forward rate constant (Kf): (speed_IP3_IRBIT * KD_IP3_IP3R_IRBIT)[s-1.uM-1] reverse rate constant (Kr): (speed_IP3_IRBIT * KD_IP3R_IRBIT)[s-1] user defined (speed_IP3_IRBIT): 1.0[uM-1.s-1] user defined (KD_IP3_IP3R_IRBIT): 0.1[uM] user defined (KD_IP3R_IRBIT): 0.5[uM] |
|
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] |
|
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] |
|
oxoM_EX+R_MRL_M |
L1
M
|
MassAction | oxoM_EX+R_MRL_M |
|
|
reaction rate (J): (((Kf * oxoM_EX) * R_M) - (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] |
|
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): 0.2[s-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] |
|
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] |
|
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] |
|
Tubby_C+PIP2_MTubby_PIP2_M |
Tubby_PIP2
M
|
MassAction | Tubby_C+PIP2_MTubby_PIP2_M |
|
|
reaction rate (J): (((Kf * Tubby_C) * PIP2_M) - (Kr * Tubby_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_Tubby_PIP2[s-1.uM-1] reverse rate constant (Kr): (KD_Tubby_PIP2 * speed_Tubby_PIP2)[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] |
|
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): 42.0[s] user defined (Vstep): 0.1[V] user defined (Vhold): -0.06[V] user defined (VSP_start): 40.0[s] |
|
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] |
|
PIP2_MIP3_C+DAG_M |
PIP2hydr
M
|
GeneralKinetics | PIP2_MIP3_C+DAG_M |
|
|
reaction rate (J): (PIP2_M * (PLC_basal + (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] |
|
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] |
|
Ca_C+Fura2_CCa_Fura2_C |
Cabind_Fura2
C
|
MassAction | Ca_C+Fura2_CCa_Fura2_C |
|
|
reaction rate (J): (((Kf * Ca_C) * Fura2_C) - (Kr * Ca_Fura2_C))[uM.s-1]
forward rate constant (Kf): speed_Ca_Fura2[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Fura2 * kd_Fura2)[s-1] user defined (speed_Ca_Fura2): 10.0[uM-1.s-1] user defined (kd_Fura2): 0.145[uM] |
|
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.s-1.um-2.uM-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 * k5K_rest)[s-1] reverse rate constant (Kr): (0.028 * foldPIP2)[s-1] user defined (k5K_rest): 0.02[s-1] |
|
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] |
|
DAG_M+C1_dom_CC1_DAG_M |
C1bindDAG
M
|
MassAction | DAG_M+C1_dom_CC1_DAG_M |
|
|
reaction rate (J): (((Kf * DAG_M) * C1_dom_C) - (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] |
|
IP3_C |
IP3Pase_KVH
C
|
GeneralKinetics | IP3_C |
|
|
reaction rate (J): (K_IP3ase * IP3_C)[uM.s-1]
user defined (K_IP3ase): (0.13 * r_FDH_IP3ase)[s-1] user defined (r_FDH_IP3ase): 1.0[s-1] |
|
Gbeta_M+RL_MRLGbeta_M |
G2beta
M
|
MassAction | Gbeta_M+RL_MRLGbeta_M |
|
|
reaction rate (J): (((Kf * Gbeta_M) * RL_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] |
|
PI4P_MDAG_M |
PLC_on_PI4P
M
|
GeneralKinetics | PI4P_MDAG_M |
|
|
reaction rate (J): (PI4P_M * PLC_efficiency_PIP * (PLC_basal + (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] user defined (PLC_efficiency_PIP): 1.0[1] |
|
oxoM_EX+RG_GDP_MRLG_GDP_M |
L2
M
|
MassAction | oxoM_EX+RG_GDP_MRLG_GDP_M |
|
|
reaction rate (J): (((Kf * oxoM_EX) * RG_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): KfL2[s-1.uM-1] reverse rate constant (Kr): KrL2[s-1] |
|
PI_MPI4P_M |
PI4K
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_rest)[s-1] reverse rate constant (Kr): 0.0[s-1] user defined (K4_rest): 8.0E-4[s-1] |
|
Ca_Buffer_low_aff+Ca_CCa_Buffer_low_aff_Ca |
Ca_Buffering_low_aff
C
|
MassAction | Ca_Buffer_low_aff+Ca_CCa_Buffer_low_aff_Ca |
|
|
reaction rate (J): (((Kf * Ca_Buffer_low_aff) * Ca_C) - (Kr * Ca_Buffer_low_aff_Ca))[uM.s-1]
forward rate constant (Kf): speed_Ca_Buffer_low_aff[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_Buffer_low_aff * KD_Ca_Buffer_low_aff)[s-1] user defined (speed_Ca_Buffer_low_aff): 10.0[s-1.uM-1] user defined (KD_Ca_Buffer_low_aff): 1.0[uM] |
|
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] |
|
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] |
|
G_GDP_MGbeta_M+GaGTP_M |
NE_G
M
|
MassAction | G_GDP_MGbeta_M+GaGTP_M |
|
|
reaction rate (J): ((Kf * G_GDP_M) - ((Kr * Gbeta_M) * GaGTP_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] |
|
PI4P_MPI_M |
PI4Pase
M
|
MassAction | PI4P_MPI_M |
|
|
reaction rate (J): ((Kf * PI4P_M) - (Kr * PI_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): 0.12[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
P4M_dom_C+PI4P_MP4M_PI4P_M |
P4M_bind_PI4P
M
|
MassAction | P4M_dom_C+PI4P_MP4M_PI4P_M |
|
|
reaction rate (J): (((Kf * P4M_dom_C) * PI4P_M) - (Kr * P4M_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): speed_P4M_PI4P[s-1.uM-1] reverse rate constant (Kr): (KD_P4M_PI4P * speed_P4M_PI4P)[s-1] user defined (speed_P4M_PI4P): 1.0[s-1.uM-1] user defined (KD_P4M_PI4P): 1.5[uM] |
|
Ca_Buffer_high_aff+Ca_CCa_Buffer_high_aff_Ca |
Ca_Buffering_high_aff
C
|
MassAction | Ca_Buffer_high_aff+Ca_CCa_Buffer_high_aff_Ca |
|
|
reaction rate (J): (((Kf * Ca_Buffer_high_aff) * Ca_C) - (Kr * Ca_Buffer_high_aff_Ca))[uM.s-1]
forward rate constant (Kf): speed_Ca_high_aff[s-1.uM-1] reverse rate constant (Kr): (speed_Ca_high_aff * KD_Ca_high_aff)[s-1] user defined (speed_Ca_high_aff): 10.0[s-1.uM-1] user defined (KD_Ca_high_aff): 0.1[uM] |
|
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] |
|
GaGDP_PLC_MPLC_M+Ga_GDP_M |
PLCdiss
M
|
MassAction | GaGDP_PLC_MPLC_M+Ga_GDP_M |
|
|
reaction rate (J): ((Kf * GaGDP_PLC_M) - ((Kr * PLC_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] forward rate constant (Kf): 0.71[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] |
|
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] |
|
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] |
|
GaGDP_PLC_MGaGTP_PLC_M |
NE_GaP
M
|
GeneralKinetics | GaGDP_PLC_MGaGTP_PLC_M |
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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] |
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Gbeta_M+R_MRGbeta_M |
G1beta
M
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MassAction | Gbeta_M+R_MRGbeta_M |
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reaction rate (J): (((Kf * Gbeta_M) * R_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] |
Name |
Type
Electrical (Membrane Polarity)
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---|---|
C |
Compartment
(+) (-)
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Ca_store |
Compartment
(+) (-)
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EX |
Compartment
(+) (-)
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M |
Membrane
N/A
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ERM |
Membrane
N/A
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Name | Structure | BioNetGen Definition |
---|---|---|
Ca_Buffer_high_aff | C | |
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Ca_Buffer_high_aff_Ca | C | |
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IP3R_IRBIT | C | |
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IP3_PH_YFP_C | C | |
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Ca_Ca_store | Ca_store | |
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R_M | M | |
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RLGbeta_M | M | |
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RL_M | M | |
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PH_YFP_C | C | |
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PH_YFP_PIP2_M | M | |
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K_C | C | |
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KCNQ_M | M | |
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Tubby_PIP2_M | M | |
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KCNQ_PIP2_M | M | |
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K_EX | EX | |
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boundPIP2_M | M | |
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Ca_Buffer_low_aff_Ca | C | |
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P4M_dom_C | C | |
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Ca_Fura2_C | C | |
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IP3_LibraVIII_C | C | |
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GaGDP_PLC_M | M | |
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noninactiveIP3R | ERM | |
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OxoM_conc_EX | EX | |
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GaGTP_M | M | |
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inactiveIP3R | ERM | |
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LibraVIII_C | C | |
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Gbeta_M | M | |
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Fura2_C | C | |
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DAG_M | M | |
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C1_dom_C | C | |
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G_GDP_M | M | |
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RG_GDP_M | M | |
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PI_M | M | |
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PA_2AG_M | M | |
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Ca_C | C | |
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PIP2_M | M | |
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PI4P_M | M | |
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GaGTP_PLC_M | M | |
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Palk_C1 | C | |
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RLG_GDP_M | M | |
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Ga_GDP_M | M | |
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PLC_M | M | |
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IP3_C | C | |
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Tubby_C | C | |
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Palk_O4 | C | |
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RGbeta_M | M | |
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C1_DAG_M | M | |
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Palk_C2 | C | |
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Palk_C3 | C | |
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Ca_Buffer_low_aff | C | |
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IP3R_IP3 | C | |
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oxoM_EX | EX | |
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P4M_PI4P_M | M | |
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Name | Text Annotations | BioNetGen Definition |
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Name |
Type
Count
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BioNetGen Definition |
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Applications
Name | Math Type | Annotation |
---|---|---|
simulations | Deterministic (ODE) Compartmental | 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 - simulations
Species | Initial Condition | Diffusion Constant | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ca_Buffer_high_aff | 4.9721916 [uM] | 0.0
[um2/s] Ca_Buffer_high_aff_Ca |
5.0278084
[uM]
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0.0
[um2/s] | IP3R_IRBIT |
0.01
[uM]
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0.0
[um2/s] | IP3_PH_YFP_C |
0.0
[uM]
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0.0
[um2/s] | PH_YFP_C |
0.0
[uM]
|
0.0
[um2/s] | K_C |
100000.0
[uM]
|
0.0
[um2/s] | Ca_Buffer_low_aff_Ca |
1.836644
[uM]
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0.0
[um2/s] | P4M_dom_C |
0.0
[uM]
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0.0
[um2/s] | Ca_Fura2_C |
0.0
[uM]
|
0.0
[um2/s] | IP3_LibraVIII_C |
0.0
[uM]
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0.0
[um2/s] | LibraVIII_C |
0.0
[uM]
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0.0
[um2/s] | Fura2_C |
0.0
[uM]
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0.0
[um2/s] | C1_dom_C |
0.0
[uM]
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0.0
[um2/s] | Ca_C |
0.101
[uM]
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0.0
[um2/s] | Palk_C1 |
1.0
[uM]
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0.0
[um2/s] | IP3_C |
0.02
[uM]
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0.0
[um2/s] | Tubby_C |
0.0
[uM]
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0.0
[um2/s] | Palk_O4 |
0.0
[uM]
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0.0
[um2/s] | Palk_C2 |
0.0
[uM]
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0.0
[um2/s] | Palk_C3 |
0.0
[uM]
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0.0
[um2/s] | Ca_Buffer_low_aff |
18.163356
[uM]
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0.0
[um2/s] | IP3R_IP3 |
0.0
[uM]
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0.0
[um2/s] | Ca_Ca_store |
361.8635
[uM]
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0.0
[um2/s] | K_EX |
0.0
[uM]
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0.0
[um2/s] | OxoM_conc_EX |
10.0
[uM]
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0.0
[um2/s] | oxoM_EX |
0.0
[uM]
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0.0
[um2/s] | R_M |
15.87
[uM]
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0.0
[um2/s] | RLGbeta_M |
0.0
[uM]
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0.0
[um2/s] | RL_M |
0.0
[uM]
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0.0
[um2/s] | PH_YFP_PIP2_M |
0.0
[uM]
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0.0
[um2/s] | KCNQ_M |
4.0
[uM]
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0.0
[um2/s] | Tubby_PIP2_M |
0.0
[uM]
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0.0
[um2/s] | KCNQ_PIP2_M |
0.0
[uM]
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0.0
[um2/s] | boundPIP2_M |
(( - 1.0 + foldPIP2) * PIP2_M)
[uM]
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0.0
[um2/s] | GaGDP_PLC_M |
0.0
[uM]
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0.0
[um2/s] | GaGTP_M |
0.0
[uM]
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0.0
[um2/s] | Gbeta_M |
0.0
[uM]
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0.0
[um2/s] | DAG_M |
13.0
[uM]
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0.0
[um2/s] | G_GDP_M |
40.0
[uM]
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0.0
[um2/s] | RG_GDP_M |
0.0
[uM]
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0.0
[um2/s] | PI_M |
226975.0
[uM]
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0.0
[um2/s] | PA_2AG_M |
0.0
[uM]
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0.0
[um2/s] | PIP2_M |
3232.0
[uM]
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0.0
[um2/s] | PI4P_M |
4540.0
[uM]
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0.0
[um2/s] | GaGTP_PLC_M |
0.0
[uM]
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0.0
[um2/s] | RLG_GDP_M |
0.0
[uM]
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0.0
[um2/s] | Ga_GDP_M |
0.0
[uM]
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0.0
[um2/s] | PLC_M |
3.12
[uM]
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0.0
[um2/s] | RGbeta_M |
0.0
[uM]
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0.0
[um2/s] | C1_DAG_M |
0.0
[uM]
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0.0
[um2/s] | P4M_PI4P_M |
0.0
[uM]
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0.0
[um2/s] | noninactiveIP3R |
1.0
[uM]
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0.0
[um2/s] | inactiveIP3R |
0.0
[uM]
|
0.0
[um2/s]
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Name | Reaction Mapping |
---|---|
PIP2_buffering | included |
G2 | included |
r24 | excluded |
L2beta | included |
IP3R_IP3_binding | included |
NE_RLG | included |
Oxo_appl | included |
L1 | included |
DAGPase | included |
PH_YFP_PIP2 | included |
PLCassoc | included |
IP3deg_Palk | excluded |
Tubby_PIP2 | included |
reconstitution | included |
VSP | included |
r12 | excluded |
PIP2hydr | included |
GTPase_GaP | included |
Cabind_Fura2 | included |
h_reaction_IP3Rinactivation | included |
PIP5K_5Pase | included |
IP3_LibraVIII | included |
C1bindDAG | included |
IP3Pase_KVH | included |
G2beta | included |
PLC_on_PI4P | included |
L2 | included |
PI4K | included |
Ca_Buffering_low_aff | included |
G1 | included |
NE_RG | included |
NE_G | included |
PI4Pase | included |
P4M_bind_PI4P | included |
Ca_Buffering_high_aff | included |
r23 | excluded |
PLCdiss | included |
GTPase_Ga | included |
PH_YFP_IP3 | included |
PIP2bindKCNQ | included |
NE_GaP | included |
G1beta | included |
SERCA_Palk | excluded |
leak_Palk | excluded |
SERCA_flux_KVH | included |
IP3R_flux_KVH | included |
KCNQ2/3 | included |
ER_leak_flux_KVH | included |
RyR_Palk | excluded |
IP3R_Palk | excluded |
Name | End Time | Output Options |
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Oxo-M | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
VSP | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Oxo-M with TubbyR332 | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Oxo-M with fura-2 | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Oxo-M with PH-PLCd1 | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Oxo-M with LIBRAVIII | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Oxo-M with C1-domain | 600.0 [s] |
KeepEvery 10 KeepAtMost 1000 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
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Compartmental | Compartment | ERM |
Global Parameters
Name | Expression |
---|---|
KfL1 | (KrL1 / KL1)[uM-1.s-1] |
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KrL1 | 5.555555555555555[s-1] |
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KfG1 | (0.1 * KfG2)[um2.molecules-1.s-1] |
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KfG2 | 0.0026666[um2.molecules-1.s-1] |
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KrG2 | 0.68[s-1] |
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KfL2 | KfL1[uM-1.s-1] |
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KrL2 | (KL2 * KfL2) [s-1] |
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allRL | (RL_M + RLG_GDP_M + RLGbeta_M)[molecules.um-2] |
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KrG1 | (KfG1 * KG1) [s-1] |
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alpha | 100.0 [1] |
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KL1 | 2.0 [uM] |
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KL2 | (KL1 / alpha) [uM] |
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KG1 | (KG2 * alpha) [molecules.um-2] |
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KG2 | (KrG2 / KfG2) [molecules.um-2] |
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allRGbeta | (RG_GDP_M + RLG_GDP_M + RLGbeta_M + RGbeta_M)[molecules.um-2] |
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allGabg | (G_GDP_M + RG_GDP_M + RLG_GDP_M)[molecules.um-2] |
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allGaPLC | (GaGTP_PLC_M + GaGDP_PLC_M)[molecules.um-2] |
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allPIP2M | (PIP2_M + KCNQ_PIP2_M + PH_YFP_PIP2_M + boundPIP2_M)[molecules.um-2] |
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allPH_cytoplasm | (PH_YFP_C + IP3_PH_YFP_C)[uM] |
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speed_PH_PIP2 | 1.0[uM-1.s-1] |
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KD_PH_PIP2 | 2.0[uM] |
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speed_PH_IP3 | 10.0[uM-1.s-1] |
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KD_PH_IP3 | 0.1[uM] |
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K_plc | 0.3[um2.molecules-1.s-1] |
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PLC_basal | 0.0[s-1] |
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start | 100.0[s] |
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end | 120.0[s] |
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foldPIP2 | 3.0 [1] |
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KD_act_Ca_IP3R | 0.2[uM] |
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KD_IP3_IP3R | 0.1[uM] |
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IP3R | pow((h * IP3_C * Ca_C / (IP3_C + KD_IP3_IP3R) / (Ca_C + KD_act_Ca_IP3R)),3.0)[1] |
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KD_DAG_C1 | 0.2[uM] |
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speed_DAG_C1 | 10.0[uM-1.s-1] |
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activePKC | (DAG_M * PIP2_M / ((DAG_M + (1000.0 * KD_DAG_C1)) * (PIP2_M + (1000.0 * KD_PH_PIP2))))[1] |
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h | (noninactiveIP3R / (noninactiveIP3R + inactiveIP3R))[1] |
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stim_4k | (stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) [s-1] |
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stim_4k_max | 0.0023647 [s-1] |
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stim_5K_max | 0.1819 [s-1] |
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stim_5k | (stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) [s-1] |
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tau_stim_onset | 1.0[s] |
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tau_stim_recovery | 5.0[s] |
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k5k_base | 0.0181[s-1] |
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OxoMforKinases | 0.0 [uM] |
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all_IP3 | (IP3_C + IP3_LibraVIII_C + IP3_PH_YFP_C)[uM] |
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r_FDH | 1.0[1] |
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r_Palk | 0.0[1] |
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perms2pers | 1000.0[s-1] |
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uM2nM | 1000.0[uM-1] |
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removeuM | 1.0[uM-1] |
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KD_OSBP_PI4P | 0.2[uM] |
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speed_OSBP_PI4P | 10.0[uM-1.s-1] |
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speed_Tubby_PIP2 | 1.0[uM-1.s-1] |
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KD_Tubby_PIP2 | 1.5[uM] |
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r_KVH | 1.0[tbd] |
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