Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| Fura4F_C+Ca_CCa_Fura4F_C | Cabind_Fura4F | C | MassAction | |
| LibraVIII_C+IP3_CIP3_LibraVIII_C | IP3_LibraVIII | C | MassAction | |
| PI4P_MDAG_M | PLC_on_PI4P | M | GeneralKinetics | |
| RG_GDP_MGaGTP_M+RGbeta_M | NE_RG | M | MassAction | |
| oxoM_EX+R_MRL_M | L1 | M | MassAction | |
| noninactiveIP3RinactiveIP3R | h_reaction_IP3Rinactivation | ERM | GeneralKinetics | |
| PI4P_MPIP2_M | PIP5K_5Pase | M | MassAction | |
| G_GDP_MGaGTP_M+Gbeta_M | NE_G | M | MassAction | |
| GaGTP_MGa_GDP_M | GTPase_Ga | M | GeneralKinetics | |
| IP3_C | IP3deg_Palk | C | MassAction | |
| Palk_C1Palk_C2 | r12 | C | MassAction | |
| Palk_C2Palk_C3 | r23 | C | MassAction | |
| Palk_C2Palk_O4 | r24 | C | MassAction | |
| PIP2_MboundPIP2_M | PIP2_buffering | M | MassAction | |
| oxoM_EX+RGbeta_MRLGbeta_M | L2beta | M | MassAction | |
| RLG_GDP_MRLGbeta_M+GaGTP_M | NE_RLG | M | GeneralKinetics | |
| GaGDP_PLC_MGaGTP_PLC_M | NE_GaP | M | GeneralKinetics | |
| PIP2_M+PH_YFP_CPH_YFP_PIP2_M | PH_YFP_PIP2 | M | MassAction | |
| PIP2_MPI4P_M | VSP | M | MassAction | |
| Gbeta_M+R_MRGbeta_M | G1beta | M | MassAction | |
| DAG_MPA_2AG_M | DAGPase | M | GeneralKinetics | |
| PI_MPI4P_M | PI4K_4Pase | M | MassAction | |
| IP3_C+PH_YFP_CIP3_PH_YFP_C | PH_YFP_IP3 | C | MassAction | |
| IP3_C | IP3Pase_FDH | C | GeneralKinetics | |
| Gbeta_M+RL_MRLGbeta_M | G2beta | M | MassAction | |
| GaGDP_PLC_MGa_GDP_M+PLC_M | PLCdiss | M | MassAction | |
| oxoM_EX+RG_GDP_MRLG_GDP_M | L2 | M | MassAction | |
| PLC_M+GaGTP_MGaGTP_PLC_M | PLCassoc | M | MassAction | |
| G_GDP_M+R_MRG_GDP_M | G1 | M | MassAction | |
| KCNQ_M+PIP2_MKCNQ_PIP2_M | PIP2bindKCNQ | M | GeneralKinetics | |
| PIP2_MDAG_M+IP3_C | PIP2hydr | M | GeneralKinetics | |
| IP3_pipetteIP3_C | IP3_dialysis | M | MassAction | |
| GaGTP_PLC_MGaGDP_PLC_M | GTPase_GaP | M | GeneralKinetics | |
| OxoM_conc_EXoxoM_EX | Oxo_appl | EX | MassAction | |
| G_GDP_M+RL_MRLG_GDP_M | G2 | M | MassAction | |
| Gbeta_M+Ga_GDP_MG_GDP_M | reconstitution | M | GeneralKinetics | |
| C1_dom_C+DAG_MC1_DAG_M | C1bindDAG | M | MassAction | |
| PIP3PI3_4_P2 | VSP_PIP3 | M | MassAction | |
| PIP2_MPIP3 | PI3K_PTEN | M | MassAction | |
| PI3_4_P2+TAPP1_dom_CTAPP1_PI34P2_M | TAPP1_binding | M | MassAction | |
| PH_Btk_dom_C+PIP3PH_Btk_PIP3_M | PH_Btk_binding | M | MassAction | |
| PI3_4_P2PI4P_M | PI3K_on_PIP4P | M | MassAction | |
| P4M_dom_C+PI4P_MP4M_PI4P_M | P4M_PI4P_binding | M | MassAction | |
| PIP3PIP2_M | VSP_5P_PIP3 | M | MassAction | |
| PI4P_MPIP2_M | PIPKIgamma_PIP | M | MassAction | |
| PI3_4_P2PIP3 | PIPKIgamma_PI34P2 | M | MassAction | |
| PI3_4_P2PI4P_VSPbound | VSP_PI34P2 | M | MassAction | |
| PI4P_VSPboundPI4P_M | PI4P_VSPbound_release | M | MassAction |
Cabind_Fura4F Universal ID's
Cabind_Fura4F Text Annotations
IP3_LibraVIII Universal ID's
IP3_LibraVIII Text Annotations
PLC_on_PI4P Universal ID's
PLC_on_PI4P Text Annotations
NE_RG Universal ID's
NE_RG Text Annotations
L1 Universal ID's
L1 Text Annotations
h_reaction_IP3Rinactivation Universal ID's
h_reaction_IP3Rinactivation Text Annotations
PIP5K_5Pase Universal ID's
PIP5K_5Pase Text Annotations
NE_G Universal ID's
NE_G Text Annotations
GTPase_Ga Universal ID's
GTPase_Ga Text Annotations
IP3deg_Palk Universal ID's
IP3deg_Palk Text Annotations
r12 Universal ID's
r12 Text Annotations
r23 Universal ID's
r23 Text Annotations
r24 Universal ID's
r24 Text Annotations
PIP2_buffering Universal ID's
PIP2_buffering Text Annotations
L2beta Universal ID's
L2beta Text Annotations
NE_RLG Universal ID's
NE_RLG Text Annotations
NE_GaP Universal ID's
NE_GaP Text Annotations
PH_YFP_PIP2 Universal ID's
PH_YFP_PIP2 Text Annotations
VSP Universal ID's
VSP Text Annotations
G1beta Universal ID's
G1beta Text Annotations
DAGPase Universal ID's
DAGPase Text Annotations
PI4K_4Pase Universal ID's
PI4K_4Pase Text Annotations
PH_YFP_IP3 Universal ID's
PH_YFP_IP3 Text Annotations
IP3Pase_FDH Universal ID's
IP3Pase_FDH Text Annotations
G2beta Universal ID's
G2beta Text Annotations
PLCdiss Universal ID's
PLCdiss Text Annotations
L2 Universal ID's
L2 Text Annotations
PLCassoc Universal ID's
PLCassoc Text Annotations
G1 Universal ID's
G1 Text Annotations
PIP2bindKCNQ Universal ID's
PIP2bindKCNQ Text Annotations
PIP2hydr Universal ID's
PIP2hydr Text Annotations
IP3_dialysis Universal ID's
IP3_dialysis Text Annotations
GTPase_GaP Universal ID's
GTPase_GaP Text Annotations
Oxo_appl Universal ID's
Oxo_appl Text Annotations
G2 Universal ID's
G2 Text Annotations
reconstitution Universal ID's
reconstitution Text Annotations
C1bindDAG Universal ID's
C1bindDAG Text Annotations
VSP_PIP3 Universal ID's
VSP_PIP3 Text Annotations
PI3K_PTEN Universal ID's
PI3K_PTEN Text Annotations
TAPP1_binding Universal ID's
TAPP1_binding Text Annotations
PH_Btk_binding Universal ID's
PH_Btk_binding Text Annotations
PI3K_on_PIP4P Universal ID's
PI3K_on_PIP4P Text Annotations
P4M_PI4P_binding Universal ID's
P4M_PI4P_binding Text Annotations
VSP_5P_PIP3 Universal ID's
VSP_5P_PIP3 Text Annotations
PIPKIgamma_PIP Universal ID's
PIPKIgamma_PIP Text Annotations
PIPKIgamma_PI34P2 Universal ID's
PIPKIgamma_PI34P2 Text Annotations
VSP_PI34P2 Universal ID's
VSP_PI34P2 Text Annotations
PI4P_VSPbound_release Universal ID's
PI4P_VSPbound_release Text Annotations
Expressions for Cabind_Fura4F
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]
local
speed_Ca_Fura4F
10.0 [uM-1.s-1]
local
kd_Fura4F
0.77 [uM]
Expressions for IP3_LibraVIII
reaction rate
J
(((Kf * LibraVIII_C) * IP3_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]
local
speed_LibraVIII
1.0 [uM-1.s-1]
local
KD_LibraVIII
0.5 [uM]
Expressions for PLC_on_PI4P
reaction rate
J
(PI4P_M * PLC_efficiency_PIP * (PLC_basal + (GaGTP_PLC_M * K_plc))) [molecules.um-2.s-1]
global
K_plc
0.2 [um2.molecules-1.s-1]
global
PLC_basal
0.0 [s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
local
PLC_efficiency_PIP
1.0 [1]
Expressions for NE_RG
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]
Expressions for L1
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]
global
KfL1
(KrL1 / KL1) [uM-1.s-1]
reverse rate constant
Kr
KrL1 [s-1]
global
KrL1
5.555555555555555 [s-1]
Expressions for h_reaction_IP3Rinactivation
reaction rate
J
- ((KD_inh_Ca_IP3R - ((Ca_C + KD_inh_Ca_IP3R) * h)) * Kon_Ca_IP3R) [molecules.um-2.s-1]
global
IP3R
pow((h * IP3_C * Ca_C / (IP3_C + KD_IP3_IP3R) / (Ca_C + KD_act_Ca_IP3R)),3.0) [1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
local
KD_inh_Ca_IP3R
0.2 [uM]
local
Kon_Ca_IP3R
2.7 [molecules.um-2.uM-1.s-1]
Expressions for PIP5K_5Pase
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
(0.625 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
(0.45 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
Expressions for NE_G
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]
Expressions for GTPase_Ga
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]
local
Kf
0.026 [s-1]
Expressions for IP3deg_Palk
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]
global
r_Palk
0.0 [1]
reverse rate constant
Kr
0.0 [uM.s-1]
local
k3K
40.0 [s-1]
local
r_Palk_IP3ase
0.0 [1]
local
k5P
0.005 [s-1]
local
kdeg
0.4 [uM]
Expressions for r12
reaction rate
J
((Kf * Palk_C1) - (Kr * Palk_C2)) [uM.s-1]
forward rate constant
Kf
(q12 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
reverse rate constant
Kr
(q21 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
local
q12
0.74 [1]
local
q21
((VP21 / (1.0 + (kp21 * (IP3_nM ^ 3.0)))) + bp21) [1]
local
VP21
0.0949 [1]
local
IP3_nM
(IP3_C * uM2nM) [1]
global
uM2nM
1000.0 [uM-1]
local
bp21
0.11 [1]
local
kp21
5.0E-10 [1]
Expressions for r23
reaction rate
J
((Kf * Palk_C2) - (Kr * Palk_C3)) [uM.s-1]
forward rate constant
Kf
(q23 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
reverse rate constant
Kr
(q32 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
local
q23
(alpha23 * p23 * P23) [1]
global
alpha
100.0 [1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
local
q32
(alpha32 * p32 * P32) [1]
global
alpha
100.0 [1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
local
p32
(((V32 / ((k32 ^ 3.0) + (Ca_nM ^ 3.0))) + b32) * ((Vm32 * (Ca_nM ^ 7.0) / ((km32 ^ 7.0) + (Ca_nM ^ 7.0))) + bm32)) [1]
local
P32
((VP32 * (IP3_nM ^ 3.0) / (1.0 + (kp32 * (IP3_nM ^ 3.0)))) + bp32) [1]
local
alpha32
50.0 [1]
local
VP32
3.0E-12 [1]
local
IP3_nM
(ip3_Palk_scale_factor * IP3_C * uM2nM) [1]
global
uM2nM
1000.0 [uM-1]
local
bp32
0.0 [1]
local
kp32
1.5E-10 [1]
local
b32
0.005 [1]
local
km32
150.0 [1]
local
V32
7000000.0 [1]
local
bm32
0.03 [1]
local
k32
520.0 [1]
local
Ca_nM
(Ca_C * uM2nM) [1]
global
uM2nM
1000.0 [uM-1]
local
Vm32
1.06 [1]
local
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]
local
P23
((VP23 / (1.0 + (kp23 * (IP3_nM ^ 3.0)))) + bp23) [1]
local
alpha23
1000.0 [1]
local
bp23
0.001 [1]
local
VP23
0.162 [1]
local
kp23
5.0E-9 [1]
local
Vm23
0.3545 [1]
local
km23
72.0 [1]
local
b23
2.2 [1]
local
bm23
0.042 [1]
local
a23
0.9775171065493647 [1]
local
V23
1.08E-6 [1]
local
k23
2000.0 [1]
local
ip3_Palk_scale_factor
1.0 [1]
Expressions for r24
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]
local
q24
(7.84 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
local
q42
(3.6 * perms2pers) [s-1]
global
perms2pers
1000.0 [s-1]
Expressions for PIP2_buffering
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]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
speed_buffering [s-1]
local
speed_buffering
1000.0 [s-1]
Expressions for L2beta
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]
global
KfL2
KfL1 [uM-1.s-1]
reverse rate constant
Kr
KrL2 [s-1]
global
KrL2
(KL2 * KfL2) [s-1]
Expressions for NE_RLG
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]
local
Kf
0.65 [s-1]
Expressions for NE_GaP
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]
Expressions for PH_YFP_PIP2
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]
global
speed_PH_PIP2
1.0 [uM-1.s-1]
reverse rate constant
Kr
(KD_PH_PIP2 * speed_PH_PIP2) [s-1]
global
speed_PH_PIP2
1.0 [uM-1.s-1]
global
KD_PH_PIP2
2.0 [uM]
Expressions for VSP
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 * VSP_conc) [s-1]
global
VSP_conc
1.6 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kVSP
(VSPmax / (1.0 + exp((1.4 * qKT * (V - Vhalf))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
Vhalf
0.095 [V]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
VSPmax
(8.0 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
Expressions for G1beta
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]
global
KfG1
(0.1 * KfG2) [um2.molecules-1.s-1]
reverse rate constant
Kr
KrG1 [s-1]
global
KrG1
(KfG1 * KG1) [s-1]
Expressions for DAGPase
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]
local
Kf
0.05 [s-1]
Expressions for PI4K_4Pase
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 * k4K_max) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
0.003 [s-1]
local
k4K_max
2.9E-5 [s-1]
Expressions for PH_YFP_IP3
reaction rate
J
(((Kf * IP3_C) * PH_YFP_C) - (Kr * IP3_PH_YFP_C)) [uM.s-1]
forward rate constant
Kf
speed_PH_IP3 [s-1.uM-1]
global
speed_PH_IP3
10.0 [uM-1.s-1]
reverse rate constant
Kr
(KD_PH_IP3 * speed_PH_IP3) [s-1]
global
speed_PH_IP3
10.0 [uM-1.s-1]
global
KD_PH_IP3
0.1 [uM]
Expressions for IP3Pase_FDH
reaction rate
J
(K_IP3ase * IP3_C) [uM.s-1]
local
K_IP3ase
(0.08 * r_FDH_IP3ase) [s-1]
global
r_FDH
1.0 [1]
local
r_FDH_IP3ase
1.0 [s-1]
Expressions for G2beta
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]
global
KfG2
0.0026666 [um2.molecules-1.s-1]
reverse rate constant
Kr
KrG2 [s-1]
global
KrG2
0.68 [s-1]
Expressions for PLCdiss
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]
Expressions for L2
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]
global
KfL2
KfL1 [uM-1.s-1]
reverse rate constant
Kr
KrL2 [s-1]
global
KrL2
(KL2 * KfL2) [s-1]
Expressions for PLCassoc
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]
Expressions for G1
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]
global
KfG1
(0.1 * KfG2) [um2.molecules-1.s-1]
reverse rate constant
Kr
KrG1 [s-1]
global
KrG1
(KfG1 * KG1) [s-1]
Expressions for PIP2bindKCNQ
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]
local
Kr
(KD_PIP2_KCNQ * Kf) [s-1]
local
Kf
speed_PIP2_KCNQ [um2.molecules-1.s-1]
local
KD_PIP2_KCNQ
KA_PIP2_KCNQ [molecules.um-2]
local
KA_PIP2_KCNQ
2000.0 [molecules.um-2]
local
speed_PIP2_KCNQ
0.05 [um2.molecules-1.s-1]
Expressions for PIP2hydr
reaction rate
J
(PIP2_M * (PLC_basal + (K_plc * foldPIP2 * GaGTP_PLC_M))) [molecules.um-2.s-1]
global
K_plc
0.2 [um2.molecules-1.s-1]
global
PLC_basal
0.0 [s-1]
global
foldPIP2
3.0 [1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
Expressions for IP3_dialysis
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]
global
start
0.0 [s]
reverse rate constant
Kr
(0.015 * (t > start) * k_pipette) [molecules.um-2.s-1.uM-1]
global
start
0.0 [s]
local
k_pipette
0.0 [s-1]
Expressions for GTPase_GaP
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]
Expressions for Oxo_appl
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]
global
start
0.0 [s]
global
end
0.0 [s]
reverse rate constant
Kr
(50.0 * (t > end)) [s-1]
global
end
0.0 [s]
Expressions for G2
reaction rate
J
(((Kf * G_GDP_M) * RL_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]
global
KfG2
0.0026666 [um2.molecules-1.s-1]
reverse rate constant
Kr
KrG2 [s-1]
global
KrG2
0.68 [s-1]
Expressions for reconstitution
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]
local
Kf
1.0 [um2.molecules-1.s-1]
Expressions for C1bindDAG
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]
global
speed_DAG_C1
10.0 [uM-1.s-1]
reverse rate constant
Kr
(KD_DAG_C1 * speed_DAG_C1) [s-1]
global
KD_DAG_C1
0.2 [uM]
global
speed_DAG_C1
10.0 [uM-1.s-1]
Expressions for VSP_PIP3
reaction rate
J
((Kf * PIP3) - (Kr * PI3_4_P2)) [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_PIP3 * VSP_conc) [s-1]
global
VSP_conc
1.6 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kVSP_PIP3
(VSP_PIP3max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PIP3))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
VSP_PIP3max
(2.0 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
Vhalf_PIP3
0.095 [V]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
Expressions for PI3K_PTEN
reaction rate
J
((Kf * PIP2_M) - (Kr * PIP3)) [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
0.35454545 [s-1]
reverse rate constant
Kr
(0.45 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
Expressions for TAPP1_binding
reaction rate
J
(((Kf * PI3_4_P2) * TAPP1_dom_C) - (Kr * TAPP1_PI34P2_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_TAPP1_PI34P2 [s-1.uM-1]
reverse rate constant
Kr
(KD_TAPP1_PI34P2 * speed_TAPP1_PI34P2) [s-1]
local
speed_TAPP1_PI34P2
1.0 [s-1.uM-1]
local
KD_TAPP1_PI34P2
0.1 [uM]
Expressions for PH_Btk_binding
reaction rate
J
(((Kf * PH_Btk_dom_C) * PIP3) - (Kr * PH_Btk_PIP3_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_Btk_PIP3 [s-1.uM-1]
reverse rate constant
Kr
(KD_PH_Btk * speed_PH_Btk_PIP3) [s-1]
local
speed_PH_Btk_PIP3
1.0 [s-1.uM-1]
local
KD_PH_Btk
0.3 [uM]
Expressions for PI3K_on_PIP4P
reaction rate
J
((Kf * PI3_4_P2) - (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
(7.5E-4 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
7.5E-4 [s-1]
Expressions for P4M_PI4P_binding
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]
local
speed_P4M_PI4P
1.0 [s-1.uM-1]
local
KD_P4M_PI4P
1.5 [uM]
Expressions for VSP_5P_PIP3
reaction rate
J
((Kf * PIP3) - (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
(kVSP_5P_PIP3 * VSP_conc) [s-1]
global
VSP_conc
1.6 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kVSP_5P_PIP3
(VSP_5P_PIP3max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PIP3))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [tbd]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
Vhalf_PIP3
0.095 [tbd]
local
VSP_5P_PIP3max
(44.0 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
local
Vhold
-0.1 [tbd]
Expressions for PIPKIgamma_PIP
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
(kPIPKIgamma * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kPIPKIgamma
(PIPKIgamma_max / (1.0 + exp((1.56 * qKT * (V - Vhalf))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
PIPKIgamma_max
(0.0 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
Vhalf
0.057 [V]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
local
Vhold
-0.1 [V]
Expressions for PIPKIgamma_PI34P2
reaction rate
J
((Kf * PI3_4_P2) - (Kr * PIP3)) [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
(kPIPKIgamma_PI34P2 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kPIPKIgamma_PI34P2
(PIPKIgamma_PI34P2_max / (1.0 + exp((1.56 * qKT * (V - Vhalf))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
Vhalf
0.057 [V]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
PIPKIgamma_PI34P2_max
(0.0 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
Expressions for VSP_PI34P2
reaction rate
J
((Kf * PI3_4_P2) - (Kr * PI4P_VSPbound)) [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_PI34P2 * VSP_conc) [s-1]
global
VSP_conc
1.6 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kVSP_PI34P2
(VSP_PI34P2max / (1.0 + exp((1.4 * qKT * (V - Vhalf_PI34P2))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
qKT
-40.5898 [tbd]
local
Vhalf_PI34P2
0.095 [V]
local
V
(Vhold + (( - Vhold + Vcommand) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
0.0 [s]
global
end
0.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
global
Vhold
-0.1 [V]
global
Vcommand
0.16 [V]
local
VSP_PI34P2max
(0.15 * ((t > VSP_start) * (t < VSP_end))) [s-1]
global
start
0.0 [s]
global
end
0.0 [s]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
local
VSP_end
52.0 [s]
local
VSP_start
50.0 [s]
Expressions for PI4P_VSPbound_release
reaction rate
J
((Kf * PI4P_VSPbound) - (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
(5.0 * (t > VSP_end3)) [s-1]
global
end
0.0 [s]
reverse rate constant
Kr
0.0 [s-1]
local
VSP_end3
52.05 [s]
Structures
| Name | Type | Electrical |
|---|---|---|
| M | Membrane | C(+) EX(-) |
| ERM | Membrane | Ca_store(+) C(-) |
| Ca_store | Compartment | (+) (-) |
| C | Compartment | (+) (-) |
| EX | Compartment | (+) (-) |
M Universal ID's
M Text Annotations
ERM Universal ID's
ERM Text Annotations
Ca_store Universal ID's
Ca_store Text Annotations
C Universal ID's
C Text Annotations
EX Universal ID's
EX Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| 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 | ||
| PIP3 | M | ||
| PI3_4_P2 | M | ||
| TAPP1_dom_C | C | ||
| TAPP1_PI34P2_M | M | ||
| PH_Btk_dom_C | C | ||
| PH_Btk_PIP3_M | M | ||
| P4M_dom_C | C | ||
| P4M_PI4P_M | M | ||
| PI4P_VSPbound | M |
IP3_pipette Universal ID's
IP3_pipette Text Annotations
PI4P_M Universal ID's
PI4P_M Text Annotations
PH_YFP_PIP2_M Universal ID's
PH_YFP_PIP2_M Text Annotations
KCNQ_M Universal ID's
KCNQ_M Text Annotations
inactiveIP3R Universal ID's
inactiveIP3R Text Annotations
IP3_PH_YFP_C Universal ID's
IP3_PH_YFP_C Text Annotations
PI_M Universal ID's
PI_M Text Annotations
RLG_GDP_M Universal ID's
RLG_GDP_M Text Annotations
RL_M Universal ID's
RL_M Text Annotations
GaGTP_PLC_M Universal ID's
GaGTP_PLC_M Text Annotations
GaGTP_M Universal ID's
GaGTP_M Text Annotations
RLGbeta_M Universal ID's
RLGbeta_M Text Annotations
Gbeta_M Universal ID's
Gbeta_M Text Annotations
C1_dom_C Universal ID's
C1_dom_C Text Annotations
K_C Universal ID's
K_C Text Annotations
Ca_C Universal ID's
Ca_C Text Annotations
RGbeta_M Universal ID's
RGbeta_M Text Annotations
R_M Universal ID's
R_M Text Annotations
noninactiveIP3R Universal ID's
noninactiveIP3R Text Annotations
boundPIP2_M Universal ID's
boundPIP2_M Text Annotations
IP3_LibraVIII_C Universal ID's
IP3_LibraVIII_C Text Annotations
LibraVIII_C Universal ID's
LibraVIII_C Text Annotations
G_GDP_M Universal ID's
G_GDP_M Text Annotations
RG_GDP_M Universal ID's
RG_GDP_M Text Annotations
Ga_GDP_M Universal ID's
Ga_GDP_M Text Annotations
DAG_M Universal ID's
DAG_M Text Annotations
oxoM_EX Universal ID's
oxoM_EX Text Annotations
PA_2AG_M Universal ID's
PA_2AG_M Text Annotations
PLC_M Universal ID's
PLC_M Text Annotations
PH_YFP_C Universal ID's
PH_YFP_C Text Annotations
PIP2_M Universal ID's
PIP2_M Text Annotations
OxoM_conc_EX Universal ID's
OxoM_conc_EX Text Annotations
Ca_Fura4F_C Universal ID's
Ca_Fura4F_C Text Annotations
Ca_Ca_store Universal ID's
Ca_Ca_store Text Annotations
Fura4F_C Universal ID's
Fura4F_C Text Annotations
IP3_C Universal ID's
IP3_C Text Annotations
Palk_C1 Universal ID's
Palk_C1 Text Annotations
Palk_C2 Universal ID's
Palk_C2 Text Annotations
Palk_C3 Universal ID's
Palk_C3 Text Annotations
Palk_O4 Universal ID's
Palk_O4 Text Annotations
C1_DAG_M Universal ID's
C1_DAG_M Text Annotations
GaGDP_PLC_M Universal ID's
GaGDP_PLC_M Text Annotations
K_EX Universal ID's
K_EX Text Annotations
KCNQ_PIP2_M Universal ID's
KCNQ_PIP2_M Text Annotations
PIP3 Universal ID's
PIP3 Text Annotations
PI3_4_P2 Universal ID's
PI3_4_P2 Text Annotations
TAPP1_dom_C Universal ID's
TAPP1_dom_C Text Annotations
TAPP1_PI34P2_M Universal ID's
TAPP1_PI34P2_M Text Annotations
PH_Btk_dom_C Universal ID's
PH_Btk_dom_C Text Annotations
PH_Btk_PIP3_M Universal ID's
PH_Btk_PIP3_M Text Annotations
P4M_dom_C Universal ID's
P4M_dom_C Text Annotations
P4M_PI4P_M Universal ID's
P4M_PI4P_M Text Annotations
PI4P_VSPbound Universal ID's
PI4P_VSPbound Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| modelinOct2010 |
Specs -
Species Specs - Reaction 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 |
modelinOct2010 Universal ID's
modelinOct2010 Text Annotations
Specifications (Species) - modelinOct2010 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| Ca_Ca_store | 400.0 [uM] | 0.0 [um2/s] | Ca_store |
| IP3_PH_YFP_C | 0.0 [uM] | 0.0 [um2/s] | C |
| C1_dom_C | 0.0 [uM] | 0.0 [um2/s] | C |
| K_C | 100000.0 [uM] | 0.0 [um2/s] | C |
| Ca_C | 0.13 [uM] | 0.0 [um2/s] | C |
| IP3_LibraVIII_C | 0.0 [uM] | 0.0 [um2/s] | C |
| LibraVIII_C | 0.0 [uM] | 0.0 [um2/s] | C |
| PH_YFP_C | 0.0 [uM] | 0.0 [um2/s] | C |
| Ca_Fura4F_C | 0.0 [uM] | 0.0 [um2/s] | C |
| Fura4F_C | 0.0 [uM] | 0.0 [um2/s] | C |
| IP3_C | 0.02 [uM] | 0.0 [um2/s] | C |
| Palk_C1 | 1.0 [uM] | 0.0 [um2/s] | C |
| Palk_C2 | 0.0 [uM] | 0.0 [um2/s] | C |
| Palk_C3 | 0.0 [uM] | 0.0 [um2/s] | C |
| Palk_O4 | 0.0 [uM] | 0.0 [um2/s] | C |
| TAPP1_dom_C | 0.0 [uM] | 0.0 [um2/s] | C |
| PH_Btk_dom_C | 0.0 [uM] | 0.0 [um2/s] | C |
| P4M_dom_C | 0.0 [uM] | 0.0 [um2/s] | C |
| IP3_pipette | 0.0 [uM] | 0.0 [um2/s] | EX |
| oxoM_EX | 0.0 [uM] | 0.0 [um2/s] | EX |
| OxoM_conc_EX | 10.0 [uM] | 0.0 [um2/s] | EX |
| K_EX | 0.0 [uM] | 0.0 [um2/s] | EX |
| PI4P_M | 4000.0 [uM] | 0.0 [um2/s] | M |
| PH_YFP_PIP2_M | 0.0 [uM] | 0.0 [um2/s] | M |
| KCNQ_M | 4.0 [uM] | 0.0 [um2/s] | M |
| PI_M | 140000.0 [uM] | 0.0 [um2/s] | M |
| RLG_GDP_M | 0.0 [uM] | 0.0 [um2/s] | M |
| RL_M | 0.0 [uM] | 0.0 [um2/s] | M |
| GaGTP_PLC_M | 0.0 [uM] | 0.0 [um2/s] | M |
| GaGTP_M | 0.0 [uM] | 0.0 [um2/s] | M |
| RLGbeta_M | 0.0 [uM] | 0.0 [um2/s] | M |
| Gbeta_M | 0.0 [uM] | 0.0 [um2/s] | M |
| RGbeta_M | 0.0 [uM] | 0.0 [um2/s] | M |
| R_M | 500.0 [uM] | 0.0 [um2/s] | M |
| boundPIP2_M | (( - 1.0 + foldPIP2) * PIP2_M) [uM] | 0.0 [um2/s] | M |
| G_GDP_M | 40.0 [uM] | 0.0 [um2/s] | M |
| RG_GDP_M | 0.0 [uM] | 0.0 [um2/s] | M |
| Ga_GDP_M | 0.0 [uM] | 0.0 [um2/s] | M |
| DAG_M | 13.0 [uM] | 0.0 [um2/s] | M |
| PA_2AG_M | 0.0 [uM] | 0.0 [um2/s] | M |
| PLC_M | 10.0 [uM] | 0.0 [um2/s] | M |
| PIP2_M | 5000.0 [uM] | 0.0 [um2/s] | M |
| C1_DAG_M | 0.0 [uM] | 0.0 [um2/s] | M |
| GaGDP_PLC_M | 0.0 [uM] | 0.0 [um2/s] | M |
| KCNQ_PIP2_M | 0.0 [uM] | 0.0 [um2/s] | M |
| PIP3 | 1338.0 [uM] | 0.0 [um2/s] | M |
| PI3_4_P2 | 1200.0 [uM] | 0.0 [um2/s] | M |
| TAPP1_PI34P2_M | 0.0 [uM] | 0.0 [um2/s] | M |
| PH_Btk_PIP3_M | 0.0 [uM] | 0.0 [um2/s] | M |
| P4M_PI4P_M | 0.0 [uM] | 0.0 [um2/s] | M |
| PI4P_VSPbound | 0.0 [uM] | 0.0 [um2/s] | M |
| inactiveIP3R | 0.0 [uM] | 0.0 [um2/s] | ERM |
| noninactiveIP3R | 1.0 [uM] | 0.0 [um2/s] | ERM |
Specifications (Reaction) - modelinOct2010 go to Simulations
| Name | Enabled? |
|---|---|
| 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 |
| VSP_PIP3 | included |
| PI3K_PTEN | included |
| TAPP1_binding | included |
| PH_Btk_binding | included |
| PI3K_on_PIP4P | included |
| P4M_PI4P_binding | included |
| VSP_5P_PIP3 | included |
| PIPKIgamma_PIP | included |
| PIPKIgamma_PI34P2 | included |
| VSP_PI34P2 | included |
| PI4P_VSPbound_release | 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 |
Simulations - modelinOct2010 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| DFH Figures 4C and 5A "Oxo" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figures 4D and 5B "Oxo" and 6F | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 5A "UTP" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 5B "UTP" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 6B "Oxo" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 6B pipette dialysis | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 6E | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 7B | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| VSP | 60.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 8C | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 8D "4K at resting rate" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| DFH Figure 8D "4K turned off" | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 1E | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 1F | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figures 4G and 4H | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 6B | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figures 6C and 6D | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 8A except Fura, Libra, C1 | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 8A Fura | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 8A Libra, C1 | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 8B except Fura, Libra, C1 | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
| FDH Figure 8C except Fura, Libra, C1 | 600.0 |
KeepEvery 10 KeepAtMost 1000 |
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Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial61971900
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | ERM |
Events
| Name | Variable | Rate Expression |
|---|
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[um2.molecules-1.s-1] |
| PLC_basal | 0.0[s-1] |
| start | 0.0[s] |
| end | 0.0[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 | 0.2[uM] |
| speed_DAG_C1 | 10.0[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))))) [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))))) [s-1] |
| tau_stim_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] |
| qKT | -40.5898[tbd] |
| VSP_conc | 1.6[1] |
| Vstep | 0.16[V] |
| Vhold | -0.1[V] |
| Vcommand | 0.16[V] |
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Downloads
| Model Format | Model Downloads |
|---|---|
| Virtual Cell Markup Language | VCML File |
| PDF Report | Report |
| COMBINE Archive | OMEX File |
| SEDML | SEDML File |
| File Format | Application Downloads |
| BNGL | modelinOct2010.bngl |
| SBML | modelinOct2010.sbml |
| Matlab | modelinOct2010.m |
| NFSim XML | modelinOct2010.xml |