Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| Fura4F_C+Ca_CCa_Fura4F_C | Cabind_Fura4F | C | MassAction | |
| IP3_C+LIBRAvIII_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 | |
| R_M+oxoM_EXRL_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 | |
| RGbeta_M+oxoM_EXRLGbeta_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 | |
| R_M+Gbeta_MRGbeta_M | G1beta | M | MassAction | |
| DAG_MPA_2AG_M | DAGPase | M | GeneralKinetics | |
| PI_MPI4P_M | PI4K_4Pase | M | MassAction | |
| PH_YFP_C+IP3_CIP3_PH_YFP_C | PH_YFP_IP3 | C | MassAction | |
| IP3_C | IP3Pase_FDH | C | GeneralKinetics | |
| RL_M+Gbeta_MRLGbeta_M | G2beta | M | MassAction | |
| GaGDP_PLC_MGa_GDP_M+PLC_M | PLCdiss | M | MassAction | |
| RG_GDP_M+oxoM_EXRLG_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_MIP3_C+DAG_M | 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 | |
| RL_M+G_GDP_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 |
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
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 * 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]
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 * (GaGTP_PLC_M * K_plc)) [molecules.um-2.s-1]
global
K_plc
(0.2 * decrease) [um2.molecules-1.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
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 * 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]
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
(foldPIP2 * (((t < start) * k5K_rest) + ((t >= start) * (t <= end) * k5k_Oxo))) [s-1]
global
start
120.0 [s]
global
end
720.0 [s]
global
foldPIP2
3.0 [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]
global
start
120.0 [s]
global
end
720.0 [s]
global
foldPIP2
3.0 [1]
global
tau_d
130.0 [s]
global
D_P
0.0 [s-1]
local
k5K_rest
0.02 [s-1]
local
k5k_Oxo
(k5K_rest + ((stim_5k - k5K_rest + k5k_base) * scale5K * (1.0 - exp(((start - t) / tau_stim_5K_onset))))) [s-1]
global
start
120.0 [s]
global
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]
global
k5k_base
0.0181 [s-1]
global
tau_stim_5K_onset
1.0 [tbd]
local
scale5K
1.0 [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
1.0 [s-1]
Expressions for L2beta
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]
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]
global
D_P
0.0 [s-1]
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 * foldPIP2) [s-1]
global
foldPIP2
3.0 [1]
reverse rate constant
Kr
0.0 [s-1]
local
kVSP
(VSPmax / (1.0 + exp((1.5 * qKT * (V - Vhalf))))) [s-1]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
local
Vhalf
0.1 [V]
local
V
(Vhold + (( - Vhold + Vstep) * (t > VSP_start) * (t < VSP_end))) [V]
global
start
120.0 [s]
global
end
720.0 [s]
global
h
(noninactiveIP3R / (noninactiveIP3R + inactiveIP3R)) [1]
local
VSPmax
0.0 [s-1]
local
qKT
-40.5898 [A.s3.kg-1.m-2]
local
VSP_end
150.0 [s]
local
Vstep
0.1 [V]
local
Vhold
-0.06 [V]
local
VSP_start
50.0 [s]
Expressions for G1beta
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]
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
5.0 [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 * ((K4_recover * (t > end)) + (K4_rest * (t < start)) + (K4_Oxo * (t >= start) * (t <= end)))) [s-1]
global
start
120.0 [s]
global
end
720.0 [s]
global
foldPIP2
3.0 [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]
global
start
120.0 [s]
global
end
720.0 [s]
global
tau_d
130.0 [s]
global
D_P
0.0 [s-1]
local
K4_Oxo
(K4_rest + ((stim_4k - K4_rest + K4_base) * scale4K * (1.0 - exp(((start - t) / tau_stim_4K_onset))))) [s-1]
global
start
120.0 [s]
global
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]
global
tau_stim_4K_onset
1.0 [s]
local
K4_rest
2.6E-4 [s-1]
local
K4_recover
((exp(((end - t) / tau_stim_recovery)) * scale4K * (stim_4k - K4_rest + K4_base)) + K4_rest) [s-1]
global
end
720.0 [s]
global
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]
global
tau_stim_recovery
5.0 [s]
local
scale4K
0.75 [1]
local
K4_base
2.3534E-4 [s-1]
local
foldPIP2
3.0 [1]
local
tau_stim_recovery
5.0 [s]
Expressions for PH_YFP_IP3
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]
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]
global
D_P
0.0 [s-1]
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
50.0 [s-1]
Expressions for G2beta
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]
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 * 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]
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]
global
D_P
0.0 [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 * (K_plc * foldPIP2 * GaGTP_PLC_M)) [molecules.um-2.s-1]
global
K_plc
(0.2 * decrease) [um2.molecules-1.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
120.0 [s]
reverse rate constant
Kr
(0.015 * (t > start) * k_pipette) [molecules.um-2.s-1.uM-1]
global
start
120.0 [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
120.0 [s]
global
end
720.0 [s]
reverse rate constant
Kr
(50.0 * (t > end)) [s-1]
global
end
720.0 [s]
Expressions for G2
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]
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
0.2 [uM-1.s-1]
reverse rate constant
Kr
(KD_DAG_C1 * speed_DAG_C1) [s-1]
global
KD_DAG_C1
0.1 [uM]
global
speed_DAG_C1
0.2 [uM-1.s-1]
Structures
| Name | Type | Electrical |
|---|---|---|
| M | Membrane | C(+) EX(-) |
| ERM | Membrane | Ca_store(+) C(-) |
| EX | Compartment | (+) (-) |
| Ca_store | Compartment | (+) (-) |
| C | Compartment | (+) (-) |
M Universal ID's
M Text Annotations
ERM Universal ID's
ERM Text Annotations
EX Universal ID's
EX Text Annotations
Ca_store Universal ID's
Ca_store Text Annotations
C Universal ID's
C 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 |
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
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| modeling PI cycle |
Specs -
Species Specs - Reaction Simulations |
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 |
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
Specifications (Species) - modeling PI cycle go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| 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 |
| 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 | 1.0E-6 [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 |
| 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 | 2.0 [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 |
| inactiveIP3R | 0.0 [uM] | 0.0 [um2/s] | ERM |
| noninactiveIP3R | 1.0 [uM] | 0.0 [um2/s] | ERM |
Specifications (Reaction) - modeling PI cycle 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 |
| 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 - modeling PI cycle go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 4K acceleration backbone | 720.0 |
OutputTimeStep 1.0 |
| 4K acceleration InsP3_LIBRA | 720.0 |
OutputTimeStep 1.0 |
| 5K acceleration backbone | 720.0 |
OutputTimeStep 1.0 |
| 4K acceleration DAG_C1A | 720.0 |
OutputTimeStep 1.0 |
| 5K acceleration InsP3_LIBRA | 720.0 |
OutputTimeStep 1.0 |
| 5K acceleration DAG_C1A | 720.0 |
OutputTimeStep 1.0 |
| PLC decrease backbone | 720.0 |
OutputTimeStep 1.0 |
| PLC decrease InsP3_LIBRA | 720.0 |
OutputTimeStep 1.0 |
| PLC decrease DAG_C1A | 720.0 |
OutputTimeStep 1.0 |
| 4P and 5P decrease backbone | 720.0 |
OutputTimeStep 1.0 |
| 4P and 5P decrease InsP3_LIBRA | 720.0 |
OutputTimeStep 1.0 |
| 4P and 5P decrease DAG_C1A | 720.0 |
OutputTimeStep 1.0 |
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
modeling PI cycle Universal ID's
modeling PI cycle Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial2048841859
(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 * 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] |
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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 | modeling PI cycle.bngl |
| SBML | modeling PI cycle.sbml |
| Matlab | modeling PI cycle.m |
| NFSim XML | modeling PI cycle.xml |