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Name - PI cycle Figure 6, 7 & S9

BioModel ID - 189512756

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
Modeling PI cycle Deterministic (ODE) Compartmental cloned from 'Modeling PI cycle' owned by user cherubim0521 cloned from 'modelinOct2010' owned by user hillelab cloned from 'modelinOct2010' owned by user bfalken (copied from PBio519 talk) (copied from M1R activation, manuscript 1) (copied from M1R activation) (copied from PipDecay) cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab cloned from 'PipDecay' owned by user bfalken cloned from 'PipDecay' owned by user hillelab

Application - Modeling PI cycle

Specifications(Species) - Modeling PI cycle See in Dashboard
Species Initial Condition Diffusion Constant
IP3_pipette 0.0 [uM] 0.0 [um2/s]
oxoM_EX 0.0 [uM] 0.0 [um2/s]
OxoM_conc_EX 10.0 [uM] 0.0 [um2/s]
K_EX 0.0 [uM] 0.0 [um2/s]
Ca_Ca_store 400.0 [uM] 0.0 [um2/s]
IP3_PH_YFP_C 0.0 [uM] 0.0 [um2/s]
C1_dom_C 0.0 [uM] 0.0 [um2/s]
K_C 100000.0 [uM] 0.0 [um2/s]
Ca_C 0.13 [uM] 0.0 [um2/s]
IP3_LIBRAvIII_C 0.0 [uM] 0.0 [um2/s]
LIBRAvIII_C 0.0 [uM] 0.0 [um2/s]
PH_YFP_C 0.0 [uM] 0.0 [um2/s]
Ca_Fura4F_C 0.0 [uM] 0.0 [um2/s]
Fura4F_C 0.0 [uM] 0.0 [um2/s]
IP3_C 0.033 [uM] 0.0 [um2/s]
Palk_C1 1.0 [uM] 0.0 [um2/s]
Palk_C2 0.0 [uM] 0.0 [um2/s]
Palk_C3 0.0 [uM] 0.0 [um2/s]
Palk_O4 0.0 [uM] 0.0 [um2/s]
P4M_C 0.0 [uM] 0.0 [um2/s]
FAPP1_C 0.0 [uM] 0.0 [um2/s]
PI4P_M 2000.0 [uM] 0.0 [um2/s]
PH_YFP_PIP2_M 0.0 [uM] 0.0 [um2/s]
KCNQ_M 4.0 [uM] 0.0 [um2/s]
RLG_GDP_M 0.0 [uM] 0.0 [um2/s]
RL_M 0.0 [uM] 0.0 [um2/s]
GaGTP_PLC_M 0.0 [uM] 0.0 [um2/s]
GaGTP_M 0.0 [uM] 0.0 [um2/s]
RLGbeta_M 0.0 [uM] 0.0 [um2/s]
Gbeta_M 0.0 [uM] 0.0 [um2/s]
RGbeta_M 0.0 [uM] 0.0 [um2/s]
R_M 500.0 [uM] 0.0 [um2/s]
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s]
G_GDP_M 40.0 [uM] 0.0 [um2/s]
RG_GDP_M 0.0 [uM] 0.0 [um2/s]
Ga_GDP_M 0.0 [uM] 0.0 [um2/s]
DAG_M 13.0 [uM] 0.0 [um2/s]
PA_2AG_M 0.0 [uM] 0.0 [um2/s]
PLC_M 10.0 [uM] 0.0 [um2/s]
PIP2_M 5000.0 [uM] 0.0 [um2/s]
C1_DAG_M 0.0 [uM] 0.0 [um2/s]
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s]
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s]
PI_M 1400.0 [uM] 0.0 [um2/s]
P4M_PI4P_M 0.0 [uM] 0.0 [um2/s]
inactiveIP3R 0.0 [uM] 0.0 [um2/s]
noninactiveIP3R 1.0 [uM] 0.0 [um2/s]
PI_E 14000.0 [uM] 0.0 [um2/s]
PI4P_G 1000.0 [uM] 0.0 [um2/s]
PI_G 35000.0 [uM] 0.0 [um2/s]
P4M_PI4P_G 0.0 [uM] 0.0 [um2/s]
FAPP1_PI4P_G 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - Modeling PI cycle See in Dashboard
Name Reaction Mapping
Cabind_Fura4F included
IP3_LibraVIII included
PLC_on_PI4P included
NE_RG included
L1 included
h_reaction_IP3Rinactivation included
PIP5K_5Pase included
NE_G included
GTPase_Ga included
IP3deg_Palk excluded
r12 excluded
r23 excluded
r24 excluded
PIP2_buffering included
L2beta included
NE_RLG included
NE_GaP included
PH_YFP_PIP2 included
VSP included
G1beta included
DAGPase included
PI4K_4Pase_M 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
PI4K_4Pase_G included
PIP5K_5Pase_G included
PI_EX_M included
PI_EX_G included
PI4P_P4M_G included
PI4P_P4M_M included
PI4P_FAPP1_G included
Sac1_G 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 See in Dashboard
Name End Time Output Options
S Figure 9A. PtdIns4P_M_P4M 720.0 [s]

OutputTimeStep 1.0

S Figure 9D. InsP3_LIBRA 720.0 [s]

OutputTimeStep 1.0

Backbone Figure 7 720.0 [s]

OutputTimeStep 1.0

S Figure 9E. DAG_C1A 720.0 [s]

OutputTimeStep 1.0

S Figure 9C. PH domain 720.0 [s]

OutputTimeStep 1.0

S Figure 9B. FAPP1 720.0 [s]

OutputTimeStep 1.0

Figure 6G. PtdIns4P_M_P4M Sac1 720.0 [s]

OutputTimeStep 1.0

Figure 6F. PH domain Sac1 720.0 [s]

OutputTimeStep 1.0

Geometry non-spatial1595765197 See in Dashboard
(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 Golgi_Vesicle_M

Global Parameters

Global Parameters See in Dashboard
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 20.0[uM-1.s-1]
KD_PH_PIP2 2.0[uM]
speed_PH_IP3 10.0[uM-1.s-1]
KD_PH_IP3 2.0[uM]
K_plc 0.2[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 0.2[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 ((0.0023581 / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) * stim_second)[s-1]
stim_4k_max 9.0[s-1]
stim_5K_max 0.03092299998[s-1]
stim_5k (stim_5K_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases)))))[s-1]
tau_stim_onset 1.0[s]
k5k_base 0.0117624[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]
onset_second 20.0[s]
K4_base (2.41884E-4 * 6.0)[s-1]
scale4K 0.75[1]
K4_rest 0.00312[s-1]
K4_Oxo (K4_rest + ((stim_4k - K4_rest + K4_base) * (1.0 - exp(((start + tau_stim_onset - t) / tau_stim_onset)))))[s-1]
tau_second 300.0[s]
tau_Ga_PI4P_PLC 241.0[tbd]
tau_PM_PI4K 210.0[s]
star 120.0[s]
tau_PI4K 300.0[s]
speed_P4M_PI4P 0.01[um2.s-1.molecules-1]
KD_P4M_PI4P 1.5[uM]
stim_second (1.0 + ((((stim_4k_max / (1.0 + exp( - (277.77777777777777 * ( - 0.0175 + OxoMforKinases))))) - (0.0077419 * stim_4k_max)) * (1.0 - exp(((start + onset_second - t) / tau_second)))) * ((start + onset_second) < t) * (t <= end)))[s-1]
tau_PIP2_PLC 20.0[s]