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Name - hillelab: KruseVivasTraynorKaplanHille_PI-metabolism_SCG_2015

BioModel ID - 98296160

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
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

Specifications(Species) - simulations See in Dashboard
Species Initial Condition Diffusion Constant
Ca_Buffer_high_aff 4.9721916 [uM] 0.0 [um2/s]
Ca_Buffer_high_aff_Ca 5.0278084 [uM] 0.0 [um2/s]
IP3R_IRBIT 0.01 [uM] 0.0 [um2/s]
IP3_PH_YFP_C 0.0 [uM] 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] 0.0 [um2/s]
P4M_dom_C 0.0 [uM] 0.0 [um2/s]
Ca_Fura2_C 0.0 [uM] 0.0 [um2/s]
IP3_LibraVIII_C 0.0 [uM] 0.0 [um2/s]
LibraVIII_C 0.0 [uM] 0.0 [um2/s]
Fura2_C 0.0 [uM] 0.0 [um2/s]
C1_dom_C 0.0 [uM] 0.0 [um2/s]
Ca_C 0.101 [uM] 0.0 [um2/s]
Palk_C1 1.0 [uM] 0.0 [um2/s]
IP3_C 0.02 [uM] 0.0 [um2/s]
Tubby_C 0.0 [uM] 0.0 [um2/s]
Palk_O4 0.0 [uM] 0.0 [um2/s]
Palk_C2 0.0 [uM] 0.0 [um2/s]
Palk_C3 0.0 [uM] 0.0 [um2/s]
Ca_Buffer_low_aff 18.163356 [uM] 0.0 [um2/s]
IP3R_IP3 0.0 [uM] 0.0 [um2/s]
Ca_Ca_store 361.8635 [uM] 0.0 [um2/s]
K_EX 0.0 [uM] 0.0 [um2/s]
OxoM_conc_EX 10.0 [uM] 0.0 [um2/s]
oxoM_EX 0.0 [uM] 0.0 [um2/s]
R_M 15.87 [uM] 0.0 [um2/s]
RLGbeta_M 0.0 [uM] 0.0 [um2/s]
RL_M 0.0 [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]
Tubby_PIP2_M 0.0 [uM] 0.0 [um2/s]
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s]
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s]
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s]
GaGTP_M 0.0 [uM] 0.0 [um2/s]
Gbeta_M 0.0 [uM] 0.0 [um2/s]
DAG_M 13.0 [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]
PI_M 226975.0 [uM] 0.0 [um2/s]
PA_2AG_M 0.0 [uM] 0.0 [um2/s]
PIP2_M 3232.0 [uM] 0.0 [um2/s]
PI4P_M 4540.0 [uM] 0.0 [um2/s]
GaGTP_PLC_M 0.0 [uM] 0.0 [um2/s]
RLG_GDP_M 0.0 [uM] 0.0 [um2/s]
Ga_GDP_M 0.0 [uM] 0.0 [um2/s]
PLC_M 3.12 [uM] 0.0 [um2/s]
RGbeta_M 0.0 [uM] 0.0 [um2/s]
C1_DAG_M 0.0 [uM] 0.0 [um2/s]
P4M_PI4P_M 0.0 [uM] 0.0 [um2/s]
noninactiveIP3R 1.0 [uM] 0.0 [um2/s]
inactiveIP3R 0.0 [uM] 0.0 [um2/s]
Specifications(Reaction) - simulations See in Dashboard
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
Simulations - simulations See in Dashboard
Name End Time Output Options
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

Geometry non-spatial754981975 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 ERM

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 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 0.3[um2.molecules-1.s-1]
PLC_basal 0.0[s-1]
start 100.0[s]
end 120.0[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]
KD_OSBP_PI4P 0.2[uM]
speed_OSBP_PI4P 10.0[uM-1.s-1]
speed_Tubby_PIP2 1.0[uM-1.s-1]
KD_Tubby_PIP2 1.5[uM]
r_KVH 1.0[tbd]