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Name - hillelab: JungSR_PAR2_desensitization2015

BioModel ID - 100961371

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
modelinOct2010 Deterministic (ODE) Compartmental cloned from 'modelinOct2010' owned by user bfalken 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 - modelinOct2010

Specifications(Species) - modelinOct2010 See in Dashboard
Species Initial Condition Diffusion Constant
AP_EX 0.0 [uM] 0.0 [um2/s]
K_EX 0.0 [uM] 0.0 [um2/s]
IP3_pipette 0.0 [uM] 0.0 [um2/s]
AP_conc_EX 100.0 [uM] 0.0 [um2/s]
dynamin 10.0 [uM] 0.0 [um2/s]
C1_dom_C 0.0 [uM] 0.0 [um2/s]
IP3_C 0.015 [uM] 0.0 [um2/s]
Ca_Fura4F_C 0.0 [uM] 0.0 [um2/s]
K_C 100000.0 [uM] 0.0 [um2/s]
Fura4F_C 0.0 [uM] 0.0 [um2/s]
Arrestin2 7.5 [uM] 0.0 [um2/s]
IP3_LibraVIII_C 0.0 [uM] 0.0 [um2/s]
IP3_PH_YFP_C 0.0 [uM] 0.0 [um2/s]
LibraVIII_C 0.0 [uM] 0.0 [um2/s]
Palk_C1 1.0 [uM] 0.0 [um2/s]
PH_YFP_C 0.0 [uM] 0.0 [um2/s]
PKC_cyto 1.0 [uM] 0.0 [um2/s]
Palk_C2 0.0 [uM] 0.0 [um2/s]
Ca_C 0.13 [uM] 0.0 [um2/s]
Palk_O4 0.0 [uM] 0.0 [um2/s]
Palk_C3 0.0 [uM] 0.0 [um2/s]
Arrestin1 7.5 [uM] 0.0 [um2/s]
Ca_Ca_store 400.0 [uM] 0.0 [um2/s]
RLPAC_M 0.0 [uM] 0.0 [um2/s]
endocytosis 0.0 [uM] 0.0 [um2/s]
PI_M 140000.0 [uM] 0.0 [um2/s]
KCNQ_M 0.0 [uM] 0.0 [um2/s]
G_GDP_M 40.0 [uM] 0.0 [um2/s]
PH_YFP_PIP2_M 0.0 [uM] 0.0 [um2/s]
RLPA2_M 0.0 [uM] 0.0 [um2/s]
PA_2AG_M 0.0 [uM] 0.0 [um2/s]
RLGbeta_M 0.0 [uM] 0.0 [um2/s]
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s]
PLC_M 10.0 [uM] 0.0 [um2/s]
GaGTP_M 0.0 [uM] 0.0 [um2/s]
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s]
RLP_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 5000.0 [uM] 0.0 [um2/s]
Ga_GDP_M 0.0 [uM] 0.0 [um2/s]
RG_GDP_M 0.0 [uM] 0.0 [um2/s]
PIP2_M 5000.0 [uM] 0.0 [um2/s]
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s]
DAG_M 13.0 [uM] 0.0 [um2/s]
RL_M 0.0 [uM] 0.0 [um2/s]
GaGTP_PLC_M 0.0 [uM] 0.0 [um2/s]
RLG_GDP_M 0.0 [uM] 0.0 [um2/s]
PKC_DAG_M 0.0 [uM] 0.0 [um2/s]
RP_M 0.0 [uM] 0.0 [um2/s]
C1_DAG_M 0.0 [uM] 0.0 [um2/s]
PI4P_M 3600.0 [uM] 0.0 [um2/s]
RLPA1 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) - modelinOct2010 See in Dashboard
Name Reaction Mapping
PIP5K_5Pase included
PH_YFP_PIP2 included
NE_RLG included
reaction 1 for phosphorylation of ligand bound receptor included
reconstitution included
G2 included
DAGPase included
GTPase_Ga included
PLCassoc included
PH_YFP_IP3 included
r12 excluded
L2 included
clathrin formation rate included
h_reaction_IP3Rinactivation included
L1 included
PLC_on_PI4P included
reaction 2 for phosphorylation of receptor included
NE_G included
ligand2 included
r24 excluded
IP3deg_Palk excluded
PI4K_4Pase included
IP3_dialysis included
IP3_LibraVIII included
VSP included
G1beta included
NE_GaP included
IP3Pase_FDH included
arrestin binding included
r23 excluded
PIP2bindKCNQ included
pinching included
G2beta included
PIP2hydr included
Oxo_appl included
PLCdiss included
G1 included
GTPase_GaP included
PKC_DAG binding included
C1bindDAG included
PIP2_buffering included
NE_RG included
Cabind_Fura4F included
L2beta included
Arrestin 1 included
RLPA1 to clathrin included
SERCA_flux_FDH included
KCNQ2/3 included
SERCA_Palk excluded
leak_Palk excluded
IP3R_flux_FDH included
RyR_Palk excluded
IP3R_Palk excluded
ER_leak_flux_FDH included
Simulations - modelinOct2010 See in Dashboard
Name End Time Output Options
Figure 7 1000.0 [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 40.0[uM]
KL2 2.0[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 0.1[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 1.0E-4[s-1]
start 100.0[s]
end 1000.0[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 2.0[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 0.15[s-1]
stim_5K_max 5.75[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]
kf_R_M 1.0E-4[s-1]
kr_RP_M 2.0[s-1]
Kp2 0.2[molecules.um-2]
kf_R_M_stim 0.01[tbd]