Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PI4P_MPIP2_M PIP5K_5Pase M MassAction
PH_YFP_C+PIP2_MPH_YFP_PIP2_M PH_YFP_PIP2 M MassAction
RLG_GDP_MRLGbeta_M+GaGTP_M NE_RLG M GeneralKinetics
RL_MRLP_M reaction 1 for phosphorylation of ligand bound receptor M GeneralKinetics
Gbeta_M+Ga_GDP_MG_GDP_M reconstitution M GeneralKinetics
RL_M+G_GDP_MRLG_GDP_M G2 M MassAction
DAG_MPA_2AG_M DAGPase M GeneralKinetics
GaGTP_MGa_GDP_M GTPase_Ga M GeneralKinetics
PLC_M+GaGTP_MGaGTP_PLC_M PLCassoc M MassAction
IP3_C+PH_YFP_CIP3_PH_YFP_C PH_YFP_IP3 C MassAction
Palk_C1Palk_C2 r12 C MassAction
RG_GDP_M+AP_EXRLG_GDP_M L2 M MassAction
dynamin+RLPA2_MRLPAC_M clathrin formation rate M GeneralKinetics
noninactiveIP3RinactiveIP3R h_reaction_IP3Rinactivation ERM GeneralKinetics
R_M+AP_EXRL_M L1 M MassAction
PI4P_MDAG_M PLC_on_PI4P M GeneralKinetics
R_MRP_M reaction 2 for phosphorylation of receptor M GeneralKinetics
G_GDP_MGaGTP_M+Gbeta_M NE_G M MassAction
RP_M+AP_EXRLP_M ligand2 M MassAction
Palk_C2Palk_O4 r24 C MassAction
IP3_C IP3deg_Palk C MassAction
PI_MPI4P_M PI4K_4Pase M MassAction
IP3_pipetteIP3_C IP3_dialysis M MassAction
LibraVIII_C+IP3_CIP3_LibraVIII_C IP3_LibraVIII C MassAction
PIP2_MPI4P_M VSP M MassAction
Gbeta_M+R_MRGbeta_M G1beta M MassAction
GaGDP_PLC_MGaGTP_PLC_M NE_GaP M GeneralKinetics
IP3_C IP3Pase_FDH C GeneralKinetics
RLP_M+Arrestin2RLPA2_M arrestin binding M GeneralKinetics
Palk_C2Palk_C3 r23 C MassAction
KCNQ_M+PIP2_MKCNQ_PIP2_M PIP2bindKCNQ M GeneralKinetics
RLPAC_M+dynaminendocytosis pinching M GeneralKinetics
Gbeta_M+RL_MRLGbeta_M G2beta M MassAction
PIP2_MIP3_C+DAG_M PIP2hydr M GeneralKinetics
AP_conc_EXAP_EX Oxo_appl EX MassAction
GaGDP_PLC_MGa_GDP_M+PLC_M PLCdiss M MassAction
R_M+G_GDP_MRG_GDP_M G1 M MassAction
GaGTP_PLC_MGaGDP_PLC_M GTPase_GaP M GeneralKinetics
DAG_M+PKC_cytoPKC_DAG_M PKC_DAG binding M GeneralKinetics
C1_dom_C+DAG_MC1_DAG_M C1bindDAG M MassAction
PIP2_MboundPIP2_M PIP2_buffering M MassAction
RG_GDP_MGaGTP_M+RGbeta_M NE_RG M MassAction
Fura4F_C+Ca_CCa_Fura4F_C Cabind_Fura4F C MassAction
RGbeta_M+AP_EXRLGbeta_M L2beta M MassAction
RLP_M+Arrestin1RLPA1 Arrestin 1 M MassAction
RLPA1RLPAC_M RLPA1 to clathrin M MassAction

Structures

Name
Type
Electrical
M Membrane C(+)   EX(-)
ERM Membrane Ca_store(+)   C(-)
EX Compartment (+)   (-)
C Compartment (+)   (-)
Ca_store Compartment (+)   (-)

Species

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
modelinOct2010 Specs - Species
Specs - Reaction
Simulations
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

Specifications (Species) - modelinOct2010 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
AP_EX 0.0 [uM] 0.0 [um2/s] EX
K_EX 0.0 [uM] 0.0 [um2/s] EX
IP3_pipette 0.0 [uM] 0.0 [um2/s] EX
AP_conc_EX 100.0 [uM] 0.0 [um2/s] EX
dynamin 10.0 [uM] 0.0 [um2/s] C
C1_dom_C 0.0 [uM] 0.0 [um2/s] C
IP3_C 0.015 [uM] 0.0 [um2/s] C
Ca_Fura4F_C 0.0 [uM] 0.0 [um2/s] C
K_C 100000.0 [uM] 0.0 [um2/s] C
Fura4F_C 0.0 [uM] 0.0 [um2/s] C
Arrestin2 7.5 [uM] 0.0 [um2/s] C
IP3_LibraVIII_C 0.0 [uM] 0.0 [um2/s] C
IP3_PH_YFP_C 0.0 [uM] 0.0 [um2/s] C
LibraVIII_C 0.0 [uM] 0.0 [um2/s] C
Palk_C1 1.0 [uM] 0.0 [um2/s] C
PH_YFP_C 0.0 [uM] 0.0 [um2/s] C
PKC_cyto 1.0 [uM] 0.0 [um2/s] C
Palk_C2 0.0 [uM] 0.0 [um2/s] C
Ca_C 0.13 [uM] 0.0 [um2/s] C
Palk_O4 0.0 [uM] 0.0 [um2/s] C
Palk_C3 0.0 [uM] 0.0 [um2/s] C
Arrestin1 7.5 [uM] 0.0 [um2/s] C
Ca_Ca_store 400.0 [uM] 0.0 [um2/s] Ca_store
RLPAC_M 0.0 [uM] 0.0 [um2/s] M
endocytosis 0.0 [uM] 0.0 [um2/s] M
PI_M 140000.0 [uM] 0.0 [um2/s] M
KCNQ_M 0.0 [uM] 0.0 [um2/s] M
G_GDP_M 40.0 [uM] 0.0 [um2/s] M
PH_YFP_PIP2_M 0.0 [uM] 0.0 [um2/s] M
RLPA2_M 0.0 [uM] 0.0 [um2/s] M
PA_2AG_M 0.0 [uM] 0.0 [um2/s] M
RLGbeta_M 0.0 [uM] 0.0 [um2/s] M
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s] M
PLC_M 10.0 [uM] 0.0 [um2/s] M
GaGTP_M 0.0 [uM] 0.0 [um2/s] M
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s] M
RLP_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 5000.0 [uM] 0.0 [um2/s] M
Ga_GDP_M 0.0 [uM] 0.0 [um2/s] M
RG_GDP_M 0.0 [uM] 0.0 [um2/s] M
PIP2_M 5000.0 [uM] 0.0 [um2/s] M
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s] M
DAG_M 13.0 [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
RLG_GDP_M 0.0 [uM] 0.0 [um2/s] M
PKC_DAG_M 0.0 [uM] 0.0 [um2/s] M
RP_M 0.0 [uM] 0.0 [um2/s] M
C1_DAG_M 0.0 [uM] 0.0 [um2/s] M
PI4P_M 3600.0 [uM] 0.0 [um2/s] M
RLPA1 0.0 [uM] 0.0 [um2/s] M
noninactiveIP3R 1.0 [uM] 0.0 [um2/s] ERM
inactiveIP3R 0.0 [uM] 0.0 [um2/s] ERM

Specifications (Reaction) - modelinOct2010 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Figure 7 1000.0

KeepEvery 10

KeepAtMost 1000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial754981975

(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 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]

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