Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Fura4F_C+Ca_CCa_Fura4F_C Cabind_Fura4F C MassAction
LibraVIII_C+IP3_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
oxoM_EX+R_MRL_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
oxoM_EX+RGbeta_MRLGbeta_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
Gbeta_M+R_MRGbeta_M G1beta M MassAction
DAG_MPA_2AG_M DAGPase M GeneralKinetics
PI_MPI4P_M PI4K_4Pase M MassAction
IP3_C+PH_YFP_CIP3_PH_YFP_C PH_YFP_IP3 C MassAction
IP3_C IP3Pase_FDH C GeneralKinetics
Gbeta_M+RL_MRLGbeta_M G2beta M MassAction
GaGDP_PLC_MGa_GDP_M+PLC_M PLCdiss M MassAction
oxoM_EX+RG_GDP_MRLG_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_MDAG_M+IP3_C 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
G_GDP_M+RL_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
PIP3PI3_4_P2 VSP_PIP3 M MassAction
PIP2_MPIP3 PI3K_PTEN M MassAction
PI3_4_P2+TAPP1_dom_CTAPP1_PI34P2_M TAPP1_binding M MassAction
PH_Btk_dom_C+PIP3PH_Btk_PIP3_M PH_Btk_binding M MassAction
PI3_4_P2PI4P_M PI3K_on_PIP4P M MassAction
P4M_dom_C+PI4P_MP4M_PI4P_M P4M_PI4P_binding M MassAction
PIP3PIP2_M VSP_5P_PIP3 M MassAction
PI4P_MPIP2_M PIPKIgamma_PIP M MassAction
PI3_4_P2PIP3 PIPKIgamma_PI34P2 M MassAction
PI3_4_P2PI4P_VSPbound VSP_PI34P2 M MassAction
PI4P_VSPboundPI4P_M PI4P_VSPbound_release M MassAction

Structures

Name
Type
Electrical
M Membrane C(+)   EX(-)
ERM Membrane Ca_store(+)   C(-)
Ca_store Compartment (+)   (-)
C Compartment (+)   (-)
EX 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 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
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 0.02 [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
TAPP1_dom_C 0.0 [uM] 0.0 [um2/s] C
PH_Btk_dom_C 0.0 [uM] 0.0 [um2/s] C
P4M_dom_C 0.0 [uM] 0.0 [um2/s] C
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
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 13.0 [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
PIP3 1338.0 [uM] 0.0 [um2/s] M
PI3_4_P2 1200.0 [uM] 0.0 [um2/s] M
TAPP1_PI34P2_M 0.0 [uM] 0.0 [um2/s] M
PH_Btk_PIP3_M 0.0 [uM] 0.0 [um2/s] M
P4M_PI4P_M 0.0 [uM] 0.0 [um2/s] M
PI4P_VSPbound 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) - modelinOct2010 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
VSP_PIP3 included
PI3K_PTEN included
TAPP1_binding included
PH_Btk_binding included
PI3K_on_PIP4P included
P4M_PI4P_binding included
VSP_5P_PIP3 included
PIPKIgamma_PIP included
PIPKIgamma_PI34P2 included
VSP_PI34P2 included
PI4P_VSPbound_release 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 - modelinOct2010 go to Specifications

Name
End Time
Output Options
DFH Figures 4C and 5A "Oxo" 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figures 4D and 5B "Oxo" and 6F 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 5A "UTP" 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 5B "UTP" 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 6B "Oxo" 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 6B pipette dialysis 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 6E 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 7B 600.0

KeepEvery 10

KeepAtMost 1000

VSP 60.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 8C 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 8D "4K at resting rate" 600.0

KeepEvery 10

KeepAtMost 1000

DFH Figure 8D "4K turned off" 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 1E 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 1F 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figures 4G and 4H 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 6B 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figures 6C and 6D 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A except Fura, Libra, C1 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A Fura 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 8A Libra, C1 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 8B except Fura, Libra, C1 600.0

KeepEvery 10

KeepAtMost 1000

FDH Figure 8C except Fura, Libra, C1 600.0

KeepEvery 10

KeepAtMost 1000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial61971900

(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[um2.molecules-1.s-1]
PLC_basal 0.0[s-1]
start 0.0[s]
end 0.0[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]
qKT -40.5898[tbd]
VSP_conc 1.6[1]
Vstep 0.16[V]
Vhold -0.1[V]
Vcommand 0.16[V]

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 modelinOct2010.bngl
SBML modelinOct2010.sbml
Matlab modelinOct2010.m
NFSim XML modelinOct2010.xml