Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PIP2_MboundPIP2_M PIP2_buffering M MassAction
RL_M+G_GDP_MRLG_GDP_M G2 M MassAction
Palk_C2Palk_O4 r24 C MassAction
oxoM_EX+RGbeta_MRLGbeta_M L2beta M MassAction
IP3_C+IP3R_IRBITIP3R_IP3 IP3R_IP3_binding C MassAction
RLG_GDP_MRLGbeta_M+GaGTP_M NE_RLG M GeneralKinetics
OxoM_conc_EXoxoM_EX Oxo_appl EX MassAction
oxoM_EX+R_MRL_M L1 M MassAction
DAG_MPA_2AG_M DAGPase M GeneralKinetics
PIP2_M+PH_YFP_CPH_YFP_PIP2_M PH_YFP_PIP2 M MassAction
PLC_M+GaGTP_MGaGTP_PLC_M PLCassoc M MassAction
IP3_C IP3deg_Palk C MassAction
Tubby_C+PIP2_MTubby_PIP2_M Tubby_PIP2 M MassAction
Gbeta_M+Ga_GDP_MG_GDP_M reconstitution M GeneralKinetics
PIP2_MPI4P_M VSP M MassAction
Palk_C1Palk_C2 r12 C MassAction
PIP2_MIP3_C+DAG_M PIP2hydr M GeneralKinetics
GaGTP_PLC_MGaGDP_PLC_M GTPase_GaP M GeneralKinetics
Ca_C+Fura2_CCa_Fura2_C Cabind_Fura2 C MassAction
noninactiveIP3RinactiveIP3R h_reaction_IP3Rinactivation ERM GeneralKinetics
PI4P_MPIP2_M PIP5K_5Pase M MassAction
IP3_C+LibraVIII_CIP3_LibraVIII_C IP3_LibraVIII C MassAction
DAG_M+C1_dom_CC1_DAG_M C1bindDAG M MassAction
IP3_C IP3Pase_KVH C GeneralKinetics
Gbeta_M+RL_MRLGbeta_M G2beta M MassAction
PI4P_MDAG_M PLC_on_PI4P M GeneralKinetics
oxoM_EX+RG_GDP_MRLG_GDP_M L2 M MassAction
PI_MPI4P_M PI4K M MassAction
Ca_Buffer_low_aff+Ca_CCa_Buffer_low_aff_Ca Ca_Buffering_low_aff C MassAction
G_GDP_M+R_MRG_GDP_M G1 M MassAction
RG_GDP_MGaGTP_M+RGbeta_M NE_RG M MassAction
G_GDP_MGbeta_M+GaGTP_M NE_G M MassAction
PI4P_MPI_M PI4Pase M MassAction
P4M_dom_C+PI4P_MP4M_PI4P_M P4M_bind_PI4P M MassAction
Ca_Buffer_high_aff+Ca_CCa_Buffer_high_aff_Ca Ca_Buffering_high_aff C MassAction
Palk_C2Palk_C3 r23 C MassAction
GaGDP_PLC_MPLC_M+Ga_GDP_M PLCdiss M MassAction
GaGTP_MGa_GDP_M GTPase_Ga M GeneralKinetics
PH_YFP_C+IP3_CIP3_PH_YFP_C PH_YFP_IP3 C MassAction
KCNQ_M+PIP2_MKCNQ_PIP2_M PIP2bindKCNQ M GeneralKinetics
GaGDP_PLC_MGaGTP_PLC_M NE_GaP M GeneralKinetics
Gbeta_M+R_MRGbeta_M G1beta M MassAction

Structures

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

Species

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
simulations 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) - simulations go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Ca_Buffer_high_aff 4.9721916 [uM] 0.0 [um2/s] C
Ca_Buffer_high_aff_Ca 5.0278084 [uM] 0.0 [um2/s] C
IP3R_IRBIT 0.01 [uM] 0.0 [um2/s] C
IP3_PH_YFP_C 0.0 [uM] 0.0 [um2/s] C
PH_YFP_C 0.0 [uM] 0.0 [um2/s] C
K_C 100000.0 [uM] 0.0 [um2/s] C
Ca_Buffer_low_aff_Ca 1.836644 [uM] 0.0 [um2/s] C
P4M_dom_C 0.0 [uM] 0.0 [um2/s] C
Ca_Fura2_C 0.0 [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
Fura2_C 0.0 [uM] 0.0 [um2/s] C
C1_dom_C 0.0 [uM] 0.0 [um2/s] C
Ca_C 0.101 [uM] 0.0 [um2/s] C
Palk_C1 1.0 [uM] 0.0 [um2/s] C
IP3_C 0.02 [uM] 0.0 [um2/s] C
Tubby_C 0.0 [uM] 0.0 [um2/s] C
Palk_O4 0.0 [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
Ca_Buffer_low_aff 18.163356 [uM] 0.0 [um2/s] C
IP3R_IP3 0.0 [uM] 0.0 [um2/s] C
Ca_Ca_store 361.8635 [uM] 0.0 [um2/s] Ca_store
K_EX 0.0 [uM] 0.0 [um2/s] EX
OxoM_conc_EX 10.0 [uM] 0.0 [um2/s] EX
oxoM_EX 0.0 [uM] 0.0 [um2/s] EX
R_M 15.87 [uM] 0.0 [um2/s] M
RLGbeta_M 0.0 [uM] 0.0 [um2/s] M
RL_M 0.0 [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
Tubby_PIP2_M 0.0 [uM] 0.0 [um2/s] M
KCNQ_PIP2_M 0.0 [uM] 0.0 [um2/s] M
boundPIP2_M (( - 1.0 + foldPIP2) * PIP2_M) [uM] 0.0 [um2/s] M
GaGDP_PLC_M 0.0 [uM] 0.0 [um2/s] M
GaGTP_M 0.0 [uM] 0.0 [um2/s] M
Gbeta_M 0.0 [uM] 0.0 [um2/s] M
DAG_M 13.0 [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
PI_M 226975.0 [uM] 0.0 [um2/s] M
PA_2AG_M 0.0 [uM] 0.0 [um2/s] M
PIP2_M 3232.0 [uM] 0.0 [um2/s] M
PI4P_M 4540.0 [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
Ga_GDP_M 0.0 [uM] 0.0 [um2/s] M
PLC_M 3.12 [uM] 0.0 [um2/s] M
RGbeta_M 0.0 [uM] 0.0 [um2/s] M
C1_DAG_M 0.0 [uM] 0.0 [um2/s] M
P4M_PI4P_M 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) - simulations go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Oxo-M 600.0

KeepEvery 10

KeepAtMost 1000

VSP 600.0

KeepEvery 10

KeepAtMost 1000

Oxo-M with TubbyR332 600.0

KeepEvery 10

KeepAtMost 1000

Oxo-M with fura-2 600.0

KeepEvery 10

KeepAtMost 1000

Oxo-M with PH-PLCd1 600.0

KeepEvery 10

KeepAtMost 1000

Oxo-M with LIBRAVIII 600.0

KeepEvery 10

KeepAtMost 1000

Oxo-M with C1-domain 600.0

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 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]

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