Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| AKAP_PLBAKAP_pPLB | PLB_phosphorylation | c0 | HMMIrreversible | |
| R2_cAMPR2 | R2_cAMP_unloading_PDE | c0 | HMMIrreversible | |
| R2_cAMPR2+cAMP | R2_cAMP_unloading | c0 | GeneralKinetics | |
| AKAP+PLBAKAP_PLB | AKAP_PLb_binding | c0 | MassAction | |
| cAMP | cAMP_degradation | c0 | HMMIrreversible | |
| AC+GsGsAC | activate_AC | c0 | MassAction | |
| GsACAC+pGs | deactivate_AC | c0 | HMMIrreversible | |
| C+R2R2C2 | PKA_holoenzyme_formation | c0 | GeneralKinetics | |
| ATPcAMP | produce_cAMP | c0 | HMMIrreversible | |
| cAMP+R2C2R2C1+C | C1_Release | c0 | GeneralKinetics | |
| pPLBPLB | dephosphorylate_PLB | c0 | HMMIrreversible | |
| cAMP+R2C1R2_cAMP+C | C2_Release | c0 | GeneralKinetics | |
| AKAP+pPLBAKAP_pPLB | AKAP-pPLB_dissociation | c0 | MassAction |
PLB_phosphorylation Universal ID's
PLB_phosphorylation Text Annotations
R2_cAMP_unloading_PDE Universal ID's
R2_cAMP_unloading_PDE Text Annotations
R2_cAMP_unloading Universal ID's
R2_cAMP_unloading Text Annotations
AKAP_PLb_binding Universal ID's
AKAP_PLb_binding Text Annotations
cAMP_degradation Universal ID's
cAMP_degradation Text Annotations
activate_AC Universal ID's
activate_AC Text Annotations
deactivate_AC Universal ID's
deactivate_AC Text Annotations
PKA_holoenzyme_formation Universal ID's
PKA_holoenzyme_formation Text Annotations
produce_cAMP Universal ID's
produce_cAMP Text Annotations
C1_Release Universal ID's
C1_Release Text Annotations
dephosphorylate_PLB Universal ID's
dephosphorylate_PLB Text Annotations
C2_Release Universal ID's
C2_Release Text Annotations
AKAP-pPLB_dissociation Universal ID's
AKAP-pPLB_dissociation Text Annotations
Expressions for PLB_phosphorylation
reaction rate
J
((Vmax * AKAP_PLB) / (Km + AKAP_PLB)) [uM.s-1]
Km (1/2 max)
Km
12.5 [uM]
max reaction rate
Vmax
(2.0 * AKAP_PLB * (C / ((2.0 * R2C2) + R2C1 + C)) * kcat_PKA) [uM.s-1]
local
kcat_PKA
21.0 [s-1]
Expressions for R2_cAMP_unloading_PDE
reaction rate
J
((Vmax * R2_cAMP) / (Km + R2_cAMP)) [uM.s-1]
Km (1/2 max)
Km
2.0 [uM]
max reaction rate
Vmax
(kcat * PDE) [uM.s-1]
local
kcat
0.2 [s-1]
Expressions for R2_cAMP_unloading
reaction rate
J
((Kf * R2_cAMP) - (Kr * cAMP * R2)) [uM.s-1]
local
Kr
0.3 [s-1.uM-1]
local
Kf
1.0E-5 [s-1]
Expressions for AKAP_PLb_binding
reaction rate
J
(((Kf * AKAP) * PLB) - (Kr * AKAP_PLB)) [uM.s-1]
forward rate constant
Kf
0.179 [s-1.uM-1]
reverse rate constant
Kr
0.0024 [s-1]
Expressions for cAMP_degradation
reaction rate
J
((Vmax * cAMP) / (Km + cAMP)) [uM.s-1]
Km (1/2 max)
Km
1.3 [uM]
max reaction rate
Vmax
(kcat_PDE * PDE4) [uM.s-1]
local
kcat_PDE
2.0 [s-1]
Expressions for activate_AC
reaction rate
J
(((Kf * AC) * Gs) - (Kr * GsAC)) [uM.s-1]
forward rate constant
Kf
(GsF * AC_On) [s-1.uM-1]
global
AC_On
0.0 [tbd]
global
GsF
0.5 [tbd]
reverse rate constant
Kr
(0.005 * AC_On) [s-1]
global
AC_On
0.0 [tbd]
Expressions for deactivate_AC
reaction rate
J
((Vmax * GsAC) / (Km + GsAC)) [uM.s-1]
Km (1/2 max)
Km
10.0 [uM]
max reaction rate
Vmax
((kcat_PKA * C) * PKA_AC_Fraction) [uM.s-1]
global
PKA_AC_Fraction
0.05 [tbd]
local
kcat_PKA
21.0 [s-1]
Expressions for PKA_holoenzyme_formation
reaction rate
J
((Kf * C * R2) - (Kr * R2C2)) [uM.s-1]
local
Kr
1.86E-4 [s-1]
local
Kf
0.799 [s-1.uM-1]
Expressions for produce_cAMP
reaction rate
J
((Vmax * ATP) / (Km + ATP)) [uM.s-1]
Km (1/2 max)
Km
315.0 [uM]
max reaction rate
Vmax
((kcat_AC * GsAC) + (kcat_AC * AC_baseline)) [uM.s-1]
global
kcat_AC
1.4 [tbd]
Expressions for C1_Release
reaction rate
J
(((cAMP ^ h) / ((Kd_cAMP ^ h) + (cAMP ^ h))) * R2C2) [uM.s-1]
local
Kd_cAMP
2.9 [tbd]
local
h
1.4 [tbd]
Expressions for dephosphorylate_PLB
reaction rate
J
((Vmax * pPLB) / (Km + pPLB)) [uM.s-1]
Km (1/2 max)
Km
2.7 [uM]
max reaction rate
Vmax
(2.5 * PP) [uM.s-1]
Expressions for C2_Release
reaction rate
J
(((cAMP ^ h) / ((Kd_cAMP ^ h) + (cAMP ^ h))) * R2C1) [uM.s-1]
local
Kd_cAMP
2.9 [tbd]
local
h
1.4 [tbd]
Expressions for AKAP-pPLB_dissociation
reaction rate
J
(((Kf * AKAP) * pPLB) - (Kr * AKAP_pPLB)) [uM.s-1]
forward rate constant
Kf
0.179 [s-1.uM-1]
reverse rate constant
Kr
(0.0024 * nR) [s-1]
global
nR
1.0 [tbd]
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| R2 | c0 | ||
| AC_baseline | c0 | ||
| C | c0 | ||
| AKAP | c0 | ||
| PDE | c0 | ||
| GsAC | c0 | ||
| AKAP_PLB | c0 | ||
| PLB | c0 | ||
| AKAP_pPLB | c0 | ||
| pPLB | c0 | ||
| PP | c0 | ||
| ATP | c0 | ||
| pGs | c0 | ||
| R2C1 | c0 | ||
| R2C2 | c0 | ||
| PDE4 | c0 | ||
| R2_cAMP | c0 | ||
| cAMP | c0 | ||
| AC | c0 | ||
| Gs | c0 |
R2 Universal ID's
R2 Text Annotations
AC_baseline Universal ID's
AC_baseline Text Annotations
C Universal ID's
C Text Annotations
AKAP Universal ID's
AKAP Text Annotations
PDE Universal ID's
PDE Text Annotations
GsAC Universal ID's
GsAC Text Annotations
AKAP_PLB Universal ID's
AKAP_PLB Text Annotations
PLB Universal ID's
PLB Text Annotations
AKAP_pPLB Universal ID's
AKAP_pPLB Text Annotations
pPLB Universal ID's
pPLB Text Annotations
PP Universal ID's
PP Text Annotations
ATP Universal ID's
ATP Text Annotations
pGs Universal ID's
pGs Text Annotations
R2C1 Universal ID's
R2C1 Text Annotations
R2C2 Universal ID's
R2C2 Text Annotations
PDE4 Universal ID's
PDE4 Text Annotations
R2_cAMP Universal ID's
R2_cAMP Text Annotations
cAMP Universal ID's
cAMP Text Annotations
AC Universal ID's
AC Text Annotations
Gs Universal ID's
Gs Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| PLB 2.0uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| PLB 0.2uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| PLB 5.0uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| cAMP_PDE_Gs_param |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| Copy of PLB 0.2uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from PLB 0.2uM) (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| Copy of PLB 2.0uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from Copy of PLB 0.2uM) (copied from PLB 0.2uM) (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
| PLB 38uM |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from Copy of PLB 2.0uM) (copied from Copy of PLB 0.2uM) (copied from PLB 0.2uM) (copied from PLB 2.0uM) cloned from 'Copy of Application0' owned by user Marc.Rigatti (copied from Application0) |
PLB 2.0uM Universal ID's
PLB 2.0uM Text Annotations
PLB 0.2uM Universal ID's
PLB 0.2uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
Copy of PLB 0.2uM Universal ID's
Copy of PLB 0.2uM Text Annotations
Copy of PLB 2.0uM Universal ID's
Copy of PLB 2.0uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
Specifications (Species) - PLB 2.0uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.2 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 0.2 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.5 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - PLB 2.0uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - PLB 2.0uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation1 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
PLB 2.0uM Universal ID's
PLB 2.0uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - PLB 0.2uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.2 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 0.2 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.5 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - PLB 0.2uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - PLB 0.2uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation7 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
PLB 0.2uM Universal ID's
PLB 0.2uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - PLB 5.0uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.2 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 5.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.25 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - PLB 5.0uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - PLB 5.0uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation13 | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| PDE_0.2 | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| PDE_0.3 | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| PDE_0.4 | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| AC_0.15_PDE_0.3 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of PDE_0.4 | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of AC_0.15_PDE_0.3 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
PLB 5.0uM Universal ID's
PLB 5.0uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - cAMP_PDE_Gs_param go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.15 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 2.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 1.0 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.25 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - cAMP_PDE_Gs_param go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | excluded |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | excluded |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | excluded |
| C2_Release | included |
| AKAP-pPLB_dissociation | excluded |
Simulations - cAMP_PDE_Gs_param go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| AC_0.2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Simulation2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| AC_0.15 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of AC_0.15 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| AC_0.15 PDE_0.2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline AC PDE_0.2 | 4999.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of AC_0.15 PDE_0.2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of AC_0.15 PDE_0.2 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
cAMP_PDE_Gs_param Universal ID's
cAMP_PDE_Gs_param Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - Copy of PLB 0.2uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.15 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 0.2 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.75 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - Copy of PLB 0.2uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - Copy of PLB 0.2uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation3 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
Copy of PLB 0.2uM Universal ID's
Copy of PLB 0.2uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - Copy of PLB 2.0uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.15 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 2.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.75 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - Copy of PLB 2.0uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - Copy of PLB 2.0uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation4 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
Copy of PLB 2.0uM Universal ID's
Copy of PLB 2.0uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 5000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - PLB 38uM go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| R2 | 0.19907870489108428 [uM] | 0.0 [um2/s] | c0 |
| AC_baseline | 0.15 [uM] | 0.0 [um2/s] | c0 |
| C | 0.027848889674816232 [uM] | 0.0 [um2/s] | c0 |
| AKAP | 0.02 [uM] | 0.0 [um2/s] | c0 |
| PDE | 0.2 [uM] | 0.0 [um2/s] | c0 |
| GsAC | 0.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_PLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PLB | 38.0 [uM] | 0.0 [um2/s] | c0 |
| AKAP_pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| pPLB | 1.0E-6 [uM] | 0.0 [um2/s] | c0 |
| PP | 0.01 [uM] | 0.0 [um2/s] | c0 |
| ATP | 5000.0 [uM] | 0.0 [um2/s] | c0 |
| pGs | 0.0 [uM] | 0.0 [um2/s] | c0 |
| R2C1 | 0.05738370344261173 [uM] | 0.0 [um2/s] | c0 |
| R2C2 | 0.0573837034412846 [uM] | 0.0 [um2/s] | c0 |
| PDE4 | 0.2 [uM] | 0.0 [um2/s] | c0 |
| R2_cAMP | 10.686153888225018 [uM] | 0.0 [um2/s] | c0 |
| cAMP | 0.49196111583075475 [uM] | 0.0 [um2/s] | c0 |
| AC | 0.5 [uM] | 0.0 [um2/s] | c0 |
| Gs | 0.75 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - PLB 38uM go to Simulations
| Name | Enabled? |
|---|---|
| PLB_phosphorylation | included |
| R2_cAMP_unloading_PDE | included |
| R2_cAMP_unloading | included |
| AKAP_PLb_binding | included |
| cAMP_degradation | included |
| activate_AC | included |
| deactivate_AC | included |
| PKA_holoenzyme_formation | included |
| produce_cAMP | included |
| C1_Release | included |
| dephosphorylate_PLB | included |
| C2_Release | included |
| AKAP-pPLB_dissociation | included |
Simulations - PLB 38uM go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Baseline cAMP low | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~1uM | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~0.62uM | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~0.62uM increased PP | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~0.62uM Km PP 10 vs 2.7 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~0.62uM Km PP 5 | 10000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Baseline cAMP low PLB 50 | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Baseline cAMP low | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Baseline cAMP low PLB 50 | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Copy of Baseline cAMP low PLB 50 | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Copy of Copy of Baseline cAMP low PLB 50 | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Copy of Copy of Baseline cAMP low PLB 50 1 | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Baseline cAMP ~0.62uM | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Baseline cAMP ~0.62uM Increased PP | 30000.0 |
KeepEvery 1 KeepAtMost 1000 |
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
PLB 38uM Universal ID's
PLB 38uM Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| AC_Stimulation | on condition: (t > 15000.0) | AC_On --> 1.0 |
Geometry non-spatial1509593381
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| AC_On | 0.0[tbd] |
| kcat_AC | 1.4[tbd] |
| PKA_AC_Fraction | 0.05[tbd] |
| nR | 1.0[tbd] |
| GsF | 0.5[tbd] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
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 | PLB 2.0uM.bngl , PLB 0.2uM.bngl , PLB 5.0uM.bngl , cAMP_PDE_Gs_param.bngl , Copy of PLB 0.2uM.bngl , Copy of PLB 2.0uM.bngl , PLB 38uM.bngl |
| SBML | PLB 2.0uM.sbml , PLB 0.2uM.sbml , PLB 5.0uM.sbml , cAMP_PDE_Gs_param.sbml , Copy of PLB 0.2uM.sbml , Copy of PLB 2.0uM.sbml , PLB 38uM.sbml |
| Matlab | PLB 2.0uM.m , PLB 0.2uM.m , PLB 5.0uM.m , cAMP_PDE_Gs_param.m , Copy of PLB 0.2uM.m , Copy of PLB 2.0uM.m , PLB 38uM.m |
| NFSim XML | PLB 2.0uM.xml , PLB 0.2uM.xml , PLB 5.0uM.xml , cAMP_PDE_Gs_param.xml , Copy of PLB 0.2uM.xml , Copy of PLB 2.0uM.xml , PLB 38uM.xml |