Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| PKA_BBB_Unnamed_compartment+C_Unnamed_compartmentPKA_C_BB_Unnamed_compartment | r0 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_B_Unnamed_compartmentPKA_B_C_Unnamed_compartment | reaction4 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_C_BB_Unnamed_compartmentPKA_B_C_Unnamed_compartment | reaction18 | Unnamed compartment | MassAction | |
| PKA_BBB_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment | reaction7 | Unnamed compartment | MassAction |
r0 Universal ID's
r0 Text Annotations
reaction4 Universal ID's
reaction4 Text Annotations
reaction18 Universal ID's
reaction18 Text Annotations
reaction7 Universal ID's
reaction7 Text Annotations
Expressions for r0
reaction rate
J
(((Kf * PKA_BBB_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_C_BB_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(C_kr / C_kd) [s-1.uM-1]
global
C_kr
2.3 [s-1]
global
C_kd
4.4E-7 [uM]
reverse rate constant
Kr
(C_kr * F1) [s-1]
global
C_kr
2.3 [s-1]
global
F1
3220.0 [1]
Expressions for reaction4
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_B_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(C_kr / C_kd) [s-1.uM-1]
global
C_kr
2.3 [s-1]
global
C_kd
4.4E-7 [uM]
reverse rate constant
Kr
(C_kr * F1 * F2) [s-1]
global
C_kr
2.3 [s-1]
global
F1
3220.0 [1]
global
F2
906.0 [tbd]
Expressions for reaction18
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_C_BB_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.3 [uM-1.s-1]
reverse rate constant
Kr
(F2 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.3 [uM-1.s-1]
global
A_kd
0.00452 [tbd]
global
F2
906.0 [tbd]
Expressions for reaction7
reaction rate
J
(((Kf * PKA_BBB_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.3 [uM-1.s-1]
reverse rate constant
Kr
(A_kd * F_A_binding) [s-1]
global
F_A_binding
0.3 [uM-1.s-1]
global
A_kd
0.00452 [tbd]
Structures
| Name | Type | Electrical |
|---|---|---|
| Unnamed compartment | Compartment | (+) (-) |
Unnamed compartment Universal ID's
Unnamed compartment Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| PKA_B_C_Unnamed_compartment | Unnamed compartment | ||
| cAMP_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_Unnamed_compartment | Unnamed compartment | ||
| PKA_C_BB_Unnamed_compartment | Unnamed compartment | ||
| PKA_BBB_Unnamed_compartment | Unnamed compartment | ||
| C_Unnamed_compartment | Unnamed compartment |
PKA_B_C_Unnamed_compartment Universal ID's
PKA_B_C_Unnamed_compartment Text Annotations
cAMP_Unnamed_compartment Universal ID's
cAMP_Unnamed_compartment Text Annotations
PKA_B_Unnamed_compartment Universal ID's
PKA_B_Unnamed_compartment Text Annotations
PKA_C_BB_Unnamed_compartment Universal ID's
PKA_C_BB_Unnamed_compartment Text Annotations
PKA_BBB_Unnamed_compartment Universal ID's
PKA_BBB_Unnamed_compartment Text Annotations
C_Unnamed_compartment Universal ID's
C_Unnamed_compartment Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| test |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
test Universal ID's
test Text Annotations
Specifications (Species) - test go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| PKA_B_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| cAMP_Unnamed_compartment | 200.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_C_BB_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_BBB_Unnamed_compartment | 0.025 [uM] | 0.0 [um2/s] | Unnamed compartment |
| C_Unnamed_compartment | 5.025 [uM] | 0.0 [um2/s] | Unnamed compartment |
Specifications (Reaction) - test go to Simulations
Simulations - test go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 1200.0 |
KeepEvery 20 KeepAtMost 6000 |
| Copy of Simulation0 | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
| Copy of Copy of Simulation0 | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
| Holo more points | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
| free R more points | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
test Universal ID's
test Text Annotations
test Universal ID's
test Text Annotations
test Universal ID's
test Text Annotations
test Universal ID's
test Text Annotations
test Universal ID's
test Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1833399091
(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 | Unnamed compartment |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| F_B_binding | 3.175[uM-1.s-1] |
| B_kd | 4.0086700000000004E-5[tbd] |
| B_factor | 5.0[tbd] |
| F_A_binding | 0.3[uM-1.s-1] |
| A_kd | 0.00452[tbd] |
| A_factor | 23.0[tbd] |
| C_kr | 2.3[s-1] |
| C_kd | 4.4E-7[uM] |
| Vm | 0.31[s-1] |
| Kf_A | 0.08[1] |
| Kr_A | 0.012[s-1] |
| Kf_B | 0.082[1] |
| Kr_B | 2.21E-4[s-1] |
| Factor | 50000.0[1] |
| FreeR_factor | 0.0[uM-1.s-1] |
| F1 | 3220.0[1] |
| F2 | 906.0[tbd] |
| F3 | 0.0[tbd] |