Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_BBB_Unnamed_compartment | reaction21 | Unnamed compartment | MassAction | |
| PKA_BBB_Unnamed_compartment+C_Unnamed_compartmentPKA_C_BB_Unnamed_compartment | r0 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_Unnamed_compartmentPKA_C_Unnamed_compartment | reaction5 | Unnamed compartment | MassAction | |
| PKA_C_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_C_BB_Unnamed_compartment | reaction6 | Unnamed compartment | MassAction |
reaction21 Universal ID's
reaction21 Text Annotations
r0 Universal ID's
r0 Text Annotations
reaction5 Universal ID's
reaction5 Text Annotations
reaction6 Universal ID's
reaction6 Text Annotations
Expressions for reaction21
reaction rate
J
(((Kf * PKA_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_BBB_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1.uM-1]
global
F_B_binding
3.175 [uM-1.s-1]
reverse rate constant
Kr
(B_kd * F_B_binding) [s-1]
global
F_B_binding
3.175 [uM-1.s-1]
global
B_kd
4.16E-4 [tbd]
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
4.397E-7 [uM]
reverse rate constant
Kr
(C_kr * F1) [s-1]
global
C_kr
2.3 [s-1]
global
F1
3218.4 [1]
Expressions for reaction5
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_Unnamed_compartment) - (Kr * PKA_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
4.397E-7 [uM]
reverse rate constant
Kr
C_kr [s-1]
global
C_kr
2.3 [s-1]
Expressions for reaction6
reaction rate
J
(((Kf * PKA_C_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_C_BB_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1.uM-1]
global
F_B_binding
3.175 [uM-1.s-1]
reverse rate constant
Kr
(F1 * B_kd * F_B_binding) [s-1]
global
F_B_binding
3.175 [uM-1.s-1]
global
B_kd
4.16E-4 [tbd]
global
F1
3218.4 [1]
Structures
| Name | Type | Electrical |
|---|---|---|
| Unnamed compartment | Compartment | (+) (-) |
Unnamed compartment Universal ID's
Unnamed compartment Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| cAMP_Unnamed_compartment | Unnamed compartment | ||
| PKA_Unnamed_compartment | Unnamed compartment | ||
| PKA_C_BB_Unnamed_compartment | Unnamed compartment | ||
| PKA_BBB_Unnamed_compartment | Unnamed compartment | ||
| C_Unnamed_compartment | Unnamed compartment | ||
| PKA_C_Unnamed_compartment | Unnamed compartment |
cAMP_Unnamed_compartment Universal ID's
cAMP_Unnamed_compartment Text Annotations
PKA_Unnamed_compartment Universal ID's
PKA_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
PKA_C_Unnamed_compartment Universal ID's
PKA_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 |
|---|---|---|---|
| cAMP_Unnamed_compartment | 200.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_Unnamed_compartment | 0.025 [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 | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| C_Unnamed_compartment | 5.025 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_C_Unnamed_compartment | 0.0 [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 |
| More points Holo | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
| More points free R | 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 | 4.16E-4[tbd] |
| B_factor | 5.0[tbd] |
| F_A_binding | 0.3[uM-1.s-1] |
| A_kd | 0.007473[tbd] |
| A_factor | 23.0[tbd] |
| C_kr | 2.3[s-1] |
| C_kd | 4.397E-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 | 3218.4[1] |
| F2 | 264.0[tbd] |
| F3 | 0.0[tbd] |