Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment | r7 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment | r2 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment | r1 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment | reaction8 | Unnamed compartment | MassAction | |
| PKA_A_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C2 | r5 | Unnamed compartment | MassAction | |
| PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2 | r6 | Unnamed compartment | MassAction | |
| PKA_AA_BB_Unnamed_compartment+C_Unnamed_compartmentPKA_AA_BB_C | r0 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_A_B_C_Unnamed_compartmentPKA_AA_BB_C | r4 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_A_B_Unnamed_compartment | reaction7 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_A_B_Unnamed_compartmentPKA_A_B_C_Unnamed_compartment | reaction4 | Unnamed compartment | MassAction |
r7 Universal ID's
r7 Text Annotations
r2 Universal ID's
r2 Text Annotations
r1 Universal ID's
r1 Text Annotations
reaction8 Universal ID's
reaction8 Text Annotations
r5 Universal ID's
r5 Text Annotations
r6 Universal ID's
r6 Text Annotations
r0 Universal ID's
r0 Text Annotations
r4 Universal ID's
r4 Text Annotations
reaction7 Universal ID's
reaction7 Text Annotations
reaction4 Universal ID's
reaction4 Text Annotations
Expressions for r7
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_A_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.2 [uM-1.s-1]
reverse rate constant
Kr
(F3 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.2 [uM-1.s-1]
global
A_kd
0.001048 [tbd]
global
F3
13.5 [tbd]
Expressions for r2
reaction rate
J
(((Kf * PKA_B_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * C_kr2) [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr2
1.0 [uM-1.s-1]
reverse rate constant
Kr
(F1 * C_kr2 * C_kd) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
2.518E-7 [uM]
global
F1
1.0 [tbd]
global
C_kr2
1.0 [uM-1.s-1]
Expressions for r1
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
C_kr2 [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr2
1.0 [uM-1.s-1]
reverse rate constant
Kr
(2.0 * C_kd2 * C_kr2 * F2) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
2.518E-7 [uM]
global
F2
2310.0 [tbd]
global
C_kd2
1.4E-6 [tbd]
global
C_kr2
1.0 [uM-1.s-1]
Expressions for reaction8
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_A_B_Unnamed_compartment) - (Kr * PKA_AA_BB_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.2 [uM-1.s-1]
reverse rate constant
Kr
(2.0 * A2_kd * F_A_binding) [s-1]
global
F_A_binding
0.2 [uM-1.s-1]
global
A2_kd
0.0057 [uM]
Expressions for r5
reaction rate
J
(((Kf * PKA_A_B_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_A_C2)) [uM.s-1]
forward rate constant
Kf
C_kr3 [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr3
1.0 [uM-1.s-1]
reverse rate constant
Kr
(F4 * C_kd2 * C_kr3 * F2) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
2.518E-7 [uM]
global
F2
2310.0 [tbd]
global
F4
206.0 [tbd]
global
C_kd2
1.4E-6 [tbd]
global
C_kr3
1.0 [uM-1.s-1]
Expressions for r6
reaction rate
J
(((Kf * PKA_B_C2_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_C2)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_A_binding) [s-1.uM-1]
global
F_A_binding
0.2 [uM-1.s-1]
reverse rate constant
Kr
(F3 * F4 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.2 [uM-1.s-1]
global
A_kd
0.001048 [tbd]
global
F3
13.5 [tbd]
global
F4
206.0 [tbd]
Expressions for r0
reaction rate
J
(((Kf * PKA_AA_BB_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_AA_BB_C)) [uM.s-1]
forward rate constant
Kf
(2.0 * C_kr5) [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr5
1.0 [uM-1.s-1]
reverse rate constant
Kr
(F7 * C_kd * C_kr5 * F1 * F3) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
2.518E-7 [uM]
global
F1
1.0 [tbd]
global
F3
13.5 [tbd]
global
C_kr5
1.0 [uM-1.s-1]
global
F7
1380.0 [tbd]
Expressions for r4
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_A_B_C_Unnamed_compartment) - (Kr * PKA_AA_BB_C)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.2 [uM-1.s-1]
reverse rate constant
Kr
(F7 * A2_kd * F_A_binding) [s-1]
global
F_A_binding
0.2 [uM-1.s-1]
global
F7
1380.0 [tbd]
global
A2_kd
0.0057 [uM]
Expressions for reaction7
reaction rate
J
(((Kf * PKA_B_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_A_B_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_A_binding) [s-1.uM-1]
global
F_A_binding
0.2 [uM-1.s-1]
reverse rate constant
Kr
(A_kd * F_A_binding) [s-1]
global
F_A_binding
0.2 [uM-1.s-1]
global
A_kd
0.001048 [tbd]
Expressions for reaction4
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_A_B_Unnamed_compartment) - (Kr * PKA_A_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
C_kr3 [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr3
1.0 [uM-1.s-1]
reverse rate constant
Kr
(F3 * C_kd * C_kr3 * F1) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
2.518E-7 [uM]
global
F1
1.0 [tbd]
global
F3
13.5 [tbd]
global
C_kr3
1.0 [uM-1.s-1]
Structures
| Name | Type | Electrical |
|---|---|---|
| Unnamed compartment | Compartment | (+) (-) |
Unnamed compartment Universal ID's
Unnamed compartment Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| PKA_B_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_C_Unnamed_compartment | Unnamed compartment | ||
| C_Unnamed_compartment | Unnamed compartment | ||
| PKA_A_B_C_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_C2_Unnamed_compartment | Unnamed compartment | ||
| PKA_A_B_Unnamed_compartment | Unnamed compartment | ||
| PKA_AA_BB_C | Unnamed compartment | ||
| PKA_B_A_C2 | Unnamed compartment | ||
| PKA_AA_BB_Unnamed_compartment | Unnamed compartment | ||
| cAMP_Unnamed_compartment | Unnamed compartment |
PKA_B_Unnamed_compartment Universal ID's
PKA_B_Unnamed_compartment Text Annotations
PKA_B_C_Unnamed_compartment Universal ID's
PKA_B_C_Unnamed_compartment Text Annotations
C_Unnamed_compartment Universal ID's
C_Unnamed_compartment Text Annotations
PKA_A_B_C_Unnamed_compartment Universal ID's
PKA_A_B_C_Unnamed_compartment Text Annotations
PKA_B_C2_Unnamed_compartment Universal ID's
PKA_B_C2_Unnamed_compartment Text Annotations
PKA_A_B_Unnamed_compartment Universal ID's
PKA_A_B_Unnamed_compartment Text Annotations
PKA_AA_BB_C Universal ID's
PKA_AA_BB_C Text Annotations
PKA_B_A_C2 Universal ID's
PKA_B_A_C2 Text Annotations
PKA_AA_BB_Unnamed_compartment Universal ID's
PKA_AA_BB_Unnamed_compartment Text Annotations
cAMP_Unnamed_compartment Universal ID's
cAMP_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_Unnamed_compartment | 0.0125 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| C_Unnamed_compartment | 5.025 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_A_B_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_C2_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_A_B_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_AA_BB_C | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_A_C2 | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_AA_BB_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| cAMP_Unnamed_compartment | 1000.0 [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 free R | 500000.0 |
KeepEvery 20 KeepAtMost 6000 |
| More points Holo | 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 | 0.0031[uM-1.s-1] |
| B_kd | 0.0029900000000000005[tbd] |
| B_factor | 5.0[tbd] |
| F_A_binding | 0.2[uM-1.s-1] |
| A_kd | 0.001048[tbd] |
| A_factor | 23.0[tbd] |
| C_kr | 0.0023[s-1] |
| C_kd | 2.518E-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] |
| B1_factor | 1.0[tbd] |
| F1 | 1.0[tbd] |
| F2 | 2310.0[tbd] |
| F3 | 13.5[tbd] |
| F4 | 206.0[tbd] |
| C_kd2 | 1.4E-6[tbd] |
| F5 | 275.0[tbd] |
| C_kr1 | 1.0[uM-1.s-1] |
| C_kr2 | 1.0[uM-1.s-1] |
| C_kr3 | 1.0[uM-1.s-1] |
| C_kr4 | 300.0[uM-1.s-1] |
| C_kr5 | 1.0[uM-1.s-1] |
| F6 | 1377.71[tbd] |
| F7 | 1380.0[tbd] |
| A2_kd | 0.0057[uM] |