Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| cAMP_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment | reaction9 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C_Unnamed_compartment | r2 | Unnamed compartment | MassAction | |
| PKA_B_C2_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment | reaction15 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_B_A_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment | reaction8 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_B_A_C2_Unnamed_compartment | reaction1 | Unnamed compartment | MassAction | |
| PKA_B_A_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment | reaction4 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_Unnamed_compartment | reaction7 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment | reaction18 | Unnamed compartment | MassAction | |
| PKA_B_C_Unnamed_compartment+C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment | r1 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_AA_BB_Unnamed_compartmentPKA_BB_AA_C_Unnamed_compartment | reaction3 | Unnamed compartment | MassAction |
reaction9 Universal ID's
reaction9 Text Annotations
r2 Universal ID's
r2 Text Annotations
reaction15 Universal ID's
reaction15 Text Annotations
reaction8 Universal ID's
reaction8 Text Annotations
reaction1 Universal ID's
reaction1 Text Annotations
reaction4 Universal ID's
reaction4 Text Annotations
reaction7 Universal ID's
reaction7 Text Annotations
reaction18 Universal ID's
reaction18 Text Annotations
r1 Universal ID's
r1 Text Annotations
reaction3 Universal ID's
reaction3 Text Annotations
Expressions for reaction9
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_A_C_Unnamed_compartment) - (Kr * PKA_BB_AA_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.003 [uM-1.s-1]
reverse rate constant
Kr
(F7 * A2_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A2_kd
3.52E-5 [tbd]
global
F7
218000.0 [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
5.0 [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
3.14E-8 [uM]
global
F1
1.0 [tbd]
global
C_kr2
5.0 [uM-1.s-1]
Expressions for reaction15
reaction rate
J
(((Kf * PKA_B_C2_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_C2_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_A_binding) [s-1.uM-1]
global
F_A_binding
0.003 [uM-1.s-1]
reverse rate constant
Kr
(F1 * F2 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A_kd
8.34E-7 [tbd]
global
F2
1.0 [tbd]
global
F1
1.0 [tbd]
Expressions for reaction8
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_A_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
0.003 [uM-1.s-1]
reverse rate constant
Kr
(2.0 * A2_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A2_kd
3.52E-5 [tbd]
Expressions for reaction1
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_B_A_C_Unnamed_compartment) - (Kr * PKA_B_A_C2_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
5.0 [uM-1.s-1]
reverse rate constant
Kr
(F4 * F2 * C_kd2 * C_kr3) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.14E-8 [uM]
global
F2
1.0 [tbd]
global
F4
125000.0 [tbd]
global
C_kd2
1.96E-5 [uM]
global
C_kr3
5.0 [uM-1.s-1]
Expressions for reaction4
reaction rate
J
(((Kf * PKA_B_A_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_B_A_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
5.0 [uM-1.s-1]
reverse rate constant
Kr
(F1 * F3 * C_kr3 * C_kd) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.14E-8 [uM]
global
F1
1.0 [tbd]
global
F3
185.0 [tbd]
global
C_kr3
5.0 [uM-1.s-1]
Expressions for reaction7
reaction rate
J
(((Kf * PKA_B_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_A_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_A_binding) [s-1.uM-1]
global
F_A_binding
0.003 [uM-1.s-1]
reverse rate constant
Kr
(A_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A_kd
8.34E-7 [tbd]
Expressions for reaction18
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_C_Unnamed_compartment) - (Kr * PKA_B_A_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_A_binding [s-1.uM-1]
global
F_A_binding
0.003 [uM-1.s-1]
reverse rate constant
Kr
(F1 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A_kd
8.34E-7 [tbd]
global
F1
1.0 [tbd]
Expressions for r1
reaction rate
J
(((Kf * PKA_B_C_Unnamed_compartment) * 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
5.0 [uM-1.s-1]
reverse rate constant
Kr
(2.0 * F2 * C_kd2 * C_kr2) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.14E-8 [uM]
global
F2
1.0 [tbd]
global
C_kd2
1.96E-5 [uM]
global
C_kr2
5.0 [uM-1.s-1]
Expressions for reaction3
reaction rate
J
(((Kf * C_Unnamed_compartment) * PKA_AA_BB_Unnamed_compartment) - (Kr * PKA_BB_AA_C_Unnamed_compartment)) [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
5.0 [uM-1.s-1]
reverse rate constant
Kr
(F3 * C_kd * C_kr5 * F1 * F7) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.14E-8 [uM]
global
F1
1.0 [tbd]
global
F3
185.0 [tbd]
global
C_kr5
5.0 [uM-1.s-1]
global
F7
218000.0 [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_C2_Unnamed_compartment | Unnamed compartment | ||
| PKA_AA_BB_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_C_Unnamed_compartment | Unnamed compartment | ||
| C_Unnamed_compartment | Unnamed compartment | ||
| PKA_BB_AA_C_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_A_C2_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_A_C_Unnamed_compartment | Unnamed compartment | ||
| cAMP_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_A_Unnamed_compartment | Unnamed compartment |
PKA_B_C2_Unnamed_compartment Universal ID's
PKA_B_C2_Unnamed_compartment Text Annotations
PKA_AA_BB_Unnamed_compartment Universal ID's
PKA_AA_BB_Unnamed_compartment Text Annotations
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_BB_AA_C_Unnamed_compartment Universal ID's
PKA_BB_AA_C_Unnamed_compartment Text Annotations
PKA_B_A_C2_Unnamed_compartment Universal ID's
PKA_B_A_C2_Unnamed_compartment Text Annotations
PKA_B_A_C_Unnamed_compartment Universal ID's
PKA_B_A_C_Unnamed_compartment Text Annotations
cAMP_Unnamed_compartment Universal ID's
cAMP_Unnamed_compartment Text Annotations
PKA_B_A_Unnamed_compartment Universal ID's
PKA_B_A_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_C2_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_AA_BB_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| 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_BB_AA_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_A_C2_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_A_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| cAMP_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_A_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 | 5000000.0 |
KeepEvery 20 KeepAtMost 6000 |
| Copy of Copy of Simulation0 | 5000000.0 |
KeepEvery 20 KeepAtMost 6000 |
| free R more points | 5000000.0 |
KeepEvery 20 KeepAtMost 6000 |
| Holo more points | 5000000.0 |
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 | 0.003175[uM-1.s-1] |
| B_kd | 0.324[tbd] |
| B_factor | 5.0[tbd] |
| F_A_binding | 0.003[uM-1.s-1] |
| A_kd | 8.34E-7[tbd] |
| A_factor | 23.0[tbd] |
| C_kr | 0.0023[s-1] |
| C_kd | 3.14E-8[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] |
| A1_factor | 226.0[tbd] |
| A2_factor | 151.0[tbd] |
| B2_factor | 602.0[tbd] |
| A2_kd | 3.52E-5[tbd] |
| spots | 2.0[uM] |
| R_A_factor | 1.0[tbd] |
| R_B_factor | 1.0[tbd] |
| F2 | 1.0[tbd] |
| F1 | 1.0[tbd] |
| F3 | 185.0[tbd] |
| F4 | 125000.0[tbd] |
| C_kd2 | 1.96E-5[uM] |
| C_kr2 | 5.0[uM-1.s-1] |
| C_kr3 | 5.0[uM-1.s-1] |
| C_kr4 | 0.0[uM-1.s-1] |
| C_kr5 | 5.0[uM-1.s-1] |
| F7 | 218000.0[tbd] |