Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| cAMP_Unnamed_compartment+PKA_B_A_C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment | reaction17 | Unnamed compartment | MassAction | |
| PKA_BB_A_Unnamed_compartment+C_Unnamed_compartmentPKA_BB_A_C_Unnamed_compartment | r3 | Unnamed compartment | MassAction | |
| PKA_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_Unnamed_compartment | reaction21 | Unnamed compartment | MassAction | |
| PKA_C_Unnamed_compartment+C_Unnamed_compartmentPKA_2C_Unnamed_compartment | reaction0 | 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_B_A_Unnamed_compartmentPKA_BB_A_Unnamed_compartment | reaction22 | Unnamed compartment | MassAction | |
| C_Unnamed_compartment+PKA_Unnamed_compartmentPKA_C_Unnamed_compartment | reaction5 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_C_Unnamed_compartmentPKA_B_C_Unnamed_compartment | reaction6 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_B_A_Unnamed_compartment | reaction7 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_2C_Unnamed_compartmentPKA_B_C2_Unnamed_compartment | reaction11 | Unnamed compartment | MassAction | |
| cAMP_Unnamed_compartment+PKA_B_C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment | reaction18 | Unnamed compartment | MassAction | |
| PKA_B_A_Unnamed_compartment+C_Unnamed_compartmentPKA_B_A_C_Unnamed_compartment | reaction4 | Unnamed compartment | MassAction | |
| PKA_B_Unnamed_compartments0 | r0 | Unnamed compartment | MassAction | |
| s0PKA_BB_A_Unnamed_compartment | r4 | Unnamed compartment | MassAction | |
| PKA_BB_A_Unnamed_compartment+cAMP_Unnamed_compartmentPKA_AA_BB_Unnamed_compartment | reaction8 | Unnamed compartment | MassAction |
reaction17 Universal ID's
reaction17 Text Annotations
r3 Universal ID's
r3 Text Annotations
reaction21 Universal ID's
reaction21 Text Annotations
reaction0 Universal ID's
reaction0 Text Annotations
r2 Universal ID's
r2 Text Annotations
r1 Universal ID's
r1 Text Annotations
reaction22 Universal ID's
reaction22 Text Annotations
reaction5 Universal ID's
reaction5 Text Annotations
reaction6 Universal ID's
reaction6 Text Annotations
reaction7 Universal ID's
reaction7 Text Annotations
reaction11 Universal ID's
reaction11 Text Annotations
reaction18 Universal ID's
reaction18 Text Annotations
reaction4 Universal ID's
reaction4 Text Annotations
r0 Universal ID's
r0 Text Annotations
r4 Universal ID's
r4 Text Annotations
reaction8 Universal ID's
reaction8 Text Annotations
Expressions for reaction17
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_A_C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1.uM-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(F9 * F5 * B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
global
F5
8.27 [tbd]
global
F9
2.288 [tbd]
Expressions for r3
reaction rate
J
(((Kf * PKA_BB_A_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_BB_A_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
C_kr4 [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr4
0.03 [uM-1.s-1]
reverse rate constant
Kr
(C_kd * C_kr4 * F5 * F3) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.27E-8 [uM]
global
F3
1600.0 [tbd]
global
C_kr4
0.03 [uM-1.s-1]
global
F5
8.27 [tbd]
Expressions for reaction21
reaction rate
J
(((Kf * PKA_Unnamed_compartment) * cAMP_Unnamed_compartment) - (Kr * PKA_B_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_B_binding) [s-1.uM-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
Expressions for reaction0
reaction rate
J
(((Kf * PKA_C_Unnamed_compartment) * C_Unnamed_compartment) - (Kr * PKA_2C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
C_kr [s-1.uM-1]
global
C_kr
0.0023 [s-1]
reverse rate constant
Kr
(2.0 * C_kd2 * C_kr) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.27E-8 [uM]
global
C_kd2
1.28E-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
C_kr2 [s-1.uM-1]
global
C_kr
0.0023 [s-1]
global
C_kr2
0.03 [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
3.27E-8 [uM]
global
F1
1.0 [tbd]
global
C_kr2
0.03 [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
0.03 [uM-1.s-1]
reverse rate constant
Kr
(C_kd2 * C_kr2 * F2) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.27E-8 [uM]
global
F2
1540.0 [tbd]
global
C_kd2
1.28E-5 [tbd]
global
C_kr2
0.03 [uM-1.s-1]
Expressions for reaction22
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_B_A_Unnamed_compartment) - (Kr * PKA_BB_A_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1.uM-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(F9 * B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
global
F9
2.288 [tbd]
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
(2.0 * C_kr) [s-1.uM-1]
global
C_kr
0.0023 [s-1]
reverse rate constant
Kr
(C_kr * C_kd) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.27E-8 [uM]
Expressions for reaction6
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_C_Unnamed_compartment) - (Kr * PKA_B_C_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1.uM-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(F1 * B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
global
F1
1.0 [tbd]
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
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
4.88E-4 [tbd]
Expressions for reaction11
reaction rate
J
(((Kf * cAMP_Unnamed_compartment) * PKA_2C_Unnamed_compartment) - (Kr * PKA_B_C2_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_B_binding) [s-1.uM-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(F2 * B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
global
F2
1540.0 [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
(F3 * A_kd * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A_kd
4.88E-4 [tbd]
global
F3
1600.0 [tbd]
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
0.03 [uM-1.s-1]
reverse rate constant
Kr
(F1 * C_kd * C_kr3 * F3) [s-1]
global
C_kr
0.0023 [s-1]
global
C_kd
3.27E-8 [uM]
global
F1
1.0 [tbd]
global
F3
1600.0 [tbd]
global
C_kr3
0.03 [uM-1.s-1]
Expressions for r0
reaction rate
J
((Kf * PKA_B_Unnamed_compartment) - (Kr * s0)) [uM.s-1]
forward rate constant
Kf
F_B_binding [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
reverse rate constant
Kr
(2.0 * B_kd * F_B_binding) [s-1]
global
F_B_binding
0.003175 [uM-1.s-1]
global
B_kd
9.7E-4 [tbd]
Expressions for r4
reaction rate
J
((Kf * s0) - (Kr * PKA_BB_A_Unnamed_compartment)) [uM.s-1]
forward rate constant
Kf
(2.0 * F_A_binding) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
reverse rate constant
Kr
(A_kd * F_A_binding * F9) [s-1]
global
F_A_binding
0.003 [uM-1.s-1]
global
A_kd
4.88E-4 [tbd]
global
F9
2.288 [tbd]
Expressions for reaction8
reaction rate
J
(((Kf * PKA_BB_A_Unnamed_compartment) * cAMP_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
0.00475 [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_A_Unnamed_compartment | Unnamed compartment | ||
| PKA_Unnamed_compartment | Unnamed compartment | ||
| 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 | ||
| PKA_BB_A_C_Unnamed_compartment | Unnamed compartment | ||
| PKA_C_Unnamed_compartment | Unnamed compartment | ||
| PKA_2C_Unnamed_compartment | Unnamed compartment | ||
| C_Unnamed_compartment | Unnamed compartment | ||
| PKA_B_A_C_Unnamed_compartment | Unnamed compartment | ||
| s0 | Unnamed compartment | ||
| PKA_BB_A_Unnamed_compartment | Unnamed compartment | ||
| cAMP_Unnamed_compartment | Unnamed compartment |
PKA_B_A_Unnamed_compartment Universal ID's
PKA_B_A_Unnamed_compartment Text Annotations
PKA_Unnamed_compartment Universal ID's
PKA_Unnamed_compartment Text Annotations
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
PKA_BB_A_C_Unnamed_compartment Universal ID's
PKA_BB_A_C_Unnamed_compartment Text Annotations
PKA_C_Unnamed_compartment Universal ID's
PKA_C_Unnamed_compartment Text Annotations
PKA_2C_Unnamed_compartment Universal ID's
PKA_2C_Unnamed_compartment Text Annotations
C_Unnamed_compartment Universal ID's
C_Unnamed_compartment Text Annotations
PKA_B_A_C_Unnamed_compartment Universal ID's
PKA_B_A_C_Unnamed_compartment Text Annotations
s0 Universal ID's
s0 Text Annotations
PKA_BB_A_Unnamed_compartment Universal ID's
PKA_BB_A_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_A_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_Unnamed_compartment | 0.011 [uM] | 0.0 [um2/s] | Unnamed compartment |
| 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 | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_BB_A_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_2C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| C_Unnamed_compartment | 0.02 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_B_A_C_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| s0 | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| PKA_BB_A_Unnamed_compartment | 0.0 [uM] | 0.0 [um2/s] | Unnamed compartment |
| cAMP_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 | 5000.0 |
KeepEvery 20 KeepAtMost 6000 |
| Copy of Copy of Simulation0 | 50000.0 |
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
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 | 9.7E-4[tbd] |
| B_factor | 5.0[tbd] |
| F_A_binding | 0.003[uM-1.s-1] |
| A_kd | 4.88E-4[tbd] |
| A_factor | 23.0[tbd] |
| C_kr | 0.0023[s-1] |
| C_kd | 3.27E-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 | 0.00475[tbd] |
| spots | 2.0[uM] |
| R_A_factor | 1.0[tbd] |
| R_B_factor | 1.0[tbd] |
| F1 | 1.0[tbd] |
| F2 | 1540.0[tbd] |
| F3 | 1600.0[tbd] |
| F4 | 1550.0[tbd] |
| C_kd2 | 1.28E-5[tbd] |
| C_kr2 | 0.03[uM-1.s-1] |
| C_kr3 | 0.03[uM-1.s-1] |
| C_kr4 | 0.03[uM-1.s-1] |
| F5 | 8.27[tbd] |
| F9 | 2.288[tbd] |