Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| Pin1A_Pin1BivAB | r4 | c0 | MassAction | |
| Pin1+LigPin1_A | r0 | c0 | MassAction | |
| Pin1+LigPin1B_ | r1 | c0 | MassAction | |
| Pin1_APin1BivBA | r6 | c0 | MassAction | |
| Pin1B_Pin1BivBA | r7 | c0 | MassAction | |
| Pin1_A+LigPin1AA | r8 | c0 | MassAction | |
| Lig+Pin1A_Pin1AA | r9 | c0 | MassAction | |
| Pin1B_+LigPin1BB | r12 | c0 | MassAction | |
| Pin1_B+LigPin1BB | r13 | c0 | MassAction | |
| Pin1_A+LigPin1BA | r16 | c0 | MassAction | |
| Pin1B_+LigPin1BA | r17 | c0 | MassAction | |
| Pin1_BPin1BivAB | r5 | c0 | MassAction | |
| Pin1_B+LigPin1AB | r20 | c0 | MassAction | |
| Pin1A_+LigPin1AB | r21 | c0 | MassAction | |
| Pin1+LigPin1A_ | r2 | c0 | MassAction | |
| Pin1+LigPin1_B | r3 | c0 | MassAction | |
| Pin1+Pin1B_Pin1B_Pin1A_ | r10 | c0 | MassAction | |
| Pin1+Pin1_BPin1_BPin1_A | r15 | c0 | MassAction | |
| Pin1+Pin1A_Pin1A_Pin1_B | r18 | c0 | MassAction | |
| Pin1+Pin1_APin1_APin1B_ | r22 | c0 | MassAction | |
| Pin1_B+Pin1Pin1A_Pin1_B | r24 | c0 | MassAction | |
| Pin1_A+Pin1Pin1_BPin1_A | r14 | c0 | MassAction | |
| Pin1B_+Pin1Pin1_APin1B_ | r23 | c0 | MassAction | |
| Pin1A_+Pin1Pin1B_Pin1A_ | r11 | c0 | MassAction |
r4 Universal ID's
r4 Text Annotations
r0 Universal ID's
r0 Text Annotations
r1 Universal ID's
r1 Text Annotations
r6 Universal ID's
r6 Text Annotations
r7 Universal ID's
r7 Text Annotations
r8 Universal ID's
r8 Text Annotations
r9 Universal ID's
r9 Text Annotations
r12 Universal ID's
r12 Text Annotations
r13 Universal ID's
r13 Text Annotations
r16 Universal ID's
r16 Text Annotations
r17 Universal ID's
r17 Text Annotations
r5 Universal ID's
r5 Text Annotations
r20 Universal ID's
r20 Text Annotations
r21 Universal ID's
r21 Text Annotations
r2 Universal ID's
r2 Text Annotations
r3 Universal ID's
r3 Text Annotations
r10 Universal ID's
r10 Text Annotations
r15 Universal ID's
r15 Text Annotations
r18 Universal ID's
r18 Text Annotations
r22 Universal ID's
r22 Text Annotations
r24 Universal ID's
r24 Text Annotations
r14 Universal ID's
r14 Text Annotations
r23 Universal ID's
r23 Text Annotations
r11 Universal ID's
r11 Text Annotations
Expressions for r4
reaction rate
J
((Kf * Pin1A_) - (Kr * Pin1BivAB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1]
reverse rate constant
Kr
5.0 [s-1]
Expressions for r0
reaction rate
J
(((Kf * Pin1) * Lig) - (Kr * Pin1_A)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
42400.0 [s-1]
Expressions for r1
reaction rate
J
(((Kf * Pin1) * Lig) - (Kr * Pin1B_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
25700.0 [s-1]
Expressions for r6
reaction rate
J
((Kf * Pin1_A) - (Kr * Pin1BivBA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1]
reverse rate constant
Kr
8.0 [s-1]
Expressions for r7
reaction rate
J
((Kf * Pin1B_) - (Kr * Pin1BivBA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1]
reverse rate constant
Kr
4.1 [s-1]
Expressions for r8
reaction rate
J
(((Kf * Pin1_A) * Lig) - (Kr * Pin1AA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
14500.0 [s-1]
Expressions for r9
reaction rate
J
(((Kf * Lig) * Pin1A_) - (Kr * Pin1AA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
42400.0 [s-1]
Expressions for r12
reaction rate
J
(((Kf * Pin1B_) * Lig) - (Kr * Pin1BB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
41400.0 [s-1]
Expressions for r13
reaction rate
J
(((Kf * Pin1_B) * Lig) - (Kr * Pin1BB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
25700.0 [s-1]
Expressions for r16
reaction rate
J
(((Kf * Pin1_A) * Lig) - (Kr * Pin1BA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
25700.0 [s-1]
Expressions for r17
reaction rate
J
(((Kf * Pin1B_) * Lig) - (Kr * Pin1BA)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
42400.0 [s-1]
Expressions for r5
reaction rate
J
((Kf * Pin1_B) - (Kr * Pin1BivAB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1]
reverse rate constant
Kr
12.0 [s-1]
Expressions for r20
reaction rate
J
(((Kf * Pin1_B) * Lig) - (Kr * Pin1AB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
14500.0 [s-1]
Expressions for r21
reaction rate
J
(((Kf * Pin1A_) * Lig) - (Kr * Pin1AB)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
41400.0 [s-1]
Expressions for r2
reaction rate
J
(((Kf * Pin1) * Lig) - (Kr * Pin1A_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
14500.0 [s-1]
Expressions for r3
reaction rate
J
(((Kf * Pin1) * Lig) - (Kr * Pin1_B)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
41400.0 [s-1]
Expressions for r10
reaction rate
J
(((Kf * Pin1) * Pin1B_) - (Kr * Pin1B_Pin1A_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
14500.0 [s-1]
Expressions for r15
reaction rate
J
(((Kf * Pin1) * Pin1_B) - (Kr * Pin1_BPin1_A)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
42400.0 [s-1]
Expressions for r18
reaction rate
J
(((Kf * Pin1) * Pin1A_) - (Kr * Pin1A_Pin1_B)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
41400.0 [s-1]
Expressions for r22
reaction rate
J
(((Kf * Pin1) * Pin1_A) - (Kr * Pin1_APin1B_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
25700.0 [s-1]
Expressions for r24
reaction rate
J
(((Kf * Pin1_B) * Pin1) - (Kr * Pin1A_Pin1_B)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
14500.0 [s-1]
Expressions for r14
reaction rate
J
(((Kf * Pin1_A) * Pin1) - (Kr * Pin1_BPin1_A)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
41400.0 [s-1]
Expressions for r23
reaction rate
J
(((Kf * Pin1B_) * Pin1) - (Kr * Pin1_APin1B_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
42400.0 [s-1]
Expressions for r11
reaction rate
J
(((Kf * Pin1A_) * Pin1) - (Kr * Pin1B_Pin1A_)) [uM.s-1]
forward rate constant
Kf
100.0 [s-1.uM-1]
reverse rate constant
Kr
25700.0 [s-1]
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| Pin1AA | c0 | ||
| Pin1BB | c0 | ||
| Pin1AB | c0 | ||
| Pin1BA | c0 | ||
| Lig | c0 | ||
| Pin1 | c0 | ||
| Pin1_B | c0 | ||
| Pin1BivAB | c0 | ||
| Pin1A_ | c0 | ||
| Pin1_A | c0 | ||
| Pin1B_ | c0 | ||
| Pin1BivBA | c0 | ||
| Pin1B_Pin1A_ | c0 | ||
| Pin1_APin1B_ | c0 | ||
| Pin1A_Pin1_B | c0 | ||
| Pin1_BPin1_A | c0 |
Pin1AA Universal ID's
Pin1AA Text Annotations
Pin1BB Universal ID's
Pin1BB Text Annotations
Pin1AB Universal ID's
Pin1AB Text Annotations
Pin1BA Universal ID's
Pin1BA Text Annotations
Lig Universal ID's
Lig Text Annotations
Pin1 Universal ID's
Pin1 Text Annotations
Pin1_B Universal ID's
Pin1_B Text Annotations
Pin1BivAB Universal ID's
Pin1BivAB Text Annotations
Pin1A_ Universal ID's
Pin1A_ Text Annotations
Pin1_A Universal ID's
Pin1_A Text Annotations
Pin1B_ Universal ID's
Pin1B_ Text Annotations
Pin1BivBA Universal ID's
Pin1BivBA Text Annotations
Pin1B_Pin1A_ Universal ID's
Pin1B_Pin1A_ Text Annotations
Pin1_APin1B_ Universal ID's
Pin1_APin1B_ Text Annotations
Pin1A_Pin1_B Universal ID's
Pin1A_Pin1_B Text Annotations
Pin1_BPin1_A Universal ID's
Pin1_BPin1_A Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| Application0 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
Application0 Universal ID's
Application0 Text Annotations
Specifications (Species) - Application0 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| Pin1AA | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1BB | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1AB | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1BA | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Lig | 37.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1 | 250.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1_B | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1BivAB | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1A_ | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1_A | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1B_ | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1BivBA | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1B_Pin1A_ | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1_APin1B_ | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1A_Pin1_B | 0.0 [uM] | 0.0 [um2/s] | c0 |
| Pin1_BPin1_A | 0.0 [uM] | 0.0 [um2/s] | c0 |
Specifications (Reaction) - Application0 go to Simulations
| Name | Enabled? |
|---|---|
| r4 | included |
| r0 | included |
| r1 | included |
| r6 | included |
| r7 | included |
| r8 | included |
| r9 | included |
| r12 | included |
| r13 | included |
| r16 | included |
| r17 | included |
| r5 | included |
| r20 | included |
| r21 | included |
| r2 | included |
| r3 | included |
| r10 | included |
| r15 | included |
| r18 | included |
| r22 | included |
| r24 | included |
| r14 | included |
| r23 | included |
| r11 | included |
Simulations - Application0 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Pin1_p131/p144_titrationsample1 | 10.0 |
KeepEvery 1 KeepAtMost 1000 |
| Pin1_p131/p144_titrationsample1_no bivalent species | 10.0 |
KeepEvery 1 KeepAtMost 1000 |
Application0 Universal ID's
Application0 Text Annotations
Application0 Universal ID's
Application0 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial120107596
(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 | c0 |
Events
| Name | Variable | Rate Expression |
|---|
Downloads
| Model Format | Model Downloads |
|---|---|
| Virtual Cell Markup Language | VCML File |
| PDF Report | Report |
| COMBINE Archive | OMEX File |
| SEDML | SEDML File |
| File Format | Application Downloads |
| BNGL | Application0.bngl |
| SBML | Application0.sbml |
| Matlab | Application0.m |
| NFSim XML | Application0.xml |