Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| pEGFR+SH2pEGFRSH2 |
r4
c0
|
GeneralKinetics | pEGFR+SH2pEGFRSH2 |
|
|
|
reaction rate (J): ((kon * SH2 * pEGFR) - (koff * pEGFRSH2))[uM.s-1]
|
|
| EGFRSH2EGFR+SH2 |
r5
c0
|
GeneralKinetics | EGFRSH2EGFR+SH2 |
|
|
|
reaction rate (J): (koff * EGFRSH2)[uM.s-1]
|
|
| pEGFRiEGFR |
r2
c0
|
GeneralKinetics | pEGFRiEGFR |
|
|
|
reaction rate (J): (ke * pEGFR)[uM.s-1]
user defined (ke): 0.1[s-1] |
|
| iEGFR |
r3
c0
|
GeneralKinetics | iEGFR |
|
|
|
reaction rate (J): (kdeg * iEGFR)[uM.s-1]
|
|
| iEGFRSH2SH2 |
r8
c0
|
GeneralKinetics | iEGFRSH2SH2 |
|
|
|
reaction rate (J): (kdeg * iEGFRSH2)[uM.s-1]
|
|
| iEGFR+SH2iEGFRSH2 |
r9
c0
|
GeneralKinetics | iEGFR+SH2iEGFRSH2 |
|
|
|
reaction rate (J): ((kon * SH2 * iEGFR) - (koff * iEGFRSH2))[uM.s-1]
|
|
| EGF+EGFRSH2pEGFRSH2 |
r6
c0
|
GeneralKinetics | EGF+EGFRSH2pEGFRSH2 |
|
|
|
reaction rate (J): ((kf * EGF * EGFRSH2) - (kr * pEGFRSH2))[uM.s-1]
|
|
| pEGFRSH2iEGFRSH2 |
r7
c0
|
GeneralKinetics | pEGFRSH2iEGFRSH2 |
|
|
|
reaction rate (J): (keSH2 * pEGFRSH2)[uM.s-1]
user defined (keSH2): 0.1[s-1] |
|
| EGFR |
r1
c0
|
GeneralKinetics | EGFR |
|
|
|
reaction rate (J): (Vsyn - (kt * EGFR))[uM.s-1]
user defined (kt): 0.01[s-1] user defined (Vsyn): 1.0[uM.s-1] |
|
| EGFR+EGFpEGFR |
r0
c0
|
GeneralKinetics | EGFR+EGFpEGFR |
|
|
|
reaction rate (J): ((kf * EGF * EGFR) - (kr * pEGFR))[uM.s-1]
|
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| c0 |
Compartment
(+) (-)
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| pEGFR | c0 | |
|
|
|
|
| iEGFR | c0 | |
|
|
|
|
| SH2 | c0 | |
|
|
|
|
| pEGFRSH2 | c0 | |
|
|
|
|
| EGFRSH2 | c0 | |
|
|
|
|
| iEGFRSH2 | c0 | |
|
|
|
|
| EGF | c0 | |
|
|
|
|
| EGFR | c0 | |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Application0 | Deterministic (ODE) Compartmental |
Application - Application0
| Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pEGFR | 0.0 [uM] | 0.0
[um2/s] | iEGFR |
0.0
[uM]
|
0.0
[um2/s] | SH2 |
0.0
[uM]
|
0.0
[um2/s] | pEGFRSH2 |
0.0
[uM]
|
0.0
[um2/s] | EGFRSH2 |
0.0
[uM]
|
0.0
[um2/s] | iEGFRSH2 |
0.0
[uM]
|
0.0
[um2/s] | EGF |
1.0
[uM]
|
0.0
[um2/s] | EGFR |
100.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| r4 | included |
| r5 | included |
| r2 | included |
| r3 | included |
| r8 | included |
| r9 | included |
| r6 | included |
| r7 | included |
| r1 | included |
| r0 | included |
| Name | End Time | Output Options |
|---|---|---|
| Complex internalizes at turnover rate; vary koff and [SH2] 1 | 120.0 [s] |
OutputTimeStep 1.0 |
| Vary EGF, no SH2 | 120.0 [s] |
OutputTimeStep 1.0 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | c0 |
Global Parameters
| Name | Expression |
|---|---|
| kf | 0.1[s-1.uM-1] |
|
|
|
| kr | 0.1[s-1] |
|
|
|
| kdeg | 0.05[s-1] |
|
|
|
| kon | 0.1[s-1.uM-1] |
|
|
|
| koff | 1.0[s-1] |
|
|
|