gorlich1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000192) Biomodels notes: This model represents a concentration gradient of RanGTP across the nuclear envelope. This gradient is generated by distribution of regulators of RanGTPase. We have taken a log linear plot of graphs generated by GENESIS and compared with the experimental graphs. The model is simulated and integrated using SBML OdeSolver with options (-n --printstep 500). Figure 4 (Simulated time course for generation of the RanGTP gradient) of the original paper (Gorlich et al., 2003) is reproduced in here. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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| Simulation | |
|---|---|
| gorlich2003_Fig4 |
Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1e-06 mole | |
| — | 1e-06 mole second^(-1.0) litre^(-1.0) | |
| — | 1000000.0 litre mole^(-1.0) second^(-1.0) | |
| — | 1.0 second^(-1.0) | |
| — | 1e-06 mole litre^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytoplasm | — | 3.0 | 0.000000000018 | |
| nucleus | — | 3.0 | 0.000000000012 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| GDP | — | 1.6 | nucleus | ✔ | |
| GTP | — | 500.0 | nucleus | ✔ | |
| RCC1 | — | 0.7 | nucleus | ✘ | |
| RCC1_Ran | — | 0.0 | nucleus | ✘ | |
| RCC1_RanGDP | — | 0.0 | nucleus | ✘ | |
| RCC1_RanGTP | — | 0.0 | nucleus | ✘ | |
| RanBP1 | — | 2.0 | cytoplasm | ✘ | |
| RanGAP | — | 0.7 | cytoplasm | ✘ | |
| RanGDP_cy | — | 5.0 | cytoplasm | ✘ | |
| RanGDP_nuc | — | 0.0 | nucleus | ✘ | |
| RanGTP_RanBP1 | — | 0.0 | cytoplasm | ✘ | |
| RanGTP_cy | — | 0.0 | cytoplasm | ✘ | |
| RanGTP_nuc | — | 0.0 | nucleus | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| Cytoplasmic_transfer | — | RanGTP_nuc = RanGTP_cy kpermRanGTP * nucleus * (RanGTP_nuc - RanGTP_cy) | |||
| GDP_dissociation | — | RCC1_RanGDP = RCC1_Ran + GDP nucleus * (r2 * RCC1_RanGDP - r7 * RCC1_Ran * GDP) | |||
| GTP_binding | — | RCC1_Ran + GTP = RCC1_RanGTP nucleus * (r3 * RCC1_Ran * GTP - r6 * RCC1_RanGTP) | |||
| Nucleoplasmic_transfer | — | RanGDP_nuc = RanGDP_cy kpermRanGDP * nucleus * (RanGDP_nuc - RanGDP_cy) | |||
| RCC1_binding | — | RanGDP_nuc + RCC1 = RCC1_RanGDP nucleus * (r1 * RanGDP_nuc * RCC1 - r8 * RCC1_RanGDP) | |||
| RanBP1_RanGDP | RanBP1_RanGDP | RanGTP_RanBP1 = RanGDP_cy + RanBP1 cytoplasm * kcat * RanGTP_RanBP1 * RanGAP / (RanGTP_RanBP1 + Km) | |||
| RanGAP_RanGDP | RanGAP_RanGDP | RanGTP_cy = RanGDP_cy cytoplasm * kcat_GAP * RanGTP_cy * RanGAP / (Km_GAP + RanGTP_cy) | |||
| RanGTP_binding | — | RanGTP_cy + RanBP1 = RanGTP_RanBP1 (kon * RanGTP_cy * RanBP1 - koff * RanGTP_RanBP1) * cytoplasm | |||
| RanGTP_release | — | RCC1_RanGTP = RanGTP_nuc + RCC1 nucleus * (r4 * RCC1_RanGTP - r5 * RanGTP_nuc * RCC1) |
| Id | Value |
|---|
| Id | Value | Reaction | |
|---|---|---|---|
| r1 | 74.0 pmicroMpsec | RCC1_binding | |
| r8 | 55.0 psec | RCC1_binding | |
| r2 | 21.0 psec | GDP_dissociation | |
| r7 | 11.0 pmicroMpsec | GDP_dissociation | |
| r3 | 0.6 pmicroMpsec | GTP_binding | |
| r6 | 19.0 psec | GTP_binding | |
| r4 | 55.0 psec | RanGTP_release | |
| r5 | 100.0 pmicroMpsec | RanGTP_release | |
| kpermRanGTP | 0.03 psec | Cytoplasmic_transfer | |
| kpermRanGDP | 0.12 psec | Nucleoplasmic_transfer | |
| kon | 0.3 pmicroMpsec | RanGTP_binding | |
| koff | 0.0004 psec | RanGTP_binding | |
| kcat | 10.8 psec | RanBP1_RanGDP (RanBP1_RanGDP) | |
| Km | 0.1 microM | RanBP1_RanGDP (RanBP1_RanGDP) | |
| kcat_GAP | 10.6 psec | RanGAP_RanGDP (RanGAP_RanGDP) | |
| Km_GAP | 0.7 microM | RanGAP_RanGDP (RanGAP_RanGDP) |
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| Trigger | Assignments |
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