santolini1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000199). Biomodels notes: "This is a model of neuronal Nitric Oxide Synthase expressed in Escherichia coli based on Santolini J. et al. J Biol Chem. (2001) 276(2):1233-43. Differing from the article, oxygen explicitly included in the reaction 2, 5 and 10 (numbers as in scheme 1 in the article). In the article the assumed oxygen concentration of 140 uM was included in the pseudo first order rate constant. Fig 2E in the article shows different time courses for citrulline and NO than the ones produced by this model. Dr. Santolini, one of the authors of the article, wrote that the legends in fig. 2E might be mixed up and should rather denote NO and NO3 instead of citrulline and NO." JWS Online curation: This model was curated by reproducing the figure 2D as described in the BioModels Notes. No additional changes were made.
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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 | |
| — | 1000000.0 litre mole^(-1.0) second^(-1.0) | |
| — | 1e-06 mole litre^(-1.0) | |
| — | 1.0 second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytosol | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| FeII | FeII | 0.0 | cytosol | ✘ | |
| FeIII | FeIII | 1.0 | cytosol | ✘ | |
| FeIII_NO | FeIII_NO | 0.0 | cytosol | ✘ | |
| FeIII_star | FeIII_star | 0.0 | cytosol | ✘ | |
| FeIII_t | FeIII_t | 0.0 | cytosol | ✘ | |
| FeII_NO | FeII_NO | 0.0 | cytosol | ✘ | |
| FeII_O2 | FeII_O2 | 0.0 | cytosol | ✘ | |
| FeII_star | FeII_star | 0.0 | cytosol | ✘ | |
| FeII_star_O2 | FeII_star_O2 | 0.0 | cytosol | ✘ | |
| NADPH | NADPH | 40.0 | cytosol | ✔ | |
| NADPplus | NADPplus | 0.0 | cytosol | ✔ | |
| NO | NO | 0.0 | cytosol | ✔ | |
| NO3 | NO3 | 0.0 | cytosol | ✔ | |
| O2 | O2 | 140.0 | cytosol | ✔ | |
| citrulline | citruline | 0.0 | cytosol | ✔ |
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 | |
|---|---|---|---|---|---|
| r1 | — | FeIII + NADPH > FeII + NADPplus cytosol * k1 * FeIII | |||
| r10 | — | FeII_NO + O2 > FeIII + NO3 cytosol * k10 * FeII_NO * O2 | |||
| r2 | — | FeII + O2 > FeII_O2 cytosol * k2 * FeII * O2 | |||
| r3 | — | FeII_O2 > FeIII_star cytosol * k3 * FeII_O2 | |||
| r4 | — | FeIII_star + {0.5}NADPH > FeII_star + {0.5}NADPplus cytosol * k4 * FeIII_star | |||
| r5 | — | FeII_star + O2 > FeII_star_O2 cytosol * k5 * FeII_star * O2 | |||
| r6 | — | FeII_star_O2 > FeIII_NO + citrulline cytosol * k6 * FeII_star_O2 | |||
| r9 | — | FeII_NO > FeII + NO cytosol * k9 * FeII_NO | |||
| rF | — | FeIII_NO > FeIII + NO cytosol * k7 * FeIII_NO | |||
| rG | — | FeIII_NO + {0.5}NADPH > FeII_NO + {0.5}NADPplus cytosol * k8 * FeIII_NO |
| Id | Value | |
|---|---|---|
| k1 | 2.6 persec | |
| k10 | 0.0013 peruMpersec | |
| k2 | 0.9 peruMpersec | |
| k3 | 26.0 persec | |
| k4 | 2.6 persec | |
| k5 | 0.9 peruMpersec | |
| k6 | 26.0 persec | |
| k7 | 5.0 persec | |
| k8 | 2.6 persec | |
| k9 | 0.0001 persec |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| FeIII_t = FeIII + FeIII_star |
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| Trigger | Assignments |
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