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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A kinetic simulation model that describes catalysis and regulation in nitric-oxide synthase.

  • J Santolini
  • S Adak
  • CM Curran
  • DJ Stuehr
J. Biol. Chem. 2001; 276 (2): 1233-1243
Abstract
After initiating NO synthesis a majority of neuronal NO synthase (nNOS) quickly partitions into a ferrous heme-NO complex. This down-regulates activity and increases enzyme K(m,O(2)). To understand this process, we developed a 10-step kinetic model in which the ferric heme-NO enzyme forms as the immediate product of catalysis, and then partitions between NO dissociation versus reduction to a ferrous heme-NO complex. Rate constants used for the model were derived from recent literature or were determined here. Computer simulations of the model precisely described both pre-steady and steady-state features of nNOS catalysis, including NADPH consumption and NO production, buildup of a heme-NO complex, changes between pre-steady and steady-state rates, and the change in enzyme K(m,O(2)) in the presence or absence of NO synthesis. The model also correctly simulated the catalytic features of nNOS mutants W409F and W409Y, which are hyperactive and display less heme-NO complex formation in the steady state. Model simulations showed how the rate of heme reduction influences several features of nNOS catalysis, including populations of NO-bound versus NO-free enzyme in the steady state and the rate of NO synthesis. The simulation predicts that there is an optimum rate of heme reduction that is close to the measured rate in nNOS. Ratio between NADPH consumption and NO synthesis is also predicted to increase with faster heme reduction. Our kinetic model is an accurate and versatile tool for understanding catalytic behavior and will provide new perspectives on NOS regulation.

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

Global parameters

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

Local parameters

Id Value Reaction

Assignment rules

Definition
FeIII_t = FeIII + FeIII_star

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments