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nazaret1

nazaret1

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v1

v1

∅ > Pyr

v2

v2

Pyr + NAD > AcCoA + NADH

v3

v3

OAA + AcCoA > Cit

v4

v4

Cit + NAD > KG + NADH

v5

v5

KG + ADP + {2.0}NAD > OAA + ATP + {2.0}NADH

v6

v6

OAA = KG

v7

v7

Pyr + ATP > OAA + ADP

v8

v8

OAA > ∅

vANT

vANT

ATP > ADP

vATP

vATP

ADP + iP + {3.0}He = ATP + H2O + {3.0}H

vleak

vleak

He > H

vresp

vresp

NADH + {0.5}O2 + {11.0}H > NAD + H2O + {10.0}He

Parameters

Global parameters
v1
v2
v3
v4
v5
v6
v7
v8

Fixed species

Initial values

Functions and Rules

Assignment rules

NADH = Nt - NAD

ADP = At - ATP

DeltaGtransport = 1.2 * F * DeltaPsi

ATPcrit = At / (1.0 + exp(-3.0 * DeltaGtransport / (R * T)) / (Kapp * iP))

JATP = kATP * (2.0 / (1.0 + exp(b * (ATP - ATPcrit))) - 1.0)

Jresp = kresp * ((Nt - NAD) / (K + Nt - NAD)) / (1.0 + exp(a * (DeltaPsi - DeltaPsim)))

Jleak = kleak * DeltaPsi

JANT = kANT * ATP

Function definitions

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


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Mitochondrial energetic metabolism: a simplified model of TCA cycle with ATP production.

  • Christine Nazaret
  • Margit Heiske
  • Kevin Thurley
  • Jean-Pierre Mazat
J. Theor. Biol. 2009; 258 (3): 455-464
Abstract
Mitochondria play a central role in cellular energetic metabolism. The essential parts of this metabolism are the tricarboxylic acid (TCA) cycle, the respiratory chain and the adenosine triphosphate (ATP) synthesis machinery. Here a simplified model of these three metabolic components with a limited set of differential equations is presented. The existence of a steady state is demonstrated and results of numerical simulations are presented. The relevance of a simple model to represent actual in vivo behavior is discussed.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000232) Biomodels notes: The model reproduces Figure 6 of the reference publication after rescaling the data. The model was integrated and simulated using Copasi v4.5 (Build 30). The time-course was run using Copasi and the data were obtained. The variables and the time were rescaled according to equation 27 of the paper, to reproduce the figure 6. The plot was done using Gnuplot. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.