weimann1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000170). Biomodels notes: "The model reproduces the time profile of the species as depicted in Fig 3A of the paper. Model successfully tested on MathSBML and Jarnac." 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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Modeling feedback loops of the Mammalian circadian oscillator.

  • Sabine Becker-Weimann
  • Jana Wolf
  • Hanspeter Herzel
  • Achim Kramer
Biophys. J. 2004; 87 (5): 3023-3034
Abstract
The suprachiasmatic nucleus governs daily variations of physiology and behavior in mammals. Within single neurons, interlocked transcriptional/translational feedback loops generate circadian rhythms on the molecular level. We present a mathematical model that reflects the essential features of the mammalian circadian oscillator to characterize the differential roles of negative and positive feedback loops. The oscillations that are obtained have a 24-h period and are robust toward parameter variations even when the positive feedback is replaced by a constantly expressed activator. This demonstrates the crucial role of the negative feedback for rhythm generation. Moreover, it explains the rhythmic phenotype of Rev-erbalpha-/- mutant mice, where a positive feedback is missing. The interplay of negative and positive feedback reveals a complex dynamics. In particular, the model explains the unexpected rescue of circadian oscillations in Per2Brdm1/Cry2-/- double-mutant mice (Per2Brdm1 single-mutant mice are arrhythmic). Here, a decrease of positive feedback strength associated with mutating the Per2 gene is compensated by the Cry2-/- mutation that simultaneously decreases the negative feedback strength. Finally, this model leads us to a testable prediction of a molecular and behavioral phenotype: circadian oscillations should be rescued when arrhythmic Per2Brdm1 mutant mice are crossed with Rev- erbalpha -/- mutant mice.

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-09 mole
3600.0 second
1e-09 mole litre^(-1.0)
2.777777777777778e-13 mole litre^(-1.0) second^(-1.0)
0.0002777777777777778 second^(-1.0)
277777.77777777775 mole^(-1.0) litre second^(-1.0)
1.0 dimensionless
Id Name Spatial dimensions Size
Cytoplasm Cytoplasm 3.0 1.0
Nucleus Nucleus 3.0 1.0
Id Name Initial quantity Compartment Fixed
y1 Per2 or Cry mRNA 0.2 Cytoplasm (Cytoplasm)
y2 PER2_CRY_complex_cytoplasm 0.0 Cytoplasm (Cytoplasm)
y3 PER2_CRY_complex_nucleus 1.1 Nucleus (Nucleus)
y4 Bmal1 mRNA 0.8 Cytoplasm (Cytoplasm)
y5 BMAL1_cytoplasm 1.0 Cytoplasm (Cytoplasm)
y6 BMAL1_nucleus 1.0 Nucleus (Nucleus)
y7 Active BMAL1 1.05 Nucleus (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
Active_BMAL1_degradation Active_BMAL1_degradation y7 > ∅

Nucleus * k7d * y7
BMAL1_activation BMAL1_activation y6 > y7

Nucleus * k6a * y6
BMAL1_deactivation BMAL1_deactivation y7 > y6

Nucleus * k7a * y7
BMAL1_nuclear_export BMAL1_nuclear_export y6 > y5

Nucleus * k6t * y6
BMAL1_nuclear_import BMAL1_nuclear_import y5 > y6

Cytoplasm * k5t * y5
BMAL1_translation BMAL1_translation ∅ > y5

Cytoplasm * k5b * y4
Bmal1_mRNA_degradation Bmal1_mRNA_degradation y4 > ∅

Cytoplasm * k4d * y4
Bmal1_transcription Bmal1_transcription ∅ > y4

Cytoplasm * trans_Bmal1
cytoplasmic_BMAL1_degradation cytoplasmic_BMAL1_degradation y5 > ∅

Cytoplasm * k5d * y5
cytoplasmic_per2_cry_complex_degradation cytoplasmic_per2_cry_complex_degradation y2 > ∅

Cytoplasm * k2d * y2
nuclear_BMAL1_degradation nuclear_BMAL1_degradation y6 > ∅

Nucleus * k6d * y6
nuclear_per2_cry_complex_degradation nuclear_per2_cry_complex_degradation y3 > ∅

Nucleus * k3d * y3
per2_cry_complex_formation per2_cry_complex_formation ∅ > y2

Cytoplasm * k2b * pow(y1, q)
per2_cry_mRNA_degradation per2_cry_mRNA_degradation y1 > ∅

Cytoplasm * k1d * y1
per2_cry_nuclear_export per2_cry_nuclear_export y3 > y2

Nucleus * k3t * y3
per2_cry_nuclear_import per2_cry_nuclear_import y2 > y3

Cytoplasm * k2t * y2
per2_cry_transcription per2_cry_transcription ∅ > y1

Cytoplasm * trans_per2_cry

Global parameters

Id Value
c 0.01 nM
hill_coeff 8.0 dimensionless
k1b 1.0 nM
k1d 0.12
k1i 0.56 nM
k2b 0.3 nM_inv_hr_inv
k2d 0.05
k2t 0.24
k3d 0.12
k3t 0.02
k4b 2.16 nM
k4d 0.75
k5b 0.24
k5d 0.06
k5t 0.45
k6a 0.09
k6d 0.12
k6t 0.06
k7a 0.003
k7d 0.09
q 2.0 dimensionless
r 3.0 dimensionless
trans_Bmal1 <assignment rule> nM_per_hour
trans_per2_cry <assignment rule> nM_per_hour
v1b 9.0 nM_per_hour
v4b 3.6 nM_per_hour
y5_y6_y7 <assignment rule> nM

Local parameters

Id Value Reaction

Assignment rules

Definition
y5_y6_y7 = y5 + y6 + y7
trans_Bmal1 = v4b * pow(y3, r) / (pow(k4b, r) + pow(y3, r))
trans_per2_cry = v1b * (y7 + c) / (k1b * (1.0 + pow(y3 / k1i, hill_coeff)) + y7 + c)

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments