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BIOMD0000000170 - Weimann2004_CircadianOscillator

 

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Reference Publication
Publication ID: 15347590
Becker-Weimann S, Wolf J, Herzel H, Kramer A.
Modeling feedback loops of the Mammalian circadian oscillator.
Biophys. J. 2004 Nov; 87(5): 3023-3034
Institute for Theoretical Biology, and Laboratory of Chronobiology--Institute of Medical Immunology (Charité), Humboldt-University Berlin, 10115 Berlin, Germany.  [more]
Model
Original Model: BIOMD0000000170.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL8378813456
Submission Date: 08 May 2008 11:57:24 UTC
Last Modification Date: 16 May 2012 10:04:56 UTC
Creation Date: 16 Apr 2008 11:56:13 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:is Gene Ontology circadian rhythm
set #2
bqbiol:isPartOf KEGG Pathway hsa04710
set #3
bqbiol:occursIn Taxonomy Mammalia
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.

Model
Publication ID: 15347590 Submission Date: 08 May 2008 11:57:24 UTC Last Modification Date: 16 May 2012 10:04:56 UTC Creation Date: 16 Apr 2008 11:56:13 UTC
Mathematical expressions
Reactions
per2_cry_transcription per2_cry_mRNA_degradation per2_cry_complex_formation cytoplasmic_per2_cry_complex_degradation
per2_cry_nuclear_import per2_cry_nuclear_export nuclear_per2_cry_complex_degradation Bmal1_transcription
Bmal1_mRNA_degradation BMAL1_translation cytoplasmic_BMAL1_degradation BMAL1_nuclear_import
BMAL1_nuclear_export nuclear_BMAL1_degradation BMAL1_activation BMAL1_deactivation
Active_BMAL1_degradation      
Rules
Assignment Rule (variable: trans_per2_cry) Assignment Rule (variable: trans_Bmal1) Assignment Rule (variable: y5_y6_y7)  
Physical entities
Compartments Species
Nucleus PER2_CRY_complex_nucleus BMAL1_nucleus Active BMAL1
Cytoplasm Per2 or Cry mRNA PER2_CRY_complex_cytoplasm Bmal1 mRNA
BMAL1_cytoplasm    
Global parameters
trans_per2_cry v1b c k1b
k1i hill_coeff trans_Bmal1 v4b
r k4b y5_y6_y7 k1d
k2b q k2d k2t
k3t k3d k4d k5b
k5d k5t k6t k6d
k6a k7a k7d  
Reactions (17)
 
 per2_cry_transcription  → [Per2 or Cry mRNA];  
 
 per2_cry_mRNA_degradation [Per2 or Cry mRNA] → ;  
 
 per2_cry_complex_formation  → [PER2_CRY_complex_cytoplasm];   {Per2 or Cry mRNA}
 
 cytoplasmic_per2_cry_complex_degradation [PER2_CRY_complex_cytoplasm] → ;  
 
 per2_cry_nuclear_import [PER2_CRY_complex_cytoplasm] → [PER2_CRY_complex_nucleus];  
 
 per2_cry_nuclear_export [PER2_CRY_complex_nucleus] → [PER2_CRY_complex_cytoplasm];  
 
 nuclear_per2_cry_complex_degradation [PER2_CRY_complex_nucleus] → ;  
 
 Bmal1_transcription  → [Bmal1 mRNA];  
 
 Bmal1_mRNA_degradation [Bmal1 mRNA] → ;  
 
 BMAL1_translation  → [BMAL1_cytoplasm];   {Bmal1 mRNA}
 
 cytoplasmic_BMAL1_degradation [BMAL1_cytoplasm] → ;  
 
 BMAL1_nuclear_import [BMAL1_cytoplasm] → [BMAL1_nucleus];  
 
 BMAL1_nuclear_export [BMAL1_nucleus] → [BMAL1_cytoplasm];  
 
 nuclear_BMAL1_degradation [BMAL1_nucleus] → ;  
 
 BMAL1_activation [BMAL1_nucleus] → [Active BMAL1];  
 
 BMAL1_deactivation [Active BMAL1] → [BMAL1_nucleus];  
 
 Active_BMAL1_degradation [Active BMAL1] → ;  
 
Rules (3)
 
 Assignment Rule (name: trans_per2_cry) trans_per2_cry = v1b*(y7+c)/(k1b*(1+(y3/k1i)^hill_coeff)+y7+c)
 
 Assignment Rule (name: trans_Bmal1) trans_Bmal1 = v4b*y3^r/(k4b^r+y3^r)
 
 Assignment Rule (name: y5_y6_y7) y5_y6_y7 = y5+y6+y7
 
   Nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 PER2_CRY_complex_nucleus
Compartment: Nucleus
Initial concentration: 1.1
 
 BMAL1_nucleus
Compartment: Nucleus
Initial concentration: 1.0
 
 Active BMAL1
Compartment: Nucleus
Initial concentration: 1.05
 
   Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Per2 or Cry mRNA
Compartment: Cytoplasm
Initial concentration: 0.2
 
 PER2_CRY_complex_cytoplasm
Compartment: Cytoplasm
Initial concentration: 0.0
 
 Bmal1 mRNA
Compartment: Cytoplasm
Initial concentration: 0.8
 
 BMAL1_cytoplasm
Compartment: Cytoplasm
Initial concentration: 1.0
 
Global Parameters (27)
 
   trans_per2_cry  
 
   v1b
Value: 9.0   (Units: nM_per_hour)
Constant
 
   c
Value: 0.01   (Units: nM)
Constant
 
   k1b
Value: 1.0   (Units: nM)
Constant
 
   k1i
Value: 0.56   (Units: nM)
Constant
 
   hill_coeff
Value: 8.0   (Units: dimensionless)
Constant
 
   trans_Bmal1  
 
   v4b
Value: 3.6   (Units: nM_per_hour)
Constant
 
   r
Value: 3.0   (Units: dimensionless)
Constant
 
   k4b
Value: 2.16   (Units: nM)
Constant
 
   y5_y6_y7
Value: 3.05   (Units: nM)
 
   k1d
Value: 0.12   (Units: hr_inv)
Constant
 
   k2b
Value: 0.3   (Units: nM_inv_hr_inv)
Constant
 
   q
Value: 2.0   (Units: dimensionless)
Constant
 
   k2d
Value: 0.05   (Units: hr_inv)
Constant
 
   k2t
Value: 0.24   (Units: hr_inv)
Constant
 
   k3t
Value: 0.02   (Units: hr_inv)
Constant
 
   k3d
Value: 0.12   (Units: hr_inv)
Constant
 
   k4d
Value: 0.75   (Units: hr_inv)
Constant
 
   k5b
Value: 0.24   (Units: hr_inv)
Constant
 
   k5d
Value: 0.06   (Units: hr_inv)
Constant
 
   k5t
Value: 0.45   (Units: hr_inv)
Constant
 
   k6t
Value: 0.06   (Units: hr_inv)
Constant
 
   k6d
Value: 0.12   (Units: hr_inv)
Constant
 
   k6a
Value: 0.09   (Units: hr_inv)
Constant
 
   k7a
Value: 0.0030   (Units: hr_inv)
Constant
 
   k7d
Value: 0.09   (Units: hr_inv)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000170

Curator's comment: (updated: 02 May 2008 01:16:14 BST)

The plot corresponds to Fig 3A of the paper. MathSBML was used to simulate the model.

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