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BIOMD0000000021 - Leloup1999_CircClock

 

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Reference Publication
Publication ID: 10366496
Leloup JC, Goldbeter A.
Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in drosophila
J. Theor. Biol. 1999 Jun; 198(3): 445-459
Unite de Chronobiologie Theorique, Faculte des Sciences, Universite Libre de Bruxelles, Campus Plaine, C.P. 231, B-1050 Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000021.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6617834203
Submission Date: 13 Sep 2005 13:24:15 UTC
Last Modification Date: 25 Feb 2015 13:16:43 UTC
Creation Date: 29 Jun 2005 10:27:52 UTC
Encoders:  Nicolas Le Novère
   Bruce Shapiro
set #1
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
set #2
bqbiol:is KEGG Pathway dme04711
set #3
bqbiol:hasTaxon Taxonomy Drosophila melanogaster
set #4
bqmodel:isDerivedFrom BioModels Database Leloup1998_CircClock_LD
Notes

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 10366496 Submission Date: 13 Sep 2005 13:24:15 UTC Last Modification Date: 25 Feb 2015 13:16:43 UTC Creation Date: 29 Jun 2005 10:27:52 UTC
Mathematical expressions
Reactions
First Phosphorylation of PER First Phosphorylation of TIM Dephosphorylation of PER (1st P) Dephosphorylation of TIM (1st P)
Second Phosphorylation of PER Second Phosphorylation of TIM Dephosphorylation of PER (2nd P) Dephosphorylation of TIM (2nd P)
PER degradation TIM degradation PER-1 degradation TIM-1 degradation
PER-2 degradation TIM-2 degradation PER-TIM complex formation PER-TIM complex nucleation
PER-TIM complex degradation (cytosol) PER-TIM complex degradation (nuclear) PER mRNA production TIM mRNA production
PER production TIM production PER mRNA degradation TIM mRNA degradation
Rules
Assignment Rule (variable: Total Per) Assignment Rule (variable: Total Tim)    
Physical entities
Compartments Species
cytoplasm PER Protein (unphosphorylated) TIM Protein (unphosphorylated) PER Protein (mono-phosphorylated)
TIM Protein (mono-phosphorylated) PER Protein (bi-phosphorylated) TIM Protein (bi-phosphorylated)
Cytosolic PER-TIM Complex PER mRNA TIM mRNA
nucleus Nuclear PER-TIM Complex    
Global parameters
Total Per Total Tim V_mT V_dT
Reactions (24)
 
 First Phosphorylation of PER [PER Protein (unphosphorylated)] → [PER Protein (mono-phosphorylated)];  
 
 First Phosphorylation of TIM [TIM Protein (unphosphorylated)] → [TIM Protein (mono-phosphorylated)];  
 
 Dephosphorylation of PER (1st P) [PER Protein (mono-phosphorylated)] → [PER Protein (unphosphorylated)];  
 
 Dephosphorylation of TIM (1st P) [TIM Protein (mono-phosphorylated)] → [TIM Protein (unphosphorylated)];  
 
 Second Phosphorylation of PER [PER Protein (mono-phosphorylated)] → [PER Protein (bi-phosphorylated)];  
 
 Second Phosphorylation of TIM [TIM Protein (mono-phosphorylated)] → [TIM Protein (bi-phosphorylated)];  
 
 Dephosphorylation of PER (2nd P) [PER Protein (bi-phosphorylated)] → [PER Protein (mono-phosphorylated)];  
 
 Dephosphorylation of TIM (2nd P) [TIM Protein (bi-phosphorylated)] → [TIM Protein (mono-phosphorylated)];  
 
 PER degradation [PER Protein (unphosphorylated)] → ;  
 
 TIM degradation [TIM Protein (unphosphorylated)] → ;  
 
 PER-1 degradation [PER Protein (mono-phosphorylated)] → ;  
 
 TIM-1 degradation [TIM Protein (mono-phosphorylated)] → ;  
 
 PER-2 degradation [PER Protein (bi-phosphorylated)] → ;  
 
 TIM-2 degradation [TIM Protein (bi-phosphorylated)] → ;  
 
 PER-TIM complex formation [PER Protein (bi-phosphorylated)] + [TIM Protein (bi-phosphorylated)] ↔ [Cytosolic PER-TIM Complex];  
 
 PER-TIM complex nucleation [Cytosolic PER-TIM Complex] ↔ [Nuclear PER-TIM Complex];  
 
 PER-TIM complex degradation (cytosol) [Cytosolic PER-TIM Complex] → ;  
 
 PER-TIM complex degradation (nuclear) [Nuclear PER-TIM Complex] → ;  
 
 PER mRNA production  → [PER mRNA];   {Nuclear PER-TIM Complex}
 
 TIM mRNA production  → [TIM mRNA];   {Nuclear PER-TIM Complex}
 
 PER production  → [PER Protein (unphosphorylated)];   {PER mRNA}
 
 TIM production  → [TIM Protein (unphosphorylated)];   {TIM mRNA}
 
 PER mRNA degradation [PER mRNA] → ;  
 
 TIM mRNA degradation [TIM mRNA] → ;  
 
Rules (2)
 
 Assignment Rule (name: Pt) Total Per = CC+Cn+P0+P1+P2
 
 Assignment Rule (name: Tt) Total Tim = CC+Cn+T0+T1+T2
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 PER Protein (unphosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 TIM Protein (unphosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 PER Protein (mono-phosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 TIM Protein (mono-phosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 PER Protein (bi-phosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 TIM Protein (bi-phosphorylated)
Compartment: cytoplasm
Initial concentration: 0.0
 
 Cytosolic PER-TIM Complex
Compartment: cytoplasm
Initial concentration: 0.0
 
 PER mRNA
Compartment: cytoplasm
Initial concentration: 0.0
 
 TIM mRNA
Compartment: cytoplasm
Initial concentration: 0.0
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 Nuclear PER-TIM Complex
Compartment: nucleus
Initial concentration: 0.0
 
Global Parameters (4)
 
   Total Per
Value: NaN
 
   Total Tim
Value: NaN
 
 V_mT
Value: 0.7
Constant
 
 V_dT
Value: 2.0
Constant
 
First Phosphorylation of PER (2)
 
   K1_P
Value: 2.0
Constant
 
   V_1P
Value: 8.0
Constant
 
First Phosphorylation of TIM (2)
 
   K_1T
Value: 2.0
Constant
 
   V_1T
Value: 8.0
Constant
 
Dephosphorylation of PER (1st P) (2)
 
   K_2P
Value: 2.0
Constant
 
   V_2P
Value: 1.0
Constant
 
Dephosphorylation of TIM (1st P) (2)
 
   K_2T
Value: 2.0
Constant
 
   V_2T
Value: 1.0
Constant
 
Second Phosphorylation of PER (2)
 
   K_3P
Value: 2.0
Constant
 
   V_3P
Value: 8.0
Constant
 
Second Phosphorylation of TIM (2)
 
   K_3T
Value: 2.0
Constant
 
   V_3T
Value: 8.0
Constant
 
Dephosphorylation of PER (2nd P) (2)
 
   K_4P
Value: 2.0
Constant
 
   V_4P
Value: 1.0
Constant
 
Dephosphorylation of TIM (2nd P) (2)
 
   K_4T
Value: 2.0
Constant
 
   V_4T
Value: 1.0
Constant
 
PER degradation (1)
 
   k_d
Value: 0.01
Constant
 
TIM degradation (1)
 
   k_d
Value: 0.01
Constant
 
PER-1 degradation (1)
 
   k_d
Value: 0.01
Constant
 
TIM-1 degradation (1)
 
   k_d
Value: 0.01
Constant
 
PER-2 degradation (3)
 
   k_d
Value: 0.01
Constant
 
   V_dP
Value: 2.0
Constant
 
   K_dP
Value: 0.2
Constant
 
TIM-2 degradation (2)
 
   k_d
Value: 0.01
Constant
 
   K_dT
Value: 0.2
Constant
 
PER-TIM complex formation (2)
 
   k3
Value: 1.2
Constant
 
   k4
Value: 0.6
Constant
 
PER-TIM complex nucleation (2)
 
   k1
Value: 0.6
Constant
 
   k2
Value: 0.2
Constant
 
PER-TIM complex degradation (cytosol) (1)
 
   k_dC
Value: 0.01
Constant
 
PER-TIM complex degradation (nuclear) (1)
 
   k_dN
Value: 0.01
Constant
 
PER mRNA production (3)
 
   v_sP
Value: 1.0
Constant
 
   K_IP
Value: 1.0
Constant
 
   n
Value: 4.0
Constant
 
TIM mRNA production (3)
 
   V_sT
Value: 1.0
Constant
 
   K_IT
Value: 1.0
Constant
 
   n
Value: 4.0
Constant
 
PER production (1)
 
   k_sP
Value: 0.9
Constant
 
TIM production (1)
 
   k_sT
Value: 0.9
Constant
 
PER mRNA degradation (3)
 
   k_d
Value: 0.01
Constant
 
   V_mP
Value: 0.7
Constant
 
   K_mP
Value: 0.2
Constant
 
TIM mRNA degradation (2)
 
   k_d
Value: 0.01
Constant
 
   K_mT
Value: 0.2
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000021

Curator's comment: (updated: 19 Oct 2006 21:49:27 BST)

Figure 2A reproduced by COPASI 4 build 19

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