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BIOMD0000000171 - Leloup1998_CircClock_LD

 

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Reference Publication
Publication ID: 9486845
Leloup JC, Goldbeter A.
A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins.
J. Biol. Rhythms 1998 Feb; 13(1): 70-87
Unité de Chronobiologie Théorique des Sciences, Faculté des Sciences, Université Libre de Bruxelles, Campus Plaine, Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000171.origin
Submitter: Lukas Endler
Submission ID: MODEL0243843132
Submission Date: 08 May 2008 16:00:58 UTC
Last Modification Date: 08 Apr 2016 15:38:12 UTC
Creation Date: 08 May 2008 10:48:48 UTC
Encoders:  Lukas Endler
set #1
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
bqbiol:isPartOf KEGG Pathway Circadian rhythm - fly - Drosophila melanogaster (fruit fly)
bqbiol:hasTaxon Taxonomy Drosophila melanogaster
bqmodel:isDerivedFrom BioModels Database Goldbeter1995_CircClock
Notes

Leloup and Goldbeter, 1998

This model was created after the article by Leloup and Goldbeter, J Biol Rhythms 1998, Vol:13(1),pp70-87, pubmedID: 9486845
A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM Proteins
The parameters and initial concentrations are taken to reproduce figs. 4 D,E,F in the publication.
For a simulation without light dependent degradation of TIM_pp, change the the parameter v_dT_fac to 1.
The light/dark phases length can be set using the parameter l_d .


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 9486845 Submission Date: 08 May 2008 16:00:58 UTC Last Modification Date: 08 Apr 2016 15:38:12 UTC Creation Date: 08 May 2008 10:48:48 UTC
Mathematical expressions
Reactions
per transkription tim transkription tim mRNA decay per mRNA decay
PER tranlation TIM translation PER decay PER-p decay
PER-pp decay TIM decay TIM-p decay TIM-pp decay
Per_TIM complex formation cytopl. PER_TIM compl. decay nuclear PER_TIM compl. decay PER_TIM complex shuttling
PER phosphorylation PER-p phosphorylation PER-p dephosphorylation PER-pp dephosphorylation
TIM phosphorylation TIM-p phosphorylation TIM-p dephosphorylation TIM-pp dephosphorylation
TIM-pp light deactivation PER-pp light deactivation    
Rules
Assignment Rule (variable: total TIM) Assignment Rule (variable: total PER) Assignment Rule (variable: T2_lightdecay_rate)  
Physical entities
Compartments Species
nucleus PER_TIM complex nuclear    
cytoplasm tim mRNA per mRNA TIM
TIM-p TIM-pp PER
PER-p PER-pp PER_TIM complex cytoplasm
total TIM total PER  
Global parameters
transkr_rep_hill_coefficient degradation_rate T2_lightdecay_rate light_dark_period
v_dT_fold_incr_during_light v_dT_value_darkness    
Reactions (26)
 
 per transkription  → [per mRNA];   {PER_TIM complex nuclear}
 
 tim transkription  → [tim mRNA];   {PER_TIM complex nuclear}
 
 tim mRNA decay [tim mRNA] → ;  
 
 per mRNA decay [per mRNA] → ;  
 
 PER tranlation  → [PER];   {per mRNA}
 
 TIM translation  → [TIM];   {tim mRNA}
 
 PER decay [PER] → ;  
 
 PER-p decay [PER-p] → ;  
 
 PER-pp decay [PER-pp] → ;  
 
 TIM decay [TIM] → ;  
 
 TIM-p decay [TIM-p] → ;  
 
 TIM-pp decay [TIM-pp] → ;  
 
 Per_TIM complex formation [PER-pp] + [TIM-pp] → [PER_TIM complex cytoplasm];  
 
 cytopl. PER_TIM compl. decay [PER_TIM complex cytoplasm] → ;  
 
 nuclear PER_TIM compl. decay [PER_TIM complex nuclear] → ;  
 
 PER_TIM complex shuttling [PER_TIM complex cytoplasm] ↔ [PER_TIM complex nuclear];  
 
 PER phosphorylation [PER] → [PER-p];  
 
 PER-p phosphorylation [PER-p] → [PER-pp];  
 
 PER-p dephosphorylation [PER-p] → [PER];  
 
 PER-pp dephosphorylation [PER-pp] → [PER-p];  
 
 TIM phosphorylation [TIM] → [TIM-p];  
 
 TIM-p phosphorylation [TIM-p] → [TIM-pp];  
 
 TIM-p dephosphorylation [TIM-p] → [TIM];  
 
 TIM-pp dephosphorylation [TIM-pp] → [TIM-p];  
 
 TIM-pp light deactivation [TIM-pp] → ;  
 
 PER-pp light deactivation [PER-pp] → ;  
 
Rules (3)
 
 Assignment Rule (name: Tt) total TIM = T0+T1+T2+C+CN*nucleus/cytoplasm
 
 Assignment Rule (name: Pt) total PER = P0+P1+P2+C+CN*nucleus/cytoplasm
 
 Assignment Rule (name: v_dT) T2_lightdecay_rate = (1+(v_dT_fac-1)*ceil(sin(time/l_d*pi)*0.9))*v_dT_dark
 
  Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 PER_TIM complex nuclear
Compartment: nucleus
Initial concentration: 1.2
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 tim mRNA
Compartment: cytoplasm
Initial concentration: 1.41
 
 per mRNA
Compartment: cytoplasm
Initial concentration: 0.09
 
 TIM
Compartment: cytoplasm
Initial concentration: 0.54
 
 TIM-p
Compartment: cytoplasm
Initial concentration: 0.79
 
 TIM-pp
Compartment: cytoplasm
Initial concentration: 4.65
 
 PER
Compartment: cytoplasm
Initial concentration: 0.02
 
 PER-p
Compartment: cytoplasm
Initial concentration: 0.02
 
 PER-pp
Compartment: cytoplasm
Initial concentration: 0.01
 
 PER_TIM complex cytoplasm
Compartment: cytoplasm
Initial concentration: 0.18
 
  total TIM
Compartment: cytoplasm
 
  total PER
Compartment: cytoplasm
 
Global Parameters (6)
 
   transkr_rep_hill_coefficient
Value: 4.0   (Units: dimensionless)
Constant
 
   degradation_rate
Value: 0.01   (Units: perhour)
Constant
 
   T2_lightdecay_rate
Value: 2.0   (Units: nanoMperHour)
 
   light_dark_period
Value: 12.0   (Units: hours)
Constant
 
   v_dT_fold_incr_during_light
Value: 2.0   (Units: dimensionless)
Constant
 
   v_dT_value_darkness
Value: 2.0   (Units: nanoMperHour)
Constant
 
per transkription (2)
 
   per_max_transkr_rate
Value: 0.8   (Units: nanomolperhour)
Constant
 
   per_inh_konstant
Value: 1.0   (Units: nanomoleperlitre)
Constant
 
tim transkription (2)
 
   tim_max_transkr_rate
Value: 1.0   (Units: nanomolperhour)
Constant
 
   tim_inh_konstant
Value: 1.0   (Units: nanomoleperlitre)
Constant
 
tim mRNA decay (2)
 
   M_T_mm_decay
Value: 0.7   (Units: nanoMperHour)
Constant
 
   decay_KM_T
Value: 0.2   (Units: nanomoleperlitre)
Constant
 
per mRNA decay (2)
 
   max_M_P_decay_rate
Value: 0.8   (Units: nanoMperHour)
Constant
 
   M_P_decay_Km
Value: 0.2   (Units: nanomoleperlitre)
Constant
 
PER tranlation (1)
 
   PER_translation_rate
Value: 0.9   (Units: perhour)
Constant
 
TIM translation (1)
 
   TIM_translation_rate
Value: 0.9   (Units: perhour)
Constant
 
Per_TIM complex formation (2)
 
   T_P_ass_rate
Value: 1.2   (Units: pernMperHour)
Constant
 
   C_diss_rate
Value: 0.6   (Units: perhour)
Constant
 
cytopl. PER_TIM compl. decay (1)
 
   C_decay_rate
Value: 0.01   (Units: perhour)
Constant
 
nuclear PER_TIM compl. decay (1)
 
   CN_decay_rate
Value: 0.01   (Units: perhour)
Constant
 
PER_TIM complex shuttling (2)
 
   C_import_rate
Value: 1.2   (Units: perhour)
Constant
 
   C_export_rate
Value: 0.2   (Units: perhour)
Constant
 
PER phosphorylation (2)
 
   P0_phos_rate
Value: 8.0   (Units: nanoMperHour)
Constant
 
   P0_kinase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
PER-p phosphorylation (2)
 
   P1_phosph_rate
Value: 8.0   (Units: nanoMperHour)
Constant
 
   P1_kinase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
PER-p dephosphorylation (2)
 
   P1_phosphatase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
   P1_dephos_rate
Value: 1.0   (Units: nanoMperHour)
Constant
 
PER-pp dephosphorylation (2)
 
   P2_dephos_rate
Value: 1.0   (Units: nanoMperHour)
Constant
 
   P2_phosphatase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
TIM phosphorylation (2)
 
   T0_phos_rate
Value: 8.0   (Units: nanoMperHour)
Constant
 
   T0_kinase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
TIM-p phosphorylation (2)
 
   T1_phosph_rate
Value: 8.0   (Units: nanoMperHour)
Constant
 
   T1_kinase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
TIM-p dephosphorylation (2)
 
   T1_phosphatase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
   T1_dephos_rate
Value: 1.0   (Units: nanoMperHour)
Constant
 
TIM-pp dephosphorylation (2)
 
   T2_dephos_rate
Value: 1.0   (Units: nanoMperHour)
Constant
 
   T2_phosphatase_KM
Value: 2.0   (Units: nanomoleperlitre)
Constant
 
TIM-pp light deactivation (1)
 
   T2_light_deact_KM
Value: 0.2   (Units: nanomoleperlitre)
Constant
 
PER-pp light deactivation (2)
 
   P2_light_deactivation_rate
Value: 2.0   (Units: nanoMperHour)
Constant
 
   P2_light_deactivation_KM
Value: 0.2   (Units: nanomoleperlitre)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000171

Curator's comment: (updated: 08 May 2008 14:14:39 BST)

The model has been simulated using copasi 4.3(build 25)
For fig 4A one parameter, v_dT_fac, has been changed to 1 and the starting point of the simulation had to be changed to +32 hours to better fit the figure in the publication.

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