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BIOMD0000000016 - Goldbeter1995_CircClock

 

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Reference Publication
Publication ID: 8587874
Goldbeter A.
A model for circadian oscillations in the Drosophila period protein (PER).
Proc. Biol. Sci. 1995 Sep; 261(1362): 319-324
Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000016.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6617161845
Submission Date: 13 Sep 2005 13:13:05 UTC
Last Modification Date: 25 Feb 2015 13:08:26 UTC
Creation Date: 29 Jun 2005 10:17:21 UTC
Encoders:  Nicolas Le Novère
   Bruce Shapiro
set #1
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
bqbiol:hasTaxon Taxonomy Drosophila melanogaster
bqbiol:is KEGG Pathway Circadian rhythm - fly - Drosophila melanogaster (fruit fly)
Notes

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: 8587874 Submission Date: 13 Sep 2005 13:13:05 UTC Last Modification Date: 25 Feb 2015 13:08:26 UTC Creation Date: 29 Jun 2005 10:17:21 UTC
Mathematical expressions
Reactions
transcription of PER translation of PER first phosphorylation of PER removal of the first PER phosphate
second phosphorylation of PER removal of the second PER phosphate translocation of PER to the nucleus translocation of PER to the cytoplasm
degradation of PER mRNA degradation of PER    
Rules
Assignment Rule (variable: total PER)      
Physical entities
Compartments Species
default EmptySet    
CYTOPLASM PER mRNA unphosphorylated PER monophosphorylated PER
biphosphorylated PER total PER  
NUCLEUS nuclear PER    
Reactions (10)
 
 transcription of PER [EmptySet] → [PER mRNA];   {nuclear PER}
 
 translation of PER [EmptySet] → [unphosphorylated PER];   {PER mRNA}
 
 first phosphorylation of PER [unphosphorylated PER] → [monophosphorylated PER];  
 
 removal of the first PER phosphate [monophosphorylated PER] → [unphosphorylated PER];  
 
 second phosphorylation of PER [monophosphorylated PER] → [biphosphorylated PER];  
 
 removal of the second PER phosphate [biphosphorylated PER] → [monophosphorylated PER];  
 
 translocation of PER to the nucleus [biphosphorylated PER] → [nuclear PER];  
 
 translocation of PER to the cytoplasm [nuclear PER] → [biphosphorylated PER];  
 
 degradation of PER mRNA [PER mRNA] → [EmptySet];  
 
 degradation of PER [biphosphorylated PER] → [EmptySet];  
 
Rules (1)
 
 Assignment Rule (name: Pt) total PER = P0+P1+P2+Pn
 
   Spatial dimensions: 3.0  Compartment size: 1.0E-15
 
 EmptySet
Compartment: default
Initial amount: 0.0
Constant
 
  Spatial dimensions: 3.0  Compartment size: 1.0E-15
 
 PER mRNA
Compartment: CYTOPLASM
Initial concentration: 0.1
 
 unphosphorylated PER
Compartment: CYTOPLASM
Initial concentration: 0.25
 
 monophosphorylated PER
Compartment: CYTOPLASM
Initial concentration: 0.25
 
 biphosphorylated PER
Compartment: CYTOPLASM
Initial concentration: 0.25
 
  total PER
Compartment: CYTOPLASM
Initial concentration: 1.0
 
 NUCLEUS Spatial dimensions: 3.0  Compartment size: 1.0E-15
 
 nuclear PER
Compartment: NUCLEUS
Initial concentration: 0.25
 
transcription of PER (3)
 
   Vs
Value: 0.76
Constant
 
   KI
Value: 1.0
Constant
 
   n
Value: 4.0
Constant
 
translation of PER (1)
 
   ks
Value: 0.38
Constant
 
first phosphorylation of PER (2)
 
   V1
Value: 3.2
Constant
 
   K1
Value: 2.0
Constant
 
removal of the first PER phosphate (2)
 
   V2
Value: 1.58
Constant
 
   K2
Value: 2.0
Constant
 
second phosphorylation of PER (2)
 
   V3
Value: 5.0
Constant
 
   K3
Value: 2.0
Constant
 
removal of the second PER phosphate (2)
 
   V4
Value: 2.5
Constant
 
   K4
Value: 2.0
Constant
 
translocation of PER to the nucleus (1)
 
   k1
Value: 1.9
Constant
 
translocation of PER to the cytoplasm (1)
 
   k2
Value: 1.3
Constant
 
degradation of PER mRNA (2)
 
   Km
Value: 0.5
Constant
 
   Vm
Value: 0.65
Constant
 
degradation of PER (2)
 
   Vd
Value: 0.95
Constant
 
   Kd
Value: 0.2
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000016

Curator's comment: (updated: 06 Aug 2007 13:20:48 BST)

Figure 2 reproduced with COPASI 4.1 (build 21)

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