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BIOMD0000000078 - Leloup2003_CircClock_LD

 

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Reference Publication
Publication ID: 12775757
Leloup JC, Goldbeter A.
Toward a detailed computational model for the mammalian circadian clock.
Proc. Natl. Acad. Sci. U.S.A. 2003 Jun; 100(12): 7051-7056
Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles, Campus Plaine, C. P. 231, B-1050 Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000078.origin
Submitter: Enuo He
Submission ID: MODEL4108701438
Submission Date: 27 Nov 2006 13:49:08 UTC
Last Modification Date: 11 Jul 2012 19:31:48 UTC
Creation Date: 17 Oct 2006 16:43:58 UTC
Encoders:  Enuo He
set #1
bqbiol:hasVersion KEGG Pathway Circadian rhythm - Homo sapiens (human)
set #2
bqbiol:isVersionOf Gene Ontology entrainment of circadian clock
set #3
bqmodel:isDerivedFrom BioModels Database Leloup1999_CircClock
set #4
bqbiol:hasTaxon Taxonomy Mammalia
Notes

This model is described in the paper Toward a detailed computational model for the mammalian circadian clock . In this model only interlocked negative and positive regulation of Per, Cry, Bmal gene are involved. Some initial values were not provided, therefore they were chosen to fit the curves from the paper.

Figure2C is re-produced by odeSolver.


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: 12775757 Submission Date: 27 Nov 2006 13:49:08 UTC Last Modification Date: 11 Jul 2012 19:31:48 UTC Creation Date: 17 Oct 2006 16:43:58 UTC
Mathematical expressions
Reactions
Mb synthesized Mb translated into protein Mb nonspecific degradation Bc phosphorylation
Bc transfered from cytosolic to nuclear Mc translated into protein Mc nonspecific degradation Cc phosphorylation
Ccp specific degradation Mp synthesis Mp translated into protein Pcp specific degradation
Pc phosphorylation Cc and Pc produce complex Per_Cry PCc phosphorylation PCcp specific degradation
PCc transfered into nuclear PCnp nonspecific degradation Bcp nonspecific degradation Bnp nonspecific degradation
Mc synthesis PCn phosphorylation Mp nonspecific degradation Per_Cry and Clock_Bmal form inactive complex
Mb specific degradation Mc specific degradation Mp specific degradation Pc nonspecific degradation
Cc nonspecific degradation Pcp nonspecific degradation Ccp nonspecific degradation PCcp nonspecific degradation
PCc nonspecific degradation PCnp specific degradation Bc nonspecific degradation Bcp specific degradation
Bn phosphorylation Bnp specific degradation In nonspecific degration In specific degradation
Bn nonspecific degradation Bcp dephosphorylation Bnp dephosphorylation Ccp dephosphorylation
Pcp dephosphorylation PCnp dephosphorylation PCn nonspecific degradation PCcp dephosphorylation
Rules
Assignment Rule (variable: LD) Assignment Rule (variable: vsp)    
Physical entities
Compartments Species
cell Mb Bc Bcp
Bn Cc Mc
Ccp Mp Pc
Pcp PCc PCcp
PCn Bnp PCnp
In    
Global parameters
LD vsp    
Reactions (48)
 
 Mb synthesized  → [Mb];   {Bn}
 
 Mb translated into protein  → [Bc];   {Mb}
 
 Mb nonspecific degradation [Mb] → ;  
 
 Bc phosphorylation [Bc] → [Bcp];  
 
 Bc transfered from cytosolic to nuclear [Bc] ↔ [Bn];  
 
 Mc translated into protein  → [Cc];   {Mc}
 
 Mc nonspecific degradation [Mc] → ;  
 
 Cc phosphorylation [Cc] → [Ccp];  
 
 Ccp specific degradation [Ccp] → ;  
 
 Mp synthesis  → [Mp];   {Bn}
 
 Mp translated into protein  → [Pc];   {Mp}
 
 Pcp specific degradation [Pcp] → ;  
 
 Pc phosphorylation [Pc] → [Pcp];  
 
 Cc and Pc produce complex Per_Cry [Cc] + [Pc] ↔ [PCc];  
 
 PCc phosphorylation [PCc] → [PCcp];  
 
 PCcp specific degradation [PCcp] → ;  
 
 PCc transfered into nuclear [PCc] ↔ [PCn];  
 
 PCnp nonspecific degradation [PCnp] → ;  
 
 Bcp nonspecific degradation [Bcp] → ;  
 
 Bnp nonspecific degradation [Bnp] → ;  
 
 Mc synthesis  → [Mc];   {Bn}
 
 PCn phosphorylation [PCn] → [PCnp];  
 
 Mp nonspecific degradation [Mp] → ;  
 
 Per_Cry and Clock_Bmal form inactive complex [PCn] + [Bn] ↔ [In];  
 
 Mb specific degradation [Mb] → ;  
 
 Mc specific degradation [Mc] → ;  
 
 Mp specific degradation [Mp] → ;  
 
 Pc nonspecific degradation [Pc] → ;  
 
 Cc nonspecific degradation [Cc] → ;  
 
 Pcp nonspecific degradation [Pcp] → ;  
 
 Ccp nonspecific degradation [Ccp] → ;  
 
 PCcp nonspecific degradation [PCcp] → ;  
 
 PCc nonspecific degradation [PCc] → ;  
 
 PCnp specific degradation [PCnp] → ;  
 
 Bc nonspecific degradation [Bc] → ;  
 
 Bcp specific degradation [Bcp] → ;  
 
 Bn phosphorylation [Bn] → [Bnp];  
 
 Bnp specific degradation [Bnp] → ;  
 
 In nonspecific degration [In] → ;  
 
 In specific degradation [In] → ;  
 
 Bn nonspecific degradation [Bn] → ;  
 
 Bcp dephosphorylation [Bcp] → [Bc];  
 
 Bnp dephosphorylation [Bnp] → [Bn];  
 
 Ccp dephosphorylation [Ccp] → [Cc];  
 
 Pcp dephosphorylation [Pcp] → [Pc];  
 
 PCnp dephosphorylation [PCnp] → [PCn];  
 
 PCn nonspecific degradation [PCn] → ;  
 
 PCcp dephosphorylation [PCcp] → [PCc];  
 
Rules (2)
 
 Assignment Rule (name: parameter_0000081) LD = functionDefinition_0000005(12)
 
 Assignment Rule (name: parameter_0000082) vsp = 1.5+(1.8-1.5)*parameter_0000081
 
Functions (5)
 
 Activation of gene lambda(Vs, B, n, K, Vs*B^n/(K^n+B^n))
 
 Michaelis-Menten(irreversible) lambda(V, substrate, Km, V*substrate/(Km+substrate))
 
 mRNA translated into protein lambda(k, mRNA, k*mRNA)
 
 Inhibition of gene lambda(vsb, K, m, Bn, vsb*K^m/(K^m+Bn^m))
 
 ceiling lambda(length, ceil(sin(pi*time/length+0.001)/2))
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Mb
Compartment: cell
Initial concentration: 9.5
 
 Bc
Compartment: cell
Initial concentration: 2.0
 
 Bcp
Compartment: cell
Initial concentration: 0.0
 
 Bn
Compartment: cell
Initial concentration: 1.9
 
 Cc
Compartment: cell
Initial concentration: 0.0
 
 Mc
Compartment: cell
Initial concentration: 1.7
 
 Ccp
Compartment: cell
Initial concentration: 0.0
 
 Mp
Compartment: cell
Initial concentration: 2.5
 
 Pc
Compartment: cell
Initial concentration: 0.0
 
 Pcp
Compartment: cell
Initial concentration: 0.0
 
 PCc
Compartment: cell
Initial concentration: 0.0
 
 PCcp
Compartment: cell
Initial concentration: 0.0
 
 PCn
Compartment: cell
Initial concentration: 1.0
 
 Bnp
Compartment: cell
Initial concentration: 0.0
 
 PCnp
Compartment: cell
Initial concentration: 0.0
 
   In
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (2)
 
   LD
Value: NaN
 
   vsp
Value: NaN
 
Mb synthesized (3)
 
   vsb
Value: 1.0
Constant
 
   Kib
Value: 2.2
Constant
 
   m
Value: 2.0
Constant
 
Mb translated into protein (1)
 
   ksb
Value: 0.12
Constant
 
Mb nonspecific degradation (1)
 
   kdmb
Value: 0.01
Constant
 
Bc phosphorylation (2)
 
   V1b
Value: 0.5
Constant
 
   Kp
Value: 0.1
Constant
 
Bc transfered from cytosolic to nuclear (2)
 
   k5
Value: 0.4
Constant
 
   k6
Value: 0.2
Constant
 
Mc translated into protein (1)
 
   ksc
Value: 1.6
Constant
 
Mc nonspecific degradation (1)
 
   kdmc
Value: 0.01
Constant
 
Cc phosphorylation (2)
 
   V1c
Value: 0.6
Constant
 
   Kp
Value: 0.1
Constant
 
Ccp specific degradation (2)
 
   vdcc
Value: 0.7
Constant
 
   Kd
Value: 0.3
Constant
 
Mp synthesis (2)
 
   n
Value: 4.0
Constant
 
   Kap
Value: 0.7
Constant
 
Mp translated into protein (1)
 
   ksp
Value: 0.6
Constant
 
Pcp specific degradation (2)
 
   vdpc
Value: 0.7
Constant
 
   Kd
Value: 0.3
Constant
 
Pc phosphorylation (2)
 
   V1p
Value: 0.4
Constant
 
   Kp
Value: 0.1
Constant
 
Cc and Pc produce complex Per_Cry (2)
 
   k3
Value: 0.4
Constant
 
   k4
Value: 0.2
Constant
 
PCc phosphorylation (2)
 
   V1pc
Value: 0.4
Constant
 
   Kp
Value: 0.1
Constant
 
PCcp specific degradation (2)
 
   vdpcc
Value: 0.7
Constant
 
   Kd
Value: 0.3
Constant
 
PCc transfered into nuclear (2)
 
   k1
Value: 0.4
Constant
 
   k2
Value: 0.2
Constant
 
PCnp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Bcp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Bnp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Mc synthesis (3)
 
   vsc
Value: 1.1
Constant
 
   n
Value: 4.0
Constant
 
   Kac
Value: 0.6
Constant
 
PCn phosphorylation (2)
 
   V3pc
Value: 0.4
Constant
 
   Kp
Value: 0.1
Constant
 
Mp nonspecific degradation (1)
 
   kdmp
Value: 0.01
Constant
 
Per_Cry and Clock_Bmal form inactive complex (2)
 
   k7
Value: 0.5
Constant
 
   k8
Value: 0.1
Constant
 
Mb specific degradation (2)
 
   vmb
Value: 0.8
Constant
 
   Kmb
Value: 0.4
Constant
 
Mc specific degradation (2)
 
   vmc
Value: 1.0
Constant
 
   Kmc
Value: 0.4
Constant
 
Mp specific degradation (2)
 
   vmp
Value: 1.1
Constant
 
   Kmp
Value: 0.31
Constant
 
Pc nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Cc nonspecific degradation (1)
 
   kdnc
Value: 0.12
Constant
 
Pcp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Ccp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
PCcp nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
PCc nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
PCnp specific degradation (2)
 
   vdpcn
Value: 0.7
Constant
 
   Kd
Value: 0.3
Constant
 
Bc nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Bcp specific degradation (2)
 
   vdbc
Value: 0.5
Constant
 
   Kd
Value: 0.3
Constant
 
Bn phosphorylation (2)
 
   V3b
Value: 0.5
Constant
 
   Kp
Value: 0.1
Constant
 
Bnp specific degradation (2)
 
   vdbn
Value: 0.6
Constant
 
   Kd
Value: 0.3
Constant
 
In nonspecific degration (1)
 
   kdn
Value: 0.01
Constant
 
In specific degradation (2)
 
   vdin
Value: 0.8
Constant
 
   Kd
Value: 0.3
Constant
 
Bn nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
Bcp dephosphorylation (2)
 
   V2b
Value: 0.1
Constant
 
   Kdp
Value: 0.1
Constant
 
Bnp dephosphorylation (2)
 
   V4b
Value: 0.2
Constant
 
   Kdp
Value: 0.1
Constant
 
Ccp dephosphorylation (2)
 
   V2c
Value: 0.1
Constant
 
   Kdp
Value: 0.1
Constant
 
Pcp dephosphorylation (2)
 
   V2p
Value: 0.3
Constant
 
   Kdp
Value: 0.1
Constant
 
PCnp dephosphorylation (2)
 
   V4pc
Value: 0.1
Constant
 
   Kdp
Value: 0.1
Constant
 
PCn nonspecific degradation (1)
 
   kdn
Value: 0.01
Constant
 
PCcp dephosphorylation (2)
 
   V2pc
Value: 0.1
Constant
 
   Kdp
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000078

Curator's comment: (updated: 21 Nov 2006 11:33:33 GMT)

The figure2C in the papaer is reproduced with odeSolver.

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