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BIOMD0000000160 - Xie2007_CircClock

 

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Reference Publication
Publication ID: 17157878
Xie Z, Kulasiri D.
Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops.
J. Theor. Biol. 2007 Mar; 245(2): 290-304
Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Canterbury, New Zealand.  [more]
Model
Original Model: BIOMD0000000160.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL1029395046
Submission Date: 30 Jan 2008 23:06:46 UTC
Last Modification Date: 05 Jul 2012 14:37:46 UTC
Creation Date: 22 Jan 2008 07:26:48 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:occursIn Taxonomy Drosophila melanogaster
bqbiol:isPartOf KEGG Pathway dme04711
bqbiol:is Gene Ontology circadian rhythm
Gene Ontology regulation of circadian sleep/wake cycle, sleep
Notes

The model reproduces the oscillations for mRNA and protein species as depicted in Fig 3 of the plot. The model differs slightly from that given in the paper and this was made after a communication from the authors. The values of parameters tcvriclkp, tcdvpmt and dccpt are slightly different. Also, although it is not given in the paper, rate laws for reactions re20, re28, re35, re42, re43 and re45 are multiplied by a specie. Model was successfully tested on MathSBML


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: 17157878 Submission Date: 30 Jan 2008 23:06:46 UTC Last Modification Date: 05 Jul 2012 14:37:46 UTC Creation Date: 22 Jan 2008 07:26:48 UTC
Mathematical expressions
Reactions
CC PT association Degradation of CLK CYK dimer Degradation of CC PT dimer Degradation of PER TIM dimer
Degradation of clk mRNA clkm translation Degradation of per mRNA perm translation
per transcription vri transcription Degradation of vri mRNA vrim translation
VRI protein degradation pdp transcription Degradation of pdp mRNA pdpm translation
PDP protein degradation clk transcription CLK CYC association CLK protein degradation
CLK CYC dissociation PER TIM association PER TIM dissociation PER protein degradation
tim transcription Degradation of tim mRNA timm translation TIM protein degradation
CC PT dimer dissociation CC binding probability in per promoter CC Unbinding probability in per promoter CC Unbinding probability in vri promoter
CC binding probability in vri promoter CC Unbinding probability in pdp1 promoter CC binding probability in pdp1 promoter VRI binding clk promoter
VRI unbinding clk promoter PDP binding clk promoter PDP unbinding clk promoter CC binding probability in tim promoter
CC Unbinding probability in tim promoter      
Physical entities
Compartments Species
wholeCell CC CCPT clkp
perp clkm perm
PT vrip vrim
VRI pdpp pdpm
PDP CLK PER
timp timm TIM
CYC CCbindingPer CCbindingvri
CCbindingpdp VRIbindingclkp PDPbindingclkp
CCbindingtim    
Global parameters
dccpt bccperp ubccperp bccpt
dperm tlper tcccperp tcdvpmt
dvri tcclkp bcc dclk
ubcc bpt ubpt dper
tcccvrip tcccpdpp dvrim dpdpm
ubccpt tlvri tlpdp bccvrip
bccpdpp ubccvrip ubccpdpp tcpdpclkp
dclkm bvriclkp bpdpclkp ubvriclkp
ubpdpclkp tcvriclkp dpdp tlclk
dcc dpt dtim dtimm
tltim bcctimp ubcctimp tccctimp
npt nvri npdp  
Reactions (41)
 
 CC PT association [CC] + [PT] → [CCPT];  
 
 Degradation of CLK CYK dimer [CC] → ;  
 
 Degradation of CC PT dimer [CCPT] → ;  
 
 Degradation of PER TIM dimer [PT] → ;  
 
 Degradation of clk mRNA [clkm] → ;  
 
 clkm translation  → [CLK];   {clkm}
 
 Degradation of per mRNA [perm] → ;  
 
 perm translation  → [PER];   {perm}
 
 per transcription  → [perm];   {CCbindingPer} , {perp}
 
 vri transcription  → [vrim];   {CCbindingvri} , {vrip}
 
 Degradation of vri mRNA [vrim] → ;  
 
 vrim translation  → [VRI];   {vrim}
 
 VRI protein degradation [VRI] → ;  
 
 pdp transcription  → [pdpm];   {CCbindingpdp} , {pdpp}
 
 Degradation of pdp mRNA [pdpm] → ;  
 
 pdpm translation  → [PDP];   {pdpm}
 
 PDP protein degradation [PDP] → ;  
 
 clk transcription  → [clkm];   {VRIbindingclkp} , {clkp} , {PDPbindingclkp}
 
 CLK CYC association [CLK] + [CYC] → [CC];  
 
 CLK protein degradation [CLK] → ;  
 
 CLK CYC dissociation [CC] → [CLK] + [CYC];  
 
 PER TIM association [PER] + [TIM] → [PT];  
 
 PER TIM dissociation [PT] → [PER] + [TIM];  
 
 PER protein degradation [PER] → ;  
 
 tim transcription  → [timm];   {CCbindingtim} , {timp}
 
 Degradation of tim mRNA [timm] → ;  
 
 timm translation  → [TIM];   {timm}
 
 TIM protein degradation [TIM] → ;  
 
 CC PT dimer dissociation [CCPT] → [CC] + [PT];  
 
 CC binding probability in per promoter  → [CCbindingPer];   {CC}
 
 CC Unbinding probability in per promoter [CCbindingPer] → ;  
 
 CC Unbinding probability in vri promoter [CCbindingvri] → ;  
 
 CC binding probability in vri promoter  → [CCbindingvri];   {CC}
 
 CC Unbinding probability in pdp1 promoter [CCbindingpdp] → ;  
 
 CC binding probability in pdp1 promoter  → [CCbindingpdp];   {CC}
 
 VRI binding clk promoter  → [VRIbindingclkp];   {PDPbindingclkp} , {VRI}
 
 VRI unbinding clk promoter [VRIbindingclkp] → ;  
 
 PDP binding clk promoter  → [PDPbindingclkp];   {VRIbindingclkp} , {PDP}
 
 PDP unbinding clk promoter [PDPbindingclkp] → ;  
 
 CC binding probability in tim promoter  → [CCbindingtim];   {CC}
 
 CC Unbinding probability in tim promoter [CCbindingtim] → ;  
 
 wholeCell Spatial dimensions: 3.0  Compartment size: 1.0
 
 CC
Compartment: wholeCell
Initial concentration: 0.5566
 
 CCPT
Compartment: wholeCell
Initial concentration: 0.4982
 
   clkp
Compartment: wholeCell
Initial concentration: 0.003185
 
   perp
Compartment: wholeCell
Initial concentration: 0.003185
 
   clkm
Compartment: wholeCell
Initial concentration: 0.2583
 
   perm
Compartment: wholeCell
Initial concentration: 0.2395
 
 PT
Compartment: wholeCell
Initial concentration: 0.4014
 
   vrip
Compartment: wholeCell
Initial concentration: 0.003185
 
   vrim
Compartment: wholeCell
Initial concentration: 0.2571
 
 VRI
Compartment: wholeCell
Initial concentration: 3.175
 
   pdpp
Compartment: wholeCell
Initial concentration: 0.003185
 
   pdpm
Compartment: wholeCell
Initial concentration: 0.3175
 
 PDP
Compartment: wholeCell
Initial concentration: 4.1953
 
 CLK
Compartment: wholeCell
Initial concentration: 3.6628
 
 PER
Compartment: wholeCell
Initial concentration: 2.7527
 
   timp
Compartment: wholeCell
Initial concentration: 0.003185
 
   timm
Compartment: wholeCell
Initial concentration: 0.2395
 
 TIM
Compartment: wholeCell
Initial concentration: 2.7527
 
 CYC
Compartment: wholeCell
Initial concentration: 1.0
Constant
 
   CCbindingPer
Compartment: wholeCell
Initial amount: 0.0431
 
   CCbindingvri
Compartment: wholeCell
Initial amount: 0.0585
 
   CCbindingpdp
Compartment: wholeCell
Initial amount: 0.08
 
   VRIbindingclkp
Compartment: wholeCell
Initial amount: 0.489
 
   PDPbindingclkp
Compartment: wholeCell
Initial amount: 0.426
 
   CCbindingtim
Compartment: wholeCell
Initial amount: 0.043
 
Global Parameters (47)
 
   dccpt
Value: 15.06
Constant
 
   bccperp
Value: 0.069
Constant
 
   ubccperp
Value: 0.262
Constant
 
   bccpt
Value: 51.0
Constant
 
   dperm
Value: 0.053
Constant
 
   tlper
Value: 36.0
Constant
 
   tcccperp
Value: 11.0
Constant
 
   tcdvpmt
Value: 0.028
Constant
 
   dvri
Value: 1.226
Constant
 
   tcclkp
Value: 1.42
Constant
 
   bcc
Value: 2.349
Constant
 
   dclk
Value: 0.2
Constant
 
   ubcc
Value: 0.89
Constant
 
   bpt
Value: 1.1
Constant
 
   ubpt
Value: 2.93
Constant
 
   dper
Value: 0.62
Constant
 
   tcccvrip
Value: 16.86
Constant
 
   tcccpdpp
Value: 9.831
Constant
 
   dvrim
Value: 0.07
Constant
 
   dpdpm
Value: 0.06
Constant
 
   ubccpt
Value: 7.89
Constant
 
   tlvri
Value: 14.68
Constant
 
   tlpdp
Value: 1.87
Constant
 
   bccvrip
Value: 0.1
Constant
 
   bccpdpp
Value: 0.062
Constant
 
   ubccvrip
Value: 0.276
Constant
 
   ubccpdpp
Value: 0.145
Constant
 
   tcpdpclkp
Value: 125.54
Constant
 
   dclkm
Value: 0.643
Constant
 
   bvriclkp
Value: 1.858
Constant
 
   bpdpclkp
Value: 1.155
Constant
 
   ubvriclkp
Value: 1.043
Constant
 
   ubpdpclkp
Value: 0.952
Constant
 
   tcvriclkp
Value: 0.053
Constant
 
   dpdp
Value: 0.156
Constant
 
   tlclk
Value: 35.0
Constant
 
   dcc
Value: 0.184
Constant
 
   dpt
Value: 0.279
Constant
 
   dtim
Value: 0.62
Constant
 
   dtimm
Value: 0.053
Constant
 
   tltim
Value: 36.0
Constant
 
   bcctimp
Value: 0.069
Constant
 
   ubcctimp
Value: 0.262
Constant
 
   tccctimp
Value: 11.0
Constant
 
   npt
Value: 5.0
Constant
 
   nvri
Value: 4.0
Constant
 
   npdp
Value: 6.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000160

Curator's comment: (updated: 22 Jan 2008 19:20:13 GMT)

Plot corresponds to Fig 3 of the paper. Results obtained from MathSBML.

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