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BIOMD0000000188 - Proctor2008_p53_Mdm2_ATM

 

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Reference Publication
Publication ID: 18706112
Proctor CJ, Gray DA.
Explaining oscillations and variability in the p53-Mdm2 system.
BMC Syst Biol 2008; 2: 75
Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK. c.j.proctor@ncl.ac.uk  [more]
Model
Original Model: BIOMD0000000188.xml.origin
Submitter: Carole Proctor
Submission ID: MODEL5836973167
Submission Date: 05 Sep 2008 14:13:40 UTC
Last Modification Date: 02 Feb 2010 13:34:40 UTC
Creation Date: 01 Sep 2008 11:45:30 UTC
Encoders:  Carole Proctor
   Vijayalakshmi Chelliah
   Douglas A Gray
set #1
bqbiol:isPartOf KEGG Pathway hsa04115
bqbiol:isVersionOf Gene Ontology regulation of DNA damage response, signal transduction by p53 class mediator
bqbiol:occursIn Taxonomy Homo sapiens
set #2
bqbiol:isPartOf Reactome REACT_85
bqbiol:isVersionOf Reactome REACT_309
Notes

This model is automatically converted from the Model BIOMD0000000188 by using libsbml . According to the terms of use , this generated model is not related with Model BIOMD0000000188 any more.

Model
Publication ID: 18706112 Submission Date: 05 Sep 2008 14:13:40 UTC Last Modification Date: 02 Feb 2010 13:34:40 UTC Creation Date: 01 Sep 2008 11:45:30 UTC
Mathematical expressions
Reactions
p53mRNASynthesis p53mRNADegradation Mdm2Synthesis Mdm2mRNASynthesis1
Mdm2mRNASynthesis2 Mdm2mRNADegradation Mdm2Degradation p53Synthesis
p53Degradation P53_Mdm2Binding P53_Mdm2Release DNAdamage
DNArepair ATMactivation p53phoshorylation p53dephosorylation
Mdm2phoshorylation Mdm2dephosorylation Mdm2Pdegradation ATMInactivation
Rules
Assignment Rule (variable: totp53) Assignment Rule (variable: totMdm2)    
Events
stressCell stopStress    
Physical entities
Compartments Species
cell Mdm2 p53 Mdm2_p53
Mdm2_mRNA p53_mRNA ATMA
ATMI p53_P Mdm2_P
damDNA Sink Source
p53deg p53syn mdm2deg
mdm2syn Mdm2mRNAdeg Mdm2mRNAsyn
totp53 totMdm2  
Global parameters
IR ksynMdm2 kdegMdm2 ksynp53
kdegp53 kbinMdm2p53 krelMdm2p53 ksynMdm2mRNA
kdegMdm2mRNA kactATM kdegATMMdm2 kinactATM
kphosp53 kdephosp53 kphosMdm2 kdephosMdm2
kdam krepair kproteff ksynp53mRNA
kdegp53mRNA      
Reactions (20)
 
 p53mRNASynthesis [Source] → [p53_mRNA];  
 
 p53mRNADegradation [p53_mRNA] → [Sink];  
 
 Mdm2Synthesis [Mdm2_mRNA] → [Mdm2_mRNA] + [Mdm2] + [mdm2syn];  
 
 Mdm2mRNASynthesis1 [p53] → [p53] + [Mdm2_mRNA] + [Mdm2mRNAsyn];  
 
 Mdm2mRNASynthesis2 [p53_P] → [p53_P] + [Mdm2_mRNA] + [Mdm2mRNAsyn];  
 
 Mdm2mRNADegradation [Mdm2_mRNA] → [Sink] + [Mdm2mRNAdeg];  
 
 Mdm2Degradation [Mdm2] → [Sink] + [mdm2deg];  
 
 p53Synthesis [p53_mRNA] → [p53] + [p53_mRNA] + [p53syn];  
 
 p53Degradation [Mdm2_p53] → [Mdm2] + [p53deg];  
 
 P53_Mdm2Binding [p53] + [Mdm2] → [Mdm2_p53];  
 
 P53_Mdm2Release [Mdm2_p53] → [p53] + [Mdm2];  
 
 DNAdamage  → [damDNA];  
 
 DNArepair [damDNA] → [Sink];  
 
 ATMactivation [damDNA] + [ATMI] → [damDNA] + [ATMA];  
 
 p53phoshorylation [p53] + [ATMA] → [p53_P] + [ATMA];  
 
 p53dephosorylation [p53_P] → [p53];  
 
 Mdm2phoshorylation [Mdm2] + [ATMA] → [Mdm2_P] + [ATMA];  
 
 Mdm2dephosorylation [Mdm2_P] → [Mdm2];  
 
 Mdm2Pdegradation [Mdm2_P] → [Sink] + [mdm2deg];  
 
 ATMInactivation [ATMA] → [ATMI];  
 
Rules (2)
 
 Assignment Rule (name: totp53) totp53 = p53+Mdm2_p53+p53_P
 
 Assignment Rule (name: totMdm2) totMdm2 = Mdm2+Mdm2_p53+Mdm2_P
 
Events (2)
 
 stressCell
IR = 25
 
 stopStress
IR = 0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Mdm2
Compartment: cell
Initial amount: 5.0
 
 p53
Compartment: cell
Initial amount: 5.0
 
 Mdm2_p53
Compartment: cell
Initial amount: 95.0
 
 Mdm2_mRNA
Compartment: cell
Initial amount: 10.0
 
 p53_mRNA
Compartment: cell
Initial amount: 10.0
 
 ATMA
Compartment: cell
Initial amount: 0.0
 
 ATMI
Compartment: cell
Initial amount: 200.0
 
 p53_P
Compartment: cell
Initial amount: 0.0
 
 Mdm2_P
Compartment: cell
Initial amount: 0.0
 
 damDNA
Compartment: cell
Initial amount: 0.0
 
 Sink
Compartment: cell
Initial amount: 1.0
Constant
 
 Source
Compartment: cell
Initial amount: 1.0
Constant
 
 p53deg
Compartment: cell
Initial amount: 0.0
 
 p53syn
Compartment: cell
Initial amount: 0.0
 
 mdm2deg
Compartment: cell
Initial amount: 0.0
 
 mdm2syn
Compartment: cell
Initial amount: 0.0
 
 Mdm2mRNAdeg
Compartment: cell
Initial amount: 0.0
 
 Mdm2mRNAsyn
Compartment: cell
Initial amount: 0.0
 
  totp53
Compartment: cell
Initial amount: 0.0
 
  totMdm2
Compartment: cell
Initial amount: 0.0
 
Global Parameters (21)
 
   IR  
 
   ksynMdm2
Value: 4.95E-4   (Units: psec)
Constant
 
   kdegMdm2
Value: 4.33E-4   (Units: psec)
Constant
 
   ksynp53
Value: 0.0060   (Units: psec)
Constant
 
   kdegp53
Value: 8.25E-4   (Units: psec)
Constant
 
   kbinMdm2p53
Value: 0.001155   (Units: pmolpsec)
Constant
 
   krelMdm2p53
Value: 1.155E-5   (Units: psec)
Constant
 
   ksynMdm2mRNA
Value: 1.0E-4   (Units: psec)
Constant
 
   kdegMdm2mRNA
Value: 1.0E-4   (Units: psec)
Constant
 
   kactATM
Value: 1.0E-4   (Units: pmolpsec)
Constant
 
   kdegATMMdm2
Value: 4.0E-4   (Units: psec)
Constant
 
   kinactATM
Value: 5.0E-4   (Units: psec)
Constant
 
   kphosp53
Value: 5.0E-4   (Units: pmolpsec)
Constant
 
   kdephosp53
Value: 0.5   (Units: psec)
Constant
 
   kphosMdm2
Value: 2.0   (Units: pmolpsec)
Constant
 
   kdephosMdm2
Value: 0.5   (Units: psec)
Constant
 
   kdam
Value: 0.08   (Units: molepsecpdGy)
Constant
 
   krepair
Value: 2.0E-5   (Units: psec)
Constant
 
   kproteff
Value: 1.0   (Units: dimensionless)
Constant
 
   ksynp53mRNA
Value: 0.0010   (Units: psec)
Constant
 
   kdegp53mRNA
Value: 1.0E-4   (Units: psec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000188

Curator's comment: (updated: 05 Sep 2008 15:08:16 BST)

Comment: The model is simulated and integrated using SBML OdeSolver with options (-n --printstep 1e4 --error 1e-14 -z).

Figure 13 (for ATM model) of the original paper (Procter CJ, 2008) is reproduced in here.

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