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Table 5 List of changed and additional reactions for the ATM model

From: Explaining oscillations and variability in the p53-Mdm2 system

Reac No.a Name Term Kinetic law Parameter valuesb  
1 p53 synthesis GO:0006412 ksynp 53<#p53_mRNA> 6.0E-3 s-1 Based on p53 half-life ~20 min[12]
15 ATM activation GO:0006468 k actATM <#damDNA><#ATMI> 1.0E-4 mol-1 s-1 Phosphorylation takes place on time-scale of a few minutes. Rate of reaction depends on amount of damaged DNA and pool of ATMI.
16 ATM inactivation GO:0006470 k inactATM <#ATMA> 5.0E-4 s-1 De-phosphorylation is of the same order of magnitude as phosphorylation.
17 p53 phosphorylation GO:0006468 kphosp 53<#p53><#ATMA> 5.0E-4 mol-1 s-1 Phosphorylation takes place on time-scale of a few minutes.
18 p53 dephosphorylation GO:0006470 kdephosp 53<#p53_P> 5.0E-1 s-1 This parameter was varied to obtain oscillations.
19 Mdm2 Transcription GO:0003700 ksynMdm 2mRNA<#p53_P> 1.0E-4 s-1 Same as ARF model
20 Mdm2 phosphorylation GO:0006468 kphosMdm 2<#Mdm2><#ATMA> 2.0 mol-1 s-1 This is more rapid th.an phosphorylation of p53 by ATM [22].
21 Mdm2 de-phosphorylation GO:0006470 kdephosMdm 2<#Mdm2_P> 5.0E-1 s-1 De-phosphorylation is of the same order of magnitude as phosphorylation.
22 Mdm2 degradation enhanced by ATM GO:0043161 kdegMdm 2ATM<#Mdm2_P> 4.0E-4 s-1 Mdm2 is degraded at higher rate after phosphorylation by ATM[21].
23 p53_mRNA synthesis GO:0009299 k synp 53mRNA 1.0E-3 mol s-1 Assume turnover of mRNA is about 2 hours
24 p53_mRNA degradation GO:0006402 kdegp 53mRNA<#p53_mRNA> 1.0E-4 s-1  
  1. aReaction numbers correspond to the numbered arrows in Figures 3 and 9, bmol refers to the number of molecules