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Table 2 List of reactions for the ARF 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 k synp 53 7.8E-2 mol s-1 Based on p53 half-life ~20 min [12].
2 p53/Mdm2 binding GO:0002039 kbinMdm 2p 53<#p53><#Mdm2> 1.155E-3 mol-1 s-1 Assumed that 95% of p53 is bound to Mdm2 under normal conditions.
3 Mdm2_p53 dissociation GO:0043624 krelMdm 2p 53<#Mdm2_p53> 1.155E-5 s-1 Based on dissociation constant of ~100 molecules [56].
4 p53 degradation GO:0043161 kdegp 53<#Mdm2_p53> 8.25E-4 s-1 p53 half-life ~20 min [12].
5 Mdm2 Transcription GO:0003700 ksynMdm 2mRNA<#p53> 1.0E-4 s-1 Turnover of Mdm2_mRNA was adjusted to give period of oscillations ~5–6 h [35].
6 Mdm2_mRNA degradation GO:0006402 kdegMdm 2mRNA<#Mdm2_mRNA> 1.0E-4 s-1  
7 Mdm2 synthesis GO:0006412 ksynMdm 2<#Mdm2_mRNA> 4.95E-4 s-1 Based on Mdm2 half-life ~30 min [12].
8 Mdm2 degradation GO:0043161 kdegMdm 2<#Mdm2> 4.33E-4 s-1 Mdm2 half-life ~30 min [12].
9 DNA damage GO:0006974 k dam <#IR> 8.0E-2 s-1 Based on about 30 double strand breaks per cell per Gy irradiation [64].
10 DNA repair GO:0006281 k repair <#damDNA> 2.0E-5 s-1 This was set so that all DNA damage was repaired by ~10–16 h[65].
11 ARF activation GO:0030330 k actARF <#damDNA> 3.3E-5 s-1 ARF is activated within 1 hour of DNA damage and activity peaks at 6 h.
12 ARF/Mdm2 binding GO:0005515 kbinARFMdm 2<#ARF><#Mdm2> 1.0E-2 mol-1 s-1 This was set so that ARF/Mdm2 complexes peaks at 6–8 h after IR [23].
13 ARF degradation GO:0043161 k degARF <#ARF> 1.0E-4 s-1 Based on ARF half-life ~6 h [66].
14 ARF-dependent Mdm2 degradation GO:0043161 kdegARFMdm 2<# ARF_Mdm2> 1.0E-3 s-1 Assumed to be 3-fold faster than normal degradation 7[25].
  1. aReaction numbers correspond to the numbered arrows in Figure 3, bmol refers to the number of molecules