Table 2.

List of reactions for the ARF model

Reac No.a	Name	Term	Kinetic law	Parameter valuesb
1	p53 synthesis	GO:0006412	ksynp53	7.8E-2 mol s-1	Based on p53 half-life ~20 min [12].
2	p53/Mdm2 binding	GO:0002039	kbinMdm2p53<#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	krelMdm2p53 <#Mdm2_p53>	1.155E-5 s-1	Based on dissociation constant of ~100 molecules [56].
4	p53 degradation	GO:0043161	kdegp53<#Mdm2_p53>	8.25E-4 s-1	p53 half-life ~20 min [12].
5	Mdm2 Transcription	GO:0003700	ksynMdm2mRNA<#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	kdegMdm2mRNA<#Mdm2_mRNA>	1.0E-4 s-1
7	Mdm2 synthesis	GO:0006412	ksynMdm2<#Mdm2_mRNA>	4.95E-4 s-1	Based on Mdm2 half-life ~30 min [12].
8	Mdm2 degradation	GO:0043161	kdegMdm2<#Mdm2>	4.33E-4 s-1	Mdm2 half-life ~30 min [12].
9	DNA damage	GO:0006974	kdam<#IR>	8.0E-2 s-1	Based on about 30 double strand breaks per cell per Gy irradiation [64].
10	DNA repair	GO:0006281	krepair<#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	kactARF<#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	kbinARFMdm2<#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	kdegARF<#ARF>	1.0E-4 s-1	Based on ARF half-life ~6 h [66].
14	ARF-dependent Mdm2 degradation	GO:0043161	kdegARFMdm2<# ARF_Mdm2>	1.0E-3 s-1	Assumed to be 3-fold faster than normal degradation 7[25].

^aReaction numbers correspond to the numbered arrows in Figure 3, ^bmol refers to the number of molecules