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

1

p53 synthesis

GO:0006412

k_{synp 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

k_{phosp 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

k_{dephosp 53}<#p53_P>

5.0E-1 s^-1

This parameter was varied to obtain oscillations.

19

Mdm2 Transcription

GO:0003700

k_{synMdm 2mRNA}<#p53_P>

1.0E-4 s^-1

Same as ARF model

20

Mdm2 phosphorylation

GO:0006468

k_{phosMdm 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

k_{dephosMdm 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

k_{degMdm 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

k_{degp 53mRNA}<#p53_mRNA>

1.0E-4 s^-1