Project 3: The p53 pathway
p53 is a transcription factor that either stops the cell cycle or starts apoptosis in a situation where, for example, DNA is damaged. In normal cells, the level of p53 is maintained at a low level. If DNA damage occurs, p53 activity increases (most probably it inhibits its degradation but we assume here that DNA damage makes more p53). High p53 activity switches on the transcription of cyclin-dependent kinase inhibitors (CKIs) to stop the progression through the cycle. If the arrest lasts for too long, apoptosis is initiated.
There are other pathways by which apoptosis
can be initiated.
Myc is a transcription factor. It is involved in both cell
proliferation and apoptosis. In normal cases, it helps the cell go
through a transition from G1 to S phase. However, if it is
overexpressed, Arf is activated and in turn, activates p53. If the
level of p53 is maintained at a high level for a certain amount of
time, apoptosis is initiated (in the presence of survival factors or
not). This pathway is independent of DNA damage.
There exist some mechanisms that keep p53 at low level. For simplicity, here, we consider that apoptosis occurs when p53 is activated. Some other proteins, such as Mdm2, interact with p53 to lower its activity in the case, for example, that DNA can be repaired.
Project:
1. Build a model in Biocham of the biochemical reactions presented in
the figure above.
Hints:
Let E2F and "Survival Factors" (SF) be variables
but always equal to 1.
Let "DNA damage" (Damage) be a parameter equal to 0. If you want to
simulate DNA damage, put this paramater equal to 1.
Use the following parameters:
| Background synthesis of Arf | ksarp=0.01 | Arf-mediated synthesis of p53 | kp53p=0.2 |
| Myc-mediated synthesis of Arf | ksarpp=0.1 | Myc-mediated synthesis | kp53pp=0.1 |
| Degradation of Arf | kdarf=1 | E2F-mediated synthesis | kp53ppp=0.01 |
| Background synthesis of Myc | ksp=0.1 | DNA Damage | Damage=0 |
| E2F-mediated synthesis of Myc | kspp=0.001 | Degradation of p53 | kdp53=0.1 |
| Degradation of Myc | kd=0.1 |
2. Choose a variable "time" such that:
1 for _=>time.
to be able to track time and use time as a variable in the following condition we want to simulate:
if [time] leq 30 then preDamage else Damage for _=>p53.
where preDamage and Damage are parameters equal to 0 and 1 respectively. That way, we simulate DNA damage automatically 20 minutes after the beginning of our simulation. Explain what happens.
3. Declare a variable 'Apoptosis' that will simulate apoptosis when p53 reaches a threshold value and if after a certain amount of time (say 60), p53 is still above the threshold. Use the 'if' statement to do so.
4. Show the diagram of the protein interactions involved in this pathway using Graphviz (see Biocham documentation for help).
5. p53 alone is not directly starting
apoptosis. Apoptosis is only triggered when DNA cannot be repaired in a
certain amount of time (i.e. when p53 remains active for a long time).
There is a pathway downstream of p53 that activates apoptosis. After
searching the literature on the different networks of proteins in which
p53 is involved, you have the choice of:
=> either discussing a simple mechanism involving caspases
(activated by p53 and responsible for triggering apoptosis) and propose
a Biocham model.
=> or discussing a mechanism that would control p53 activity
(feedback mechanism involving Mdm2) and
build the corresponding Biocham model.
Note: For the Biocham model, you don't have to find parameters but
simply describe the kinetics of the biochemical reactions you propose
to use.