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Team:ITB Indonesia/Modeling/DNA damage kinetic
From 2013.igem.org
DNA Damage Kinetic
Interestingly, AFB1 oxide is not a stable substance. AFB1 oxide will going through two possible reaction : spontaneous reaction with H2O to produce a more stable and harmless AFB diol, or reacting with N7-Guanine to produce AFB-DNA adduct and damaging cell’s DNA.
Mathematical representation of this phenomena can be described by :
Parameters for DNA damage kinetic are :
| Parameter | Value |
Source |
k0 |
0,6 s-1 |
[1] |
Kd |
0,43 mg/ml |
[1] |
kcat |
35 s-1 |
[1] |
We have a problem understanding the unit of Kd (equilibrium constant for bind and unbind of AFB and DNA) because it said mg/ml. So, we hypothetize that the reaction between AFB1oxide and DNA can be assumed like enzymatic reaction (reaction equation of DNA-AFB1oxide is analogous to Michaelis-Menten kinetic), so unit on the left side will agree with the right side of the reaction.
In this model, we decide to assume that AFB1oxide is “enzyme” and DNA is “substrate”. Here is the parameter we input to Simbiology to simulate this model :
Notice that we state DNA as the substrate for Michaelis Menten equation.
Reference :
[1] Johnson, W. W., Guengerich, F. P. Reaction of aflatoxin B1 exo-8,9-epoxide with DNA: Kinetic analysis of covalent binding and DNA-induced hydrolysis.
