Team:ITB Indonesia/Modelling/DNA damage kinetic

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<h2 class="title">DNA damage kinetic</h2>
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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.  
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<p>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&rsquo;s DNA. <br />
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  Mathematical representation of this phenomena can be  described by :<br />
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  Parameters for DNA damage kinetic are :</p>
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    <td width="205" align="center" valign="middle"><strong>Parameter</strong></td>
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    <td width="205" align="center" valign="middle"><p align="center"><strong>Value</strong></p></td>
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    <td width="205" align="center" valign="middle"><p align="center"><strong>Source</strong></p></td>
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    <td width="205" align="center" valign="middle"><p>k0</p></td>
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    <td width="205" align="center" valign="middle"><p>0,6 s-1</p></td>
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    <td width="205" align="center" valign="middle"><p align="center">[1]</p></td>
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    <td width="205" align="center" valign="middle"><p>Kd</p></td>
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    <td width="205" align="center" valign="middle"><p>0,43 mg/ml</p></td>
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    <td width="205" align="center" valign="middle"><p align="center">[1]</p></td>
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    <td width="205" align="center" valign="middle"><p>kcat</p></td>
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    <td width="205" align="center" valign="middle"><p>35 s-1</p></td>
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    <td width="205" align="center" valign="middle"><p align="center">[1]</p></td>
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  <p style="border:solid #F60">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.</p>
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  <p style="border:solid #F60">In this model, we decide  to assume that AFB1oxide is &ldquo;enzyme&rdquo; and DNA is &ldquo;substrate&rdquo;. Here is the  parameter we input to Simbiology to simulate this model :<br />
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    Notice that we state DNA  as the substrate for Michaelis Menten equation.</p>
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<p><strong>Reference :</strong><br />
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  [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.</p>
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Latest revision as of 01:28, 28 September 2013

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.

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