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Team:ITB Indonesia/Modelling/DNA damage kinetic
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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 | + | <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’s DNA. <br /> |
| + | <img src="file:///C|/Users/User/AppData/Roaming/Adobe/Dreamweaver CS5/en_US/OfficeImageTemp/clip_image001.png" alt="" width="218" height="140" /><br /> | ||
| + | Mathematical representation of this phenomena can be described by :<br /> | ||
| + | <img src="file:///C|/Users/User/AppData/Roaming/Adobe/Dreamweaver CS5/en_US/OfficeImageTemp/clip_image003.png" alt="" width="148" height="25" /> <br /> | ||
| + | <img src="file:///C|/Users/User/AppData/Roaming/Adobe/Dreamweaver CS5/en_US/OfficeImageTemp/clip_image005.png" alt="" width="371" height="25" /></p> | ||
| + | <p><br /> | ||
| + | Parameters for DNA damage kinetic are :</p> | ||
| + | <table border="1" cellspacing="0" cellpadding="0"> | ||
| + | <tr> | ||
| + | <td width="205" align="center" valign="middle"><strong>Parameter</strong></td> | ||
| + | <td width="205" align="center" valign="middle"><p align="center"><strong>Value</strong></p></td> | ||
| + | <td width="205" align="center" valign="middle"><p align="center"><strong>Source</strong></p></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td width="205" align="center" valign="middle"><p>k0</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p>0,6 s-1</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p align="center">[1]</p></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td width="205" align="center" valign="middle"><p>Kd</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p>0,43 mg/ml</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p align="center">[1]</p></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td width="205" align="center" valign="middle"><p>kcat</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p>35 s-1</p></td> | ||
| + | <td width="205" align="center" valign="middle"><p align="center">[1]</p></td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | <div> | ||
| + | <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> | ||
| + | </div> | ||
| + | <div> | ||
| + | <p style="border:solid #F60">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 :<br /> | ||
| + | <img src="file:///C|/Users/User/AppData/Roaming/Adobe/Dreamweaver CS5/en_US/OfficeImageTemp/clip_image007.jpg" alt="" width="373" height="277" align="middle" /><br /> | ||
| + | Notice that we state DNA as the substrate for Michaelis Menten equation.</p> | ||
| + | </div> | ||
| + | <p><strong>Reference :</strong><br /> | ||
| + | [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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Revision as of 01:27, 28 September 2013
Please Add Title Here!
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.
