Team:SCUT-China/Modeling/Overview

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Revision as of 10:04, 17 October 2014

Overview

To prove the accuracy of kinetic equations of the related domains, we stacked the related equations according to the sequence of DEBS 1. When establishing the kinetic model of domain, we got into trouble. According to the analysis of reaction mechanism and kinetic equation we show before, the initial value of the kinetic equations on second AT domain depends on the concentration of DEBS 1, that is, the result of the kinetic equations on Module 2 are not affected by the result of previous domains.

However, if we have a further simplified model in which the second AT domain is ignored, the whole kinetic model stacked will be affected by the whole DEBS 1, including Loading, Module 1, Module 2.

Therefore, we establish two kinetic models stacked, and compare them with each other. Then we compare them with the kinetic model of the whole DEBS 1.

Aimed at the final goal of our project, we simulated the kinetic equations of chemical reactions occurring in each domain, including AT, ACP, KS, KR, ER, DH, and TE. Then we tested these equations and analyzed their feasibility.

DEBS 1 is the first part of the PKS which catalyzes and synthesizes 6dEB, the precursor of erythromycin. Its domain sequence is AT, ACP, KS, AT, KR, ACP, KS, AT, KR, ACP. Theoretically, the kinetic model of domains which have been stacked is match with the kinetic model of DEBS 1+TE.

In modeling section, we kept pace with the members who are responsible for experiment. We stacked the related equations according to the sequence of DEBS 1+TE. Meanwhile, we also simulated the kinetic equations of the whole DEBS 1+TE. Then we compared the equations of domains which have been stacked with the equation of DEBS 1+TE, and verified the feasibility of the model.

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 <div class="words">
 <p class="intro">
-We devote to dividing the polyketide synthases (PKSs) and catalyze according to specific mechanism. Therefore, as if we standardize the genes which encode independent domains of PKSs, we can synthesize new kinds of polyketides by means of permutation and combination of domains.<br/><br/>
+To prove the accuracy of kinetic equations of the related domains, we stacked the related equations according to the sequence of DEBS 1. When establishing the kinetic model of domain, we got into trouble. According to the analysis of reaction mechanism and kinetic equation we show before, the initial value of the kinetic equations on second AT domain depends on the concentration of DEBS 1, that is, the result of the kinetic equations on Module 2 are not affected by the result of previous domains.<br/><br/>
-In the process of analyzing the DEBS1 which catalyze and synthesize 6-deoxyerythronolide B (6dEB)，the precursor of erythromycin, we know that each domain has independent and specific chemical reaction and function.
+However, if we have a further simplified model in which the second AT domain is ignored, the whole kinetic model stacked will be affected by the whole DEBS 1, including Loading, Module 1, Module 2.
 </p><br/><br/>
-<table width="100%" border="0">
-  <tr>
-    <td class="title"><br/><br/>Name of domain<br/><br/></td>
-    <td class="title"><br/><br/>Function<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Acyltransfer-ase, AT<br/><br/></td>
-    <td><br/><br/>Activating the extended unit------- propionyl group<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Acyl carrier protein, ACP<br/><br/></td>
-    <td><br/><br/>Anchor the polyketide chain needed to extend<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Ketocaylsynthase, KS<br/><br/></td>
-    <td><br/><br/>Combining the propionyl group with acetyl group at the end of the polyketide chain by forming the C—C bond<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Keto-reductase, KR<br/><br/></td>
-    <td><br/><br/>Deoxidizing the extended unit and enabling it to form the β-hydroxyl ester bond<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Dehydratase, DH<br/><br/></td>
-    <td><br/><br/>Dehydrating the extended unit and enabling it to form the α, β- enol ester bond<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Enoylreductase, ER<br/><br/></td>
-    <td><br/><br/>Deoxidizing the extended unit and enabling it to form the saturated methylene<br/><br/></td>
-  </tr>
-  <tr>
-    <td><br/><br/>Thioesterase, TE<br/><br/></td>
-    <td><br/><br/>Removing the polyketide chain from PKS<br/><br/></td>
-  </tr>
-</table><br/><br/>
 <p class="intro">
-By preliminary analysis of chemical reaction and function of each domain, we can conclude that it is available to analyze their own kinetic mechanism, and it's significant. If we simulate the kinetic equations of chemical reactions occurring in each domain, we can finally establish kinetic model of PKSs related to all kinds of polyketides. <br/><br/>
+Therefore, we establish two kinetic models stacked, and compare them with each other. Then we compare them with the kinetic model of the whole DEBS 1.<br/><br/>
 Aimed at the final goal of our project, we simulated the kinetic equations of chemical reactions occurring in each domain, including AT, ACP, KS, KR, ER, DH, and TE. Then we tested these equations and analyzed their feasibility.<br/><br/>