Difference between revisions of "Team:Brasil-USP/Modeling/EnzymaticReaction"

Line 3: Line 3:
 
{{:Team:Brasil-USP/modeling/TemplateIndex}}
 
{{:Team:Brasil-USP/modeling/TemplateIndex}}
  
 +
<html>
 +
   
 +
    <div class="container jamboreh">
 +
      <br />
 +
      <div id="ToC">
 +
        <h3>Table of contents</h3>
 +
        <ul>
 +
          <li><a href="#objective">Main objective</a></li>
 +
          <li><a href="#deterministic">Deterministic modeling</a></li>
 +
          <li><a href="#enzymeproduction">RoxA and Lcp Production</a></li>
 +
          <li><a href="#hokD">Kill Switch: hokD</a></li>
 +
          <li><a href="#fitting">Fitting the parameters</a></li>
 +
          <li><a href="#fluctuations">Fluctuation analysis</a></li>
 +
        </ul>
 +
      </div>
 +
     
 +
      <p>
 +
        So far, we have modeled the production of enzymes that are capable of breaking rubber polymers, namely Lcp and RoxA. During the rubber degradation, however, no other products will be formed, only a bunch of small polymers with variable lengths. This means that, in a Michaelis-Menten fashion, our substrate and our product are the same. Then, we can ask which is the best way to model such behavior? Is Michaelis-Menten suitable? The result is partially yes, as we show below.
 +
      </p>
  
 +
      <div class="fig" style="width: 700px;">
 +
        <img style="width:700px; display: block; margin: 20px auto 20px auto;" src="/wiki/images/a/a5/Team-Brasil-USP_modeligem_ER_problem.png" />
 +
        <p>Figure 1- During the rubber degradation, Lcp and RoxA will break rubber polymers into smaller polymers. In a Michaelis-Menten fashion, our substrate and our product are the same. How can we solve it?</p>
 +
      </div>
  
 +
    </div>
 +
   
 +
    <div class="wikicontent">
 +
     
 +
      <a id="objective"></a>
 +
      <h1>The main idea</h1>
  
 +
<h1>Dynamics of the enzymatic reaction</h1>
  
 +
 +
<h1>Discussions and references</h1>
 +
 +
 +
 +
1- Cheng and Prud`Humme. Enzymatic Degradation of Guar and Substituted Guar Galactomannans, Biomacromolecules, 2000, vol 1, p.782.
 +
 +
    </div>
 
     <hr class="fancy-line" />
 
     <hr class="fancy-line" />
 
{{:Team:Brasil-USP/Templates/Foot}}
 
{{:Team:Brasil-USP/Templates/Foot}}

Revision as of 01:20, 19 September 2015

Enzymatic Reactions

Modeling results


So far, we have modeled the production of enzymes that are capable of breaking rubber polymers, namely Lcp and RoxA. During the rubber degradation, however, no other products will be formed, only a bunch of small polymers with variable lengths. This means that, in a Michaelis-Menten fashion, our substrate and our product are the same. Then, we can ask which is the best way to model such behavior? Is Michaelis-Menten suitable? The result is partially yes, as we show below.

Figure 1- During the rubber degradation, Lcp and RoxA will break rubber polymers into smaller polymers. In a Michaelis-Menten fashion, our substrate and our product are the same. How can we solve it?

The main idea

Dynamics of the enzymatic reaction

Discussions and references

1- Cheng and Prud`Humme. Enzymatic Degradation of Guar and Substituted Guar Galactomannans, Biomacromolecules, 2000, vol 1, p.782.
{{:Team:Brasil-USP/Templates/Foot}}