Team:WLC-Milwaukee/Modeling

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<h2>Protein Modeling</h2>
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<p> We are currently undergoing protein data modeling which describes the kinetics of our catalytic enzymes.</p>
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<h1>Protein Modeling</h1>
This code models Michaelis-Menten enzyme kinetics over a user inputted time duration. Product formation and enzyme-substrate complex formation are assumed irreversible. Initial concentrations of the E-S complex and product are assumed to be zero. And it does not account for the presence of inhibitors or activators.  
This code models Michaelis-Menten enzyme kinetics over a user inputted time duration. Product formation and enzyme-substrate complex formation are assumed irreversible. Initial concentrations of the E-S complex and product are assumed to be zero. And it does not account for the presence of inhibitors or activators.  
Using the law of mass action the enzyme substrate complex, and product formation chemical equations, are separated into a set of differential equations. The MATLAB ode45 function is used to solve the set of differential equations over the given time span.
Using the law of mass action the enzyme substrate complex, and product formation chemical equations, are separated into a set of differential equations. The MATLAB ode45 function is used to solve the set of differential equations over the given time span.
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<h1>xynA at pH 7.3</h1>
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INPUT CODE AND DATA???
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</br></br></br></br></br></br></br></br></br>
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<h1>XynA at pH 7.3</h1>
</br>
</br>
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<h2>Enzyme at 2-fold the Concentration of Substrate</h2>
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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<table border="1">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg">
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<tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg">
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg"></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg">
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  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg"></td>
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  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg"></td>
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</tr>
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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<tr>
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  <td> COMMENTS HERE </td>
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  <td> COMMENTS HERE </td>
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  <td> COMMENTS HERE </td>
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</tr>
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</table>
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</br>
</br>
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<h2>Enzyme at 10-fold the Concentration of Substrate</h2>
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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<table border="1">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg">
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<tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg">
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg"></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
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  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg"></td>
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  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg"></td>
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  </tr>
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>100:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/a/a6/100E_1s.jpg"></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/3/32/XynA7.3_100E_5s.jpg"></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>Increased Substrate Concentration at 15 Seconds</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg">
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
   
   
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<tr>
 
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  <td> COMMENTS HERE </td>
 
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  <td> COMMENTS HERE </td>
 
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  <td> COMMENTS HERE </td>
 
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</tr>
 
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</table>
 
</br>
</br>
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<p>DISCUSSION</p>
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<h2>Enzyme at 100-fold the Concentration of Substrate</h2>
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</br></br></br></br></br></br></br></br>
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<table border="1">
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<h1>XynA at pH 8.8</h1>
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<tr>
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/a/a6/100E_1s.jpg"></td>
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</br>
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/3/32/XynA7.3_100E_5s.jpg"></td>
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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</tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/10/XynA8.8_2E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/17/XynA8.8_2E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/0/01/XynA8.8_2E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/6/67/XynA8.8_10E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/6/66/XynA8.8_10E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_10E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
 +
<h2>100:1 Substrate-Enzyme Concentration</h2>
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 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7b/XynA8.8_100E_1s.jpg">
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<img width="33%" src=" https://static.igem.org/mediawiki/2014/8/8d/XynA8.8_100E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
 +
 
 +
<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
 +
<h2>Increased Substrate Concentration at 15 Seconds</h2>
 +
 
 +
<img width="33%" src=" https://static.igem.org/mediawiki/2014/0/01/XynA8.8_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
   
   
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<tr>
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
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  <td> COMMENTS HERE </td>
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</br>
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  <td> COMMENTS HERE </td>
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  <td> COMMENTS HERE </td>
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<p>DISCUSSION</p>
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</tr>
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</table>
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</br></br></br></br></br></br></br></br></br></br>
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<h1>YesZ at pH 7.0</h1>
</br>
</br>
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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<h2>Increased Enzyme Concentration at 15 Seconds</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/5/55/YesZ_2E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/0/04/YesZ_2E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg">
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<table border="1">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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<tr>
+
 
-
  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg"></td>
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</br>
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  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg"></td>
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  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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</tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/77/YesZ_10E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/2/25/YesZ_10E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg">
 +
 
 +
<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
 +
<h2>100:1 Substrate-Enzyme Concentration</h2>
 +
 
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/0/08/YesZ_100E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/12/YesZ_100E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg">
 +
 
 +
<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
 +
<h2>Increased Substrate Concentration at 15 Seconds</h2>
 +
 
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg">
   
   
-
<tr>
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
-
  <td> COMMENTS HERE </td>
+
-
  <td> COMMENTS HERE </td>
+
-
  <td> COMMENTS HERE </td>
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</tr>
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</table>
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</br>
</br>
<p>DISCUSSION</p>
<p>DISCUSSION</p>
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</body>-->
</html>
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Latest revision as of 02:11, 18 October 2014


Protein Modeling

We are currently undergoing protein data modeling which describes the kinetics of our catalytic enzymes.

Retrieved from "http://2014.igem.org/Team:WLC-Milwaukee/Modeling"