Team:WLC-Milwaukee/Modeling

From 2014.igem.org

(Difference between revisions)
 
(9 intermediate revisions not shown)
Line 1: Line 1:
{{Team:WLC-Test}}
{{Team:WLC-Test}}
-
<html>
 
 +
<html><body>
 +
<h2>Protein Modeling</h2>
 +
<p> We are currently undergoing protein data modeling which describes the kinetics of our catalytic enzymes.</p>
 +
</body>
 +
 +
 +
 +
 +
<!--
 +
<body>
 +
<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.
-
<h1>xynA at pH 7.3</h1>
+
INPUT CODE AND DATA???
 +
 
 +
</br></br></br></br></br></br></br></br></br>
 +
 
 +
<h1>XynA at pH 7.3</h1>
</br>
</br>
Line 12: Line 26:
<h2>2:1 Substrate-Enzyme Concentration</h2>
<h2>2:1 Substrate-Enzyme Concentration</h2>
-
<table border="1">
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg">
-
<tr>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg">
-
  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg"></td>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg">
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg"></td>
+
 
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg"></td>
+
 
-
</tr>
+
<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>
-
+
-
<tr>
+
-
As time progresses from 1 second to 15 seconds, the reaction moves to completion where almost all substrate has been catalyzed into product.
+
-
</tr>
+
-
</table>
+
</br>
</br>
Line 29: Line 38:
<h2>10:1 Substrate-Enzyme Concentration</h2>
<h2>10:1 Substrate-Enzyme Concentration</h2>
-
<table border="1">
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg">
-
<tr>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg">
-
  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg"></td>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg"></td>
+
 
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg"></td>
+
 
-
  </tr>
+
<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/a/a6/100E_1s.jpg"></td>
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/3/32/XynA7.3_100E_5s.jpg"></td>
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
 +
 
 +
 
 +
<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/2014/9/9f/XynA7.3_2E_15s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg">
 +
 
 +
   
 +
<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
   
   
-
<tr>
 
-
As time progresses from 1 second to 15 seconds, the reaction moves to completion where almost all substrate has been catalyzed into product.
 
-
</tr>
 
-
</table>
 
</br>
</br>
 +
<p>DISCUSSION</p>
 +
 +
</br></br></br></br></br></br></br></br>
 +
 +
<h1>XynA at pH 8.8</h1>
 +
 +
</br>
 +
 +
<h2>2:1 Substrate-Enzyme Concentration</h2>
 +
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/1/10/XynA8.8_2E_1s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/1/17/XynA8.8_2E_5s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/0/01/XynA8.8_2E_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>10:1 Substrate-Enzyme Concentration</h2>
 +
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/6/67/XynA8.8_10E_1s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/6/66/XynA8.8_10E_5s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_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>
<h2>100:1 Substrate-Enzyme Concentration</h2>
-
<table border="1">
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7b/XynA8.8_100E_1s.jpg">
-
<tr>
+
<img width="33%" src=" https://static.igem.org/mediawiki/2014/8/8d/XynA8.8_100E_5s.jpg">
-
  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/a/a6/100E_1s.jpg"></td>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/3/32/XynA7.3_100E_5s.jpg"></td>
+
 
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
+
<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>
-
</tr>
+
 
 +
</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">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_10E_15s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
   
   
-
<tr>
+
<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
-
As time progresses from 1 second to 15 seconds, the reaction moves to completion where almost all substrate has been catalyzed into product.
+
</br>
-
</tr>
+
 
-
</table>
+
<p>DISCUSSION</p>
 +
 
 +
</br></br></br></br></br></br></br></br></br></br>
 +
 
 +
<h1>YesZ at pH 7.0</h1>
</br>
</br>
 +
<h2>2:1 Substrate-Enzyme Concentration</h2>
 +
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/5/55/YesZ_2E_1s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/0/04/YesZ_2E_5s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_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>10:1 Substrate-Enzyme Concentration</h2>
 +
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/77/YesZ_10E_1s.jpg">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/2/25/YesZ_10E_5s.jpg">
 +
<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">
 +
<img width="33%" src="https://static.igem.org/mediawiki/2014/1/12/YesZ_100E_5s.jpg">
 +
<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>
<h2>Increased Substrate Concentration at 15 Seconds</h2>
-
<table border="1">
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg">
-
<tr>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg">
-
  <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg"></td>
+
<img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg">
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg"></td>
+
-
  <td style="padding:5px" width="33%"><img  src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
+
-
</tr>
+
   
   
-
<tr>
+
<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
-
Despite the increase in substrate concentration with a constant enzyme conentration, all substrate was catalyzed into product in similar amounts of time.
+
-
</tr>
+
-
</table>
+
</br>
</br>
<p>DISCUSSION</p>
<p>DISCUSSION</p>
 +
 +
</body>-->
</html>
</html>

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"