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Team:WLC-Milwaukee/Modeling
From 2014.igem.org
(Difference between revisions)
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<h2>2:1 Substrate-Enzyme Concentration</h2> | <h2>2:1 Substrate-Enzyme Concentration</h2> | ||
| - | < | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg"> |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg"> | |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_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> | <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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<h2>10:1 Substrate-Enzyme Concentration</h2> | <h2>10:1 Substrate-Enzyme Concentration</h2> | ||
| - | < | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg"> |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg"> | |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_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> | <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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<h2>100:1 Substrate-Enzyme Concentration</h2> | <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> | |
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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> | <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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<h2>Increased Substrate Concentration at 15 Seconds</h2> | <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"> | |
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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> | <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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<h2>2:1 Substrate-Enzyme Concentration</h2> | <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"> | |
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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> | <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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<h2>10:1 Substrate-Enzyme Concentration</h2> | <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"> | |
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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> | <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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<h2>100:1 Substrate-Enzyme Concentration</h2> | <h2>100:1 Substrate-Enzyme Concentration</h2> | ||
| - | < | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/7/7b/XynA8.8_100E_1s.jpg"> |
| - | + | <img width="33%" src=" https://static.igem.org/mediawiki/2014/8/8d/XynA8.8_100E_5s.jpg"> | |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_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> | <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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<h2>Increased Substrate Concentration at 15 Seconds</h2> | <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"> | |
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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> | <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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<table border="1"> | <table border="1"> | ||
<tr> | <tr> | ||
| - | <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/5/55/YesZ_2E_1s.jpg"></td> | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/5/55/YesZ_2E_1s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/0/04/YesZ_2E_5s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg"></td> |
</tr> | </tr> | ||
</table> | </table> | ||
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<table border="1"> | <table border="1"> | ||
<tr> | <tr> | ||
| - | <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/7/77/YesZ_10E_1s.jpg"></td> | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/7/77/YesZ_10E_1s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/2/25/YesZ_10E_5s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg"></td> |
</tr> | </tr> | ||
</table> | </table> | ||
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<table border="1"> | <table border="1"> | ||
<tr> | <tr> | ||
| - | <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/0/08/YesZ_100E_1s.jpg"></td> | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/0/08/YesZ_100E_1s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/1/12/YesZ_100E_5s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg"></td> |
</tr> | </tr> | ||
</table> | </table> | ||
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<table border="1"> | <table border="1"> | ||
<tr> | <tr> | ||
| - | <td style="padding:5px" width="33%"><img src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg"></td> | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg"></td> |
| - | <td style="padding:5px" width="33%"><img | + | <td style="padding:5px" width="33%"><img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg"></td> |
</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 15:44, 17 October 2014
|
Protein Modeling
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. INPUT CODE AND DATA???XynA at pH 7.3
2:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
10:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
100:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
Increased Substrate Concentration at 15 Seconds
Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.
DISCUSSION
XynA at pH 8.8
2:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
10:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
100:1 Substrate-Enzyme Concentration
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
Increased Substrate Concentration at 15 Seconds
Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.
DISCUSSION
YesZ at pH 7.0
2:1 Substrate-Enzyme Concentration
 |
 |
 |
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
10:1 Substrate-Enzyme Concentration
 |
 |
 |
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
100:1 Substrate-Enzyme Concentration
 |
 |
 |
As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.
Increased Substrate Concentration at 15 Seconds
|
|
|
Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.
DISCUSSION
