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Team:WLC-Milwaukee/Modeling
From 2014.igem.org
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| + | <h2>Protein Modeling</h2> | ||
| + | <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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| + | INPUT CODE AND DATA??? | ||
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<h1>XynA at pH 7.3</h1> | <h1>XynA at pH 7.3</h1> | ||
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<h2>2:1 Substrate-Enzyme Concentration</h2> | <h2>2:1 Substrate-Enzyme Concentration</h2> | ||
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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> | ||
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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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<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"> | |
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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"> | |
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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"> | |
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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/2014/5/55/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"> | |
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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/2014/7/77/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"> | |
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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/2014/0/08/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"> | |
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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/2014/7/7d/YesZ_2E_15s.jpg"> |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg"> | |
| - | + | <img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_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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</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.
