Team:SCUT/Model/N-butanol simulation

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<a href="https://2014.igem.org/Team:SCUT/Model/Overview"><img src="https://static.igem.org/mediawiki/2014/d/dc/1-01.png"></a>
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<p onclick="scroll_1()">Background</p>
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<p>Background</p>
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<p onclick="scroll_2()">Rubisco simulation</p>
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<p>Carbon dioxide fixed part</p>
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<p onclick="scroll_3()">N-butanol simulation</p>
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<p>n-butanol simulation</p>
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<a href="https://2014.igem.org/Team:SCUT/Model/Rubisco_simulation"><img src="https://static.igem.org/mediawiki/2014/c/c6/Model2-01.png"></a>
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<p>Introduction</p>
<p>Individual part</p>
<p>Individual part</p>
<p>Combine part</p>
<p>Combine part</p>
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<p>The function of Rubisco</p>
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<p>The function of RuBisCo</p>
<p>Scaffold</p>
<p>Scaffold</p>
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<p>Reference</p>
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<img src="https://static.igem.org/mediawiki/2014/1/16/3-01.png">
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<a href="https://2014.igem.org/Team:SCUT/Model/N-butanol_simulation"><img src="https://static.igem.org/mediawiki/2014/d/d2/Model3-01.png"></a>
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<p>Background</p>
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<p onclick="scroll_1()">Introduction</p>
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<p>Rubisco simulation</p>
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<p onclick="scroll_2()">Simulation</p>
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<p>N-butanol simulation</p>
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<p onclick="scroll_3()">Reference</p>
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<p>Background</p>
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<p>Rubisco simulation</p>
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<p>N-butanol simulation</p>
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<img src="https://static.igem.org/mediawiki/2014/7/7f/5-01.png">
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<a href="https://2014.igem.org/Team:SCUT/Model/Tips_for_other_teams"><img src="https://static.igem.org/mediawiki/2014/a/af/Model4-01.png"></a>
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<p>Background</p>
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<p>Outline</p>
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<p>Rubisco simulation</p>
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<p>Reference</p>
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<p>N-butanol simulation</p>
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</div>
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<div class="mainbody mainbody1" id="label_1">
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<p class="atop">
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<span>Overview</span>
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</p>
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<p class="first">
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In order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we constructed a model by Michealis-Menton kinetics and ordinary differential equation(ODE). The model shows that, with high concentrations of NADH in mitochondria, the production of n-butanol will be greatly improved.
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<p class="atop">
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<span>Introduction</span>
<span>Introduction</span>
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<p class="first">
<p class="first">
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We model the biochemical reactions of this pathway by using <span>Michealis-Menton kinetics</span> and then model them by kinetics at the beginning of the reactions when no products have been accumulated. Finally, considering the special environment of mitochondria, we<span> study the effects of the high concentrations of NADH and NADPH</span> , which is abundant in mitochondria.  
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We firstly constructed the biochemical reactions of n-butanol producing pathway by Michealis-Menton kinetics and then modeled them by kinetics at the beginning of the reactions when no products have been accumulated. Finally, considering the special environment of mitochondria, we did the work about the effects of the concentrations of NADH and NADPH, which is abundant in mitochondria.
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<span>Simulation</span>
<span>Simulation</span>
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For thiolase [erg10], the reaction is
For thiolase [erg10], the reaction is
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/e/e2/Modeling000.png">
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<p>
The rate expression is defined as
The rate expression is defined as
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/1/10/Modeling001.png">
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For 3-hydroxybutyryl-coa dehydrogenase[Hbd], the reaction is
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/9/9c/Equ_1_%2816%29.png"><br/>
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</p>
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The rate expression is defined as
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/0/01/Modeling002.png">
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</p>
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For crotonase[crt], the reaction is
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/0/08/Equ_1_%2820%29.png">
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</p>
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The rate expression is defined as
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/6/6a/Modeling003.png">
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For BtCoA dehydrogenase [ccr], the reaction is
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/8/8c/Equ_1_%2823%29.png">
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</p>
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The rate expression is defined as
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/4/4b/RB.jpg">
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</p>
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For Bldh, butyraldehyde dehydrogenase [AdH2], the reaction is
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/6/6d/Equ_1_%2826%29.png">
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The rate expression is defined as
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/3/38/Equ_1_%2827%29.png"><br/><br/>
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<img src="https://static.igem.org/mediawiki/2014/4/40/Equ_1_%2831%29.png"><br/><br/>
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<img src="https://static.igem.org/mediawiki/2014/c/ce/Equ_1_%2828%29.png"><br/><br/>
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<img src="https://static.igem.org/mediawiki/2014/1/1a/Modeling006.png" style="margin-left:28px;">
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About the initial concentration<br/>
 
We set the concentration of Actyl-CoA to 1000μM, and consider it as a constant. <br/>For simplify ,we set the concentration of NADH and NADPH to 200μM and 100μM respectively and also consider it as a constant .Concentrations of all other metabolite are set to 0 in the beginning.
We set the concentration of Actyl-CoA to 1000μM, and consider it as a constant. <br/>For simplify ,we set the concentration of NADH and NADPH to 200μM and 100μM respectively and also consider it as a constant .Concentrations of all other metabolite are set to 0 in the beginning.
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<span>Result</span>
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<p class="first" id="equ">
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<img src="https://static.igem.org/mediawiki/2014/2/2a/Nb-1.jpg"><br/>
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Figure 1.Production of n-butanol at different of concentration of enzyme
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</p>
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<p>
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We set the concentration of AcCoA as a constant to 1000μM, and the concentration of NADH,  NAD<sup>+</sup>, NADPH and NADP<sup>+</sup> to 200μM, 200μM and 100μM,100μM respectively. The concentration of other substrate are set to 0 at the beginning of the process. In figure 1, we set the concentration of enzyme range from 0 to 1mM. From the result, we can learn that overexpress the enzyme can increase the production of butanol.
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</p>
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<p id="equ">
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<img src="https://static.igem.org/mediawiki/2014/1/10/Nb-2.jpg"><br/>
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figure 2. Production of n-butanol at different of concentration of NADH and NADPH
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</p>
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<p>
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We construct the pathway into mitochondria for its high concentration of NADH and NADPH, so in figure 2 we range the concentration of NADH and NADPH from 50-200μM, 20-100μM respectively. The result shows that as the concentration is increased, the production can be improved.
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</p>
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<div class="mainbody mainbody5" id="label_5">
<p class="atop">
<p class="atop">
<span>Reference</span>
<span>Reference</span>
</p>
</p>
<p class="first">
<p class="first">
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[1] http://www.Brenda-enzymes.info/index.php <br/>
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[1]<a href="http://www.Brenda-enzymes.info/index.php"> http://www.Brenda-enzymes.info/index.php </a><br/>
[2] Gary D. Colby and Jiann-Shin Chen. Purification and Properties of 3-Hydroxybutyryl-Coenzyme A Dehydrogenase from Clostridium beijerinckii ("Clostridium butylicum") NRRL B593. Applied And Environmental Microbiology, Oct. 1992, p. 3297-3302<br/>
[2] Gary D. Colby and Jiann-Shin Chen. Purification and Properties of 3-Hydroxybutyryl-Coenzyme A Dehydrogenase from Clostridium beijerinckii ("Clostridium butylicum") NRRL B593. Applied And Environmental Microbiology, Oct. 1992, p. 3297-3302<br/>
[3] Robert M. Waterson, Francis J. Castellino, G.Michael Hass and Robert L. Hill, Purification and Characterization of. Crotonase from Clostridium acetobutylicum, J. Biol. Chem. 1972, 247:5266-5271.<br/>
[3] Robert M. Waterson, Francis J. Castellino, G.Michael Hass and Robert L. Hill, Purification and Characterization of. Crotonase from Clostridium acetobutylicum, J. Biol. Chem. 1972, 247:5266-5271.<br/>
[4] Michel Rigoulet,1 Hugo Aguilaniu,1,3 Nicole Avéret,1 Odile Bunoust,1 Organization and regulation of the cytosolic NADH metabolism in the yeast Saccharomyces cerevisiae<br/>
[4] Michel Rigoulet,1 Hugo Aguilaniu,1,3 Nicole Avéret,1 Odile Bunoust,1 Organization and regulation of the cytosolic NADH metabolism in the yeast Saccharomyces cerevisiae<br/>
-
[5] https://2012.igem.org/Team:Shenzhen/Result/YAO.Factory<br/>
+
[5] <a href="https://2012.igem.org/Team:Shenzhen/Result/YAO.Factory">https://2012.igem.org/Team:Shenzhen/Result/YAO.Factory</a><br/>
[6] RUN-TAO YAN AND JIANN-SHIN CHEN Coenzyme A-Acylating Aldehyde Dehydrogenase from Clostridium beijerinckii NRRL B592<br/>
[6] RUN-TAO YAN AND JIANN-SHIN CHEN Coenzyme A-Acylating Aldehyde Dehydrogenase from Clostridium beijerinckii NRRL B592<br/>
</p>
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Latest revision as of 15:16, 26 November 2014

Background

Carbon dioxide fixed part

n-butanol simulation

Introduction

Individual part

Combine part

The function of RuBisCo

Scaffold

Reference

Outline

Reference

Overview

In order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we constructed a model by Michealis-Menton kinetics and ordinary differential equation(ODE). The model shows that, with high concentrations of NADH in mitochondria, the production of n-butanol will be greatly improved.

Introduction

We firstly constructed the biochemical reactions of n-butanol producing pathway by Michealis-Menton kinetics and then modeled them by kinetics at the beginning of the reactions when no products have been accumulated. Finally, considering the special environment of mitochondria, we did the work about the effects of the concentrations of NADH and NADPH, which is abundant in mitochondria.

Simulation

For thiolase [erg10], the reaction is

The rate expression is defined as

For 3-hydroxybutyryl-coa dehydrogenase[Hbd], the reaction is


The rate expression is defined as

For crotonase[crt], the reaction is

The rate expression is defined as

For BtCoA dehydrogenase [ccr], the reaction is

The rate expression is defined as

For Bldh, butyraldehyde dehydrogenase [AdH2], the reaction is

The rate expression is defined as







We set the concentration of Actyl-CoA to 1000μM, and consider it as a constant.
For simplify ,we set the concentration of NADH and NADPH to 200μM and 100μM respectively and also consider it as a constant .Concentrations of all other metabolite are set to 0 in the beginning.

Result


Figure 1.Production of n-butanol at different of concentration of enzyme

We set the concentration of AcCoA as a constant to 1000μM, and the concentration of NADH, NAD+, NADPH and NADP+ to 200μM, 200μM and 100μM,100μM respectively. The concentration of other substrate are set to 0 at the beginning of the process. In figure 1, we set the concentration of enzyme range from 0 to 1mM. From the result, we can learn that overexpress the enzyme can increase the production of butanol.


figure 2. Production of n-butanol at different of concentration of NADH and NADPH

We construct the pathway into mitochondria for its high concentration of NADH and NADPH, so in figure 2 we range the concentration of NADH and NADPH from 50-200μM, 20-100μM respectively. The result shows that as the concentration is increased, the production can be improved.

Reference

[1] http://www.Brenda-enzymes.info/index.php
[2] Gary D. Colby and Jiann-Shin Chen. Purification and Properties of 3-Hydroxybutyryl-Coenzyme A Dehydrogenase from Clostridium beijerinckii ("Clostridium butylicum") NRRL B593. Applied And Environmental Microbiology, Oct. 1992, p. 3297-3302
[3] Robert M. Waterson, Francis J. Castellino, G.Michael Hass and Robert L. Hill, Purification and Characterization of. Crotonase from Clostridium acetobutylicum, J. Biol. Chem. 1972, 247:5266-5271.
[4] Michel Rigoulet,1 Hugo Aguilaniu,1,3 Nicole Avéret,1 Odile Bunoust,1 Organization and regulation of the cytosolic NADH metabolism in the yeast Saccharomyces cerevisiae
[5] https://2012.igem.org/Team:Shenzhen/Result/YAO.Factory
[6] RUN-TAO YAN AND JIANN-SHIN CHEN Coenzyme A-Acylating Aldehyde Dehydrogenase from Clostridium beijerinckii NRRL B592

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