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Team:SCUT/Model/N-butanol simulation
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Latest revision as of 15:16, 26 November 2014
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
