Team:SCUT/Model/N-butanol simulation

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 model the biochemical reactions of this pathway by using Michealis-Menton kinetics 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 study the effects of the high 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

About the initial concentration
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.

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