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Team:SCUT/Model/N-butanol simulation
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Revision as of 09:04, 14 October 2014
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
Ordinary differential equations
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
