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Team:IIT Madras/Dry lab/Modelling/Validation
From 2011.igem.org
Validation of Model
The validation was done with negative regulation of the cytochrome oxidase reaction by comparing with literature available for inhibition using azide[3]
Table 1: .
Table 2: Validation Simulation: For the same amount of inhibition of oxidative phosphorylation due to azide the growth rate increases in the presence of Proteorhodopsin. At the same time when the glucose concentration is minimal the % increase in growth rate due to Proteorhodopsin is higher.
Figure 1: Plot for % increase in growth due to Proteorhodopsin at varying glucose concentration in the absence of Azide.
According to the model the following reactions showed major flux changes due to Proteorhodopsin :
- 'adentylate kinase GTP '
- 'adenosine hydrolase'
- 'dihydroorotic acid menaquinone 8
- '3 isopropylmalate dehydrogenase'
- 'psicoselysine transport via proton symport periplasm
- 'purine nucleoside phosphorylase Deoxyadenosine '
- 'L threonine via sodium symport periplasm '
Figure 2: Plot for % increase in growth due to Proteorhodopsin at varying glucose concentration for 70% inhibition of Oxidative phosphorylation (ETC) on addition of azide.
According to the model the following reactions showed major flux changes due to Proteorhodopsin :
- 'adentylate kinase GTP '
- 'adenosine hydrolase'
- 'dihydroorotic acid menaquinone 8 '
- 'Glycolate oxidase' Needs to be done
- 'psicoselysine transport via proton symport periplasm '
- 'purine nucleoside phosphorylase Deoxyadenosine '
- 'L threonine via sodium symport periplasm '
Reaction Knockout Analysis of all the reactions didn’t have major effects on growth rates .
Figure 3: Plot for % increase in growth due to Proteorhodopsin at varying glucose concentration for complete inhibition of Oxidative phosphorylation (ETC) on addition of high concentration of azide.
According to the model the following reactions showed major flux changes due to Proteorhodopsin :
- adentylate kinase GTP
- adenosine hydrolase
- dihydroorotic acid menaquinone 8
- 3'isopropylmalatedehydrogenase'
- psicoselysine transport via proton symportperiplasm
- purine nucleoside phosphorylaseDeoxyadenosine
- L threonine via sodium symportperiplasm
