Team:IIT Madras/Dry lab/Modelling/Validation

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]. This literature states that in the presence of azide i.e, when the Electron Transport Chain is inhibited (Cytochrome oxidase in specific) the cell survivability decreases drastically. But in the presence of Proteorhodopsin this survivability is increased by 11% hence indicating an increase in growth rate. We validated our model using this literature.

Method: At 70% inhibition and complete inhibition (i.e. Cytochrome oxidase reaction flux was reduced by 70% and 100%) we varied the glucose uptake flux. We calculated growth rate for Model_WT and Model_PR and hence calculated percentage increase in cell growth rate caused due to Proteorhodopsin.
Observations: Upto 30% increase in growth rate was observed due to Proteorhodopsin at 70% inhibtion of ETC due to Azide (See Figure 1). On complete inhibition Proteorhodopsin almost seems to compensate for the ETC (See Figure 2) as stated in literature.

Table 1:

Figure 1: 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 :

1. 'adentylate kinase GTP '
2. 'adenosine hydrolase'
3. 'dihydroorotic acid menaquinone 8 '
4. 'Glycolate oxidase' Needs to be done
5. 'psicoselysine transport via proton symport periplasm '
6. 'purine nucleoside phosphorylase Deoxyadenosine '
7. 'L threonine via sodium symport periplasm '

Reaction Knockout Analysis of all the reactions didn’t have major effects on growth rates .

Figure 2: 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 :

1. adentylate kinase GTP
2. adenosine hydrolase
3. dihydroorotic acid menaquinone 8
4. 3'isopropylmalatedehydrogenase'
5. psicoselysine transport via proton symportperiplasm
6. purine nucleoside phosphorylaseDeoxyadenosine
7. L threonine via sodium symportperiplasm

Reaction Knockout Analysis of '3 isopropylmalate dehydrogenase' was lethal and the other reactions didn’t have major effects on growth rates .