Calculation of PO ratio

[TomF]

I was looking at some energetics with the yeast model.

I saw in one of the yeast model papers they calculated the model-based PO ratio by maximizing ATP production. (and got a value of 1.04 for glucose). Does anyone know the exact reaction that was optimized to obtain this number? I tried optimizing for ATPS and ATPS3m(mitochondrial synthase) but wasn't getting the quoted value.

Thanks

 

 

[Ronan Fleming]

Hi Tom,

I have not worked with a yeast model, but if the modeling of the
electron transport chain is in any way similar to that for E. coli
(e.g. iAF1260), you might get different PO ratios depending on the
partitioning of fluxes through alternate pathways in the electron
transport chain. Optimization will always find a highest yield so if
your current predictions are too high, take a look at reactions like
NADH dehydrogenases and see which ones are being used preferentially.

Ronan

--
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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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[pj]

Hey Tom,

Just to remind you that, in the presence of glucose and oxygen, yeast metabolism use that carbon source mainly through fermentation. The specific percentage that goes to fermentation and to respiratory pathways you have to see in literature and it will depend on the medium you are using, if it is a rich medium like YPD or a synthetic medium.

So in the case you mentioning I would probably guess that all reactions where ATP is synthesized were maximized for ATP production.

Regarding oxygen use, is more tricky. Since most glucose goes into fermentation, there is a kind of decoupling of total ATP production and oxygen use in mitochondria.

I think you should define the conditions you are interested to have when you do the modeling of yeast metabolism, because the results you will get probably will depend on that. For instance, if the rate of glycolysis is too high, yeast cells will experience overflow metabolism (production of too much NADH) and will start redirecting this metabolite to be used by the exterior mitochondrial NADH dehydrogenase Nde1 and to other reactions where it is consumed.

There are good revisions about all this subjects, this one is a good place to start:

http://repositorium.sdum.uminho.pt/bitstream/1822/6231/1/Ch06.pdf