compartment for new metabolites

[Jin]

Hi all,

I wanna manipulate my model with adding new metabolites. I am not sure at which compartments the new reactions are active. Is it acceptable to set the compartments of my metabolites as cytoplasm? In fact, does the compartment make have impact on predictions?

Thanks,

Jin

[Thomas Pfau]

Hi Jin,

In general , if you only add metabolites, without any reactions, it won't change anything except for the dimensions of the stoichiometric matrix, since they won't interact with anything else in the model.
If you plan to introduce new reactions that are connected to the remaining model, then it is important where those are located, as it has an influence on which metabolites are available in the respective compartment(s).

If you have no idea, where those reactions could take place the cytoplasm is a sensible choice, but you might want to try some predictive algorithms for the enzymes you introduce (i.e. where would protein löocalisation prediction tools put the enzymes catalysing your new reactions) and place them there.

Best

Thomas

Am 16.06.2020 um 16:44 schrieb Jin:

Any comment?

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[Jin]

Thanks Thomas!

On Tuesday, 16 June 2020 21:10:49 UTC+1, Thomas Pfau wrote:

Hi Jin,

In general , if you only add metabolites, without any reactions, it won't change anything except for the dimensions of the stoichiometric matrix, since they won't interact with anything else in the model.
If you plan to introduce new reactions that are connected to the remaining model, then it is important where those are located, as it has an influence on which metabolites are available in the respective compartment(s).

If you have no idea, where those reactions could take place the cytoplasm is a sensible choice, but you might want to try some predictive algorithms for the enzymes you introduce (i.e. where would protein löocalisation prediction tools put the enzymes catalysing your new reactions) and place them there.

Best

Thomas

Am 16.06.2020 um 16:44 schrieb Jin:

Any comment?

On Friday, 12 June 2020 08:49:16 UTC+1, Jin wrote:

Hi all,

I wanna manipulate my model with adding new metabolites. I am not sure at which compartments the new reactions are active. Is it acceptable to set the compartments of my metabolites as cytoplasm? In fact, does the compartment make have impact on predictions?

Thanks,

Jin

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