Depends on the specific protein. Supposing you're using E. coli:

- Insoluble intracellular (inclusion bodies): Great yields, high purity, but you need to find a good refolding protocol. This can ruin your yields.

- Soluble intracellular: Getting good yields/purity not that easy due to less pure starting sample, but may be offset by not having to refold the protein. Usually the best alternative.

- Periplasmic: Good yields, high purity, no need to refold most of the time, but not easy to scale up (I mean industrial scale) and productivity is poor.

- Extracellular: Not a good idea if you're using E. coli, almost nothing gets there except via cell lysis. Switch to yeast.

Hope it helps

Dear Jiivittha,

It all depends on the nature of your protein and the expression system. In general, material that is in the more native state of the protein will tend to be the best for purification. This is because it is more likely to be properly processed by the expression cells. Obviously, the more heterologous the expression system, the less likely that the processing will be like expression in the native organism.

Perhaps you could give some details of your protein of interest (native organism, native location, whether it has obvious post-translational modifications like disulfides or glycosylation) and expression system?

At least in E. Coli, generally the largest yields and are going to come from whatever conditions give you soluble cytosolic protein. That said, if the protein will not express solubly, proteins purified from the pellet are often purer from the get-go. Same goes for proteins shuttled to the periplasmic space. Sometimes those can essentially be used crude without further purification. As Nicholas says, it is highly dependent on the nature of your protein, its expression system and the relationship between the two.

Depends on the specific protein. Supposing you're using E. coli:

- Insoluble intracellular (inclusion bodies): Great yields, high purity, but you need to find a good refolding protocol. This can ruin your yields.

- Soluble intracellular: Getting good yields/purity not that easy due to less pure starting sample, but may be offset by not having to refold the protein. Usually the best alternative.

- Periplasmic: Good yields, high purity, no need to refold most of the time, but not easy to scale up (I mean industrial scale) and productivity is poor.

- Extracellular: Not a good idea if you're using E. coli, almost nothing gets there except via cell lysis. Switch to yeast.

Hope it helps