I have tried to remove ATP by anion exchange dowex resin, however, I have also lost proteins due to their negatively charged surfaces. Can anyone suggest the safe methods to deplete ATP from my solution without any effect on protein structure and conformation? I would highly appreciate if you can suggest a suitable way.
If you are trying to inactivate ATP in your prep, I would recommend using using low concentrations of alkaline phosphatate. It will dephosphorylate the ATP and ADP.
You might try dialysis, size exclusion columns, or centrifuge filters.
As Joshua suggest, the using a size exclusion columns that come in different formats according to the volume of sample that you have as one of the best options. We've used PD-10 columns (GE healthcare) that come in an small size which can be used in the centrifuge.
In my experience centrifuge filter devices always leave an small amount of ATP. I think because the ATP binds the filter membrane.
The idea of Steingrimur is good. Another possibility is to use apyrase, which commonly used as ATP and ADP scavenger.
Simply pass your solution through a small plug of activated carbon (decolorizing charcoal) and any aromatic cofactors, like FAD, NAD, ATP, etc will stick like glue to the charcoal. This is a common technique to remove tightly but non-covalently bound cofactors from enzymes to obtain the apoenzyme. No need to add more protein to your protein solution!
I would agree with Ana Batastinni and try Apyrase, you could always generate Apyrase conjugated beads using Potato Apyrase from Sigma and then easily remove them, although I like the AP idea but I've never tried. Please let me know how you get on with it.
I tried and liked alkaline phosphotase to dephosphorylate ATP. It works
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