pyrophoshatasing cell extract for nucleotide depletion?

Johannes Graumann graumann at
Tue Aug 6 14:09:25 EST 2002

Hash: SHA1

D.K. <dk at> wrote:
>You know, only now I realized how badly I mixed it up :(
>In fact, everything I wrote in my original reply is wrong and
>the exact opposite is correct: kinases can, albeit poorly,
>thiophosphorylate, but phosphatases cannot take thiophosphate
>off. (Yes, this time I got it right for sure :-))
>So sorry! Hexokinase part is still OK, though.
This means I could (if I stick with it) pyrophosphatase as well as 
hexokinase I suppose ... ;0)

>>> If you can provide a more detailed description of the experiment
>>> you are trying to do, odds are good there is a better solution.
>>Ok, here comes the embarrasing part (I have no idea whether this is a
>>reasonable approach) ...
>>I'm setting out to look by pulldown/masspec for the substrate of a
>>kinase. I will try pulldown straight from extract and  pulldown from
>>extract of cells that have been formaldehyde crosslinked.
>IMHO, this will work only if you are very lucky...
I'm aware of this but this is a pet project, so I'm just going for it 

>>I found some papers revferring to the stabilization of 
>>kinase/substrate complexes in the presence of g-S-ATP (albeit only for 
>>peptides in vitro) and hence the question above. I would make an 
>>extract, deplete it for ATP while providing g-S-ATP and pull down my 
>>kinase, hoping that g-S-ATP has replaced ATP and might stabilize the 
>>kinase/substrate complex. Sounds weired? - may well be ;0)
>No, it's not weird. 
^Thanks! ;0)

>IMO, in this case you really don't need to bother with ATP depletion. 
>Even if you manage to keep all cellular ATP intact, it still will be 
>diluted way below ATPgS level that you can easily provide (~ 2 mM). 
I will try that.

>Just to be sure you can desalt extract over spin or gravity column  - 
>any commercial or home made G-25 or P-6 will do. No need to complicate 
>things by introducing other stuff.
Why should the column step be necessary - someone else proposed a 
depletion from nucleotides by size exclusion (see other post in thread), 
but I don'tlike that idea. Looking for interactions I want to be quick 
about the depletion without messing up the protein stoechiometry by 
dilution even more than I do with the extraction buffer anyway ...


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