[EMBOSS] pepstats pI values (vs protparam)

[Ingo P. Korndoerfer]

o.k. ... so i will contribute why we need to know the pI.

our core activity is the purification of proteins for crystallization. a
good pI prediction helps us making better guesses at what ion exchange
media and buffer conditions might make a good starting point in the
purification. so, i guess, what we need is the pI under conditions
typically applicable to a purification. which is likely somewhat off
from "physiological", but might be diluted saline solutions, typically,
e.g., 100 mM NaCl, 10 mM Tris ... (just to give an idea about the ionic
strength, if that matters).

and while we are at it: it might be interesting for us to also be able
to guess beforehand what difference a serine or threonine
phosphorylation etc might make ...

ingo

On 28/06/2010 18:03, Peter Rice wrote:
> On 24/06/2010 11:20, Ingo P. Korndoerfer wrote:
>> oh no ... i need some help again ...
>>
>> my colleagues tell me (similar to the issue resolved last week)
>> peptstats and protparam calculate different pIs.
>>
>> alternatively, of course, if i can convince my team pepstats values
>> are better then protparam values, that would be fine, too ...
>
> That may be the easiest option for now...
>
> I checked on what protparam does ... and it is very specific to
> running 2D gels under high urea conditions. It also looks as though
> the publication does not have all the values (only a few N-terminal
> resudie values were given, for the proteins they analysed) so I have
> to dig deeper to calculate the others. The values are defined only
> for acidic proteins (and for acidic residues, values are given to 2
> decimal places, for basic residues they are to the nearest integer!
> Are there any more recent calculatioins for basic resudues we can
> use?
>
> It does lead to some interesting options, especially for eukaryote
> proteins, but we will not be able to change the calculations in time
> for this release.
>
> Meanwhile we would like to hear more from users who calculate pIs
> what conditions they are interested in (and why).
>
> regards,
>
> Peter Rice
>
>



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