On Wednesday, 31 August 2011, Jan Dohnalek wrote:
> Wasn't the original question directed to our (growing) feeling that many
> times PISA says No obvious oligomerization pattern but we already have
> evidence of dimer formation etc..
> This should happen "occasionally" as the approach implied in the
> calculations is statistical in a sense. We should not be getting such
> contradictions on a regular basis.
I think there are at least two possibilities
1) the interface seen in the crystal is a real dimer interface,
but the PISA score fails to rate it as significant
2) the protein has crystallized as a monomer even though it
[sometimes] exists in solution as a dimer. The interface
seen in the crystal is not the "real" dimer interface and
thus the PISA score is correct.
I have no idea which, if either, of these might be the case for 1OYA.
Ethan
>
> Possible I misunderstood the original point ...
>
>
> Jan
>
>
> On Thu, Sep 1, 2011 at 7:46 AM, Karthik S <biokart...@gmail.com> wrote:
>
> > http://www.ebi.ac.uk/msd-srv/prot_int/pi_ilist_css.html
> > so it depends on how many 'stable assemblies' pisa can find i suppose.
> > more interfaces and especially if stable enough will make your
> > fraction go down. i would have been more surprised or worried if that
> > conservative mutation showed radically different CSS scores say one
> > close to zero and the other one or close to it. so the exclamation
> > marks here are really pointless (since both values are close to zero).
> > hence i would ignore the CSS in these two cases. CSS is a statistical
> > measure and does not imply biological meaning. in making me (us)
> > assume the latter through this one singular value leads to all
> > misconceptions.
> >
> > --
> > Karthik
> >
> > On Wed, Aug 31, 2011 at 7:52 PM, Yuri Pompeu <yuri.pom...@ufl.edu> wrote:
> > > I was playing around with PDBe PISA and came across the following:
> > > For pdb entry 1OYA. The most promising interface has an area bury of
> > around 720A^2 and DeltaG of -10.6Kcal/mol. sym_op(y,x,-z+1) and CSS of
> > 0.039! Assembly analysis says it has no strong indications that point to
> > stable quaternary structure.
> > > This protein has been extensively studied and determined to be a dimer.
> > > Entry 3RND is the same protein with one single conservative mutation deep
> > in the active site.
> > > They align with a RMSD of 0.3 A, 99.8% sequence identity. Superposition
> > and inspection of the regions that contact
> > > the adjacent monomer shows they are basically identical.
> > > The interface here shows Area bury of 760 A^2 and DeltaG = -6.6Kcal/mol.
> > sym_op (-y,-x,-z-1/2) CSS=0.00 !
> > > Assembly analysis basically says no stable oligomers form. This enzyme
> > also is dimer according to gel filtration.
> > > Could anyone ellaborate on this please, if they feel like they have the
> > time...
> > > Cheers
> > >
> >
>
>
>
>
