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 > > > > > > > > >