I guess both of the mentioned possibilities occur and it is hard to judge which one it is for a particular case. PISA is extremely useful for clear-cut cases to judge them quick. In the "borderline" ones it remains to be the task of the research teams to prove what sort of oligomerisation state is biologically relevant. I wish we had a method that delivers a reliable answer regarding the "real state" of any protein studied...
Jan On Thu, Sep 1, 2011 at 8:41 AM, Ethan Merritt <merr...@u.washington.edu>wrote: > 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 > > > > > > > > > > > > > > > > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
