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.
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
