I get confused by these figures. As I understand it the "interface area" given in Pisa is half the loss of accessible area on forming the complex: is that right?
We're working on a complex with interface area ~500A^2, where the complex is stable enough for gel filtration, and with a measured Kd of ~2microM, Pisa estimate of DelG -2.3. Does that sound sensible? Phil On 5 Sep 2011, at 10:33, Eugene Krissinel wrote: > 720 is not an impressive size for a stable interface, but it may do depending > on molecule size and exact chemistry of the interface (h-bonds, salt bridges, > disulphides, charges etc etc). Everything is subject to chemical environment > and concentration, as usual. For these entries, PISA gives dissociation free > energy of -1 kcal/mol. Given some +/- 5 kcal/mol estimated (guessed) accuracy > of PISA, this may or may not be a stable thing. And yes, it has about 70-80% > chances to be simply an artefact of crystal packing, according to some sort > of derivations that I did in 2nd PISA paper in J.Comp.Chem. in January last > year. > > Having said all this, PISA is not an oracle and does not pretend to be > correct in 100% of instances. > > Eugene. > > > On 5 Sep 2011, at 10:14, Eleanor Dodson wrote: > >> Like Jan, I find it very useful to sort out the clear cut cases. Otherwise >> it is easy to get things wrong.. >> >> But isnt a buried surface area of 720 rather small for a stable interface? >> If there is other confirming evidence like 2 diff space groups then you feel >> more secure!! >> >> On 09/01/2011 02:27 PM, Yuri Pompeu wrote: >>> This is regarding Ethan´s point, particularly: >>>> 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 see the same exact interface in a crystal of a close homologue that >>> belongs to a different space group (hexagonal vs tetragonal system)
