This page will contain information about the ongoing CASP9 effort on POEM@HOME. The first hard target was T0531. For this target no good template structures could be found. After initial fragment model generations, we submitted the structures for structure building and rating to POEM@HOME, where we found 3 dominant folds.
The first fold is energetically most stable (and therefore usually the one we pick). It is a long extended beta sheet with many many hydrogen bonds stabilizing between the sheets.
Best raw energy structure for target T531
Usually when we discover a structure as stable as this one, we submit it immediately. This time however, we noticed that the disulfide bridges are unpaired (the red sticks, sticking out). Disulfide bridges usually stabilize the protein by a large amount of energy - therefore we also compared this structure with the remaining ones in the population.
Second best energy structure for Target T531
Obviously in this structure the disulfides are also unpaired, but at least 2 bridges are in the vicinity of each other. The last one is found in a loop allowing for the refolding of this loop.
Structure with all disulfide bridges developable
Finally the population contained a structure where all disulfide bonds can theoretically be linked. We started the simulation from here with an emphasis of disulfide bond generation and submitted the resulting structure. Obviously we cannot say yet if this structure is correct or not, because the final results are not out, but it was one of the most interesting structures to date. | 
发表于 2010-6-9 10:17:55
