Results - April 2008

In the recent months we succeeded folding various proteins. The fold presented on the images above is 1UXD (PDB-Database link). The fructose repressor originating from Escheria Coli is able to bind DNA via a helix-turn-helix motif. One possible folding pathway discovered by POEM@HOME was rendered using three different representations, which are accessible via the three images underneath. To produce a continuous motion a linear interpolation was constructed with Chimera between the POEM states.
On the first video the forming of the three helices can be observed, which happens before the protein folds into a compact structure by a few mainchain rotations. The second movie contains a ball and stick representation, where one can see, that at the end of the folding process, the mainchain remains static mainly, while the sidechains remain flexible. This is due to the fact, that a mainchain rotation always implies a big change in energy, because a lot of atoms are displaced. The last (lower) movie shows the folding process in sphere representation (green = hydrophilic, prefers vicinity to water, white = hydrophobic, dislikes water). Here the best noticable characteristic of protein folding is, that the protein approaches a tightly packed structure with a hydrophobic core.
Movie 1 and 3 clarify the two competing protein folding theories: Hydrophobic collapse and secondary structure formation. The folding of 1UXD suggests, that both mechanism coexist. Higher resolution versions of the movies will be available shortly on the forums.