Results - December 2007


On the left we show the unfolded starting conformation of a so-called tryptophan zipper, one of the smallest proteins with a stable 3D structure. On the right we show the overlay of the structure folded by POEM@HOME (pink) with the experimental one (turquoi se). The ribbon like structures indicate what is called a beta-sheet protein conformation. Most proteins of this size are not stable, but i n this designed peptide stability is achieved by clustering the tryptophane sidechains on one side of the beta-sheet.


These sidechains do not like to be in water (hydrophobic effect) and our model correctly predicts their clustering in agreement with experiment. The average error (called root mean square deviation) of each atom in the folded structure is 1.38 Å, roughly the “diameter” of water molecule for comparison. The folded structure agrees with the experiment to experimental resolution. Small beta-hairpins have a number of biological functions, which makes it interesting to study them. Among other things they modulate the entry of viruses into the cell (like the HIV virus).


On the left we show the unfolded starting conformation of the HIV accessory protein, another protein the HIV virus needs to enter the cell. On the right we show the overlay of the structure folded with POEM@HOME (blue) with the experimental conformation of this 40 amino-acid th ree-helix bundle. The average error for each atom in the folded structure is just 2.56 Å, again within experimental resolution. We have fol ded both proteins in three independent simulations each (we are working on movies). These results show that POEM@HOME is working, thanks fo r all your contributions and happy holidays.