1117: Ultra-compact 17-residue Marburg virus inhibitor
|Name:||1117: Ultra-compact 17-residue Marburg virus inhibitor|
|Expired:||07/30/2015 - 23:00|
|Description:||This is the third in our series of Marburg inhibitor peptide puzzles. We'd like you to design a 17-residue peptide that's able to inhibit the Marburg glycoprotein, a viral surface protein that allows the Marburg virus to infect cells. Seventeen residues might seem quite small, but smaller size can make it easier for a peptide to pass through barriers, such as the gut-blood barrier or the blood-brain barrier, and can also make it less likely to trigger an immune response. It's also quite easy to synthesize a peptide this small, which can mean both that we can make large amounts and that we can include unnatural amino acids or other chemical modifications that would not be possible in a protein that's expressed in bacteria or yeast, but which might aid function or stability. The flip side, though, is that it's more challenging to design something that folds well and binds with high affinity and specificity in this small size range -- but that's the challenge!
We'd like nice, compact designs that bury a sizable hydrophobic core, have no voids in their cores, have lots of secondary structure (helices and sheets) and have good disulfide bonding patterns. Players should also try to maximize contacts (especially hydrophobic contacts) between the peptide and the target. We suspect that designs with a helix lying across a two-standed sheet will work best in this puzzle, but that's not carved in stone. We're giving you a bonus for forming at least two disulfide bonds, as well as a strong bonus for making a good hydrophobic core. This puzzle also uses the fragment filter, so make sure that your designed segments have good fragment quality! (The fragment filter will unfortunately penalize the target as well as the design, but that affects everyone equally and gives no one an advantage.)
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