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975: Ebola glycoprotein 30-residue inhibitory peptide design

Closed since over 11 years ago

Intermediate Overall Design

Summary

Created
August 27, 2014
Expires
Max points
100
Description

Based on player feedback, we are posting a second anti-Ebola peptide design puzzle, this time with a slightly longer peptide. We would like you to design a small (30-residue) peptide that can bind to and block the Ebola glycoprotein. The glycoprotein is a viral surface protein that allows the Ebola virus to enter human cells. A small peptide inhibitor of this protein would therefore represent a candidate therapeutic for treating this deadly disease. We are starting you with a hotspot "stub" that was the top-scoring result from the earlier stub-finding puzzle, number 846 (congratulations to AnthropicDreams). We have extended this stub with twenty-seven additional residues that you can design.


A small peptide in this size range probably won't fold the way a protein would. Some considerations -- good hydrophobic packing, lack of holes in the core, good hydrogen bonding, presence of secondary structure, etc. -- will be the same, but in addition, heavy disulfide cross-linking is often necessary for stability in this size range. You will get a considerable bonus for forming up to three disulfide bonds (for a total of five, counting the two disulfide bonds already present in the Ebola target protein). Many natural plant and animal toxins are small peptides, and it is common to see three disulfide bonds in a "leapfrog" pattern (i.e. cys1-cys4, cys2-cys5, cys3-cys6) for maximal stability. The starting point for this puzzle has three disulfides in this "leapfrog" pattern, but this might not represent the optimal disulfide placement or peptide structure. Feel free to improve on this!


Note: Server maintenance is scheduled for Wednesday, Sept. 3rd, from 8:00 am to 11:00 am PST. This puzzle is scheduled to terminate just prior to the scheduled downtime.

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Comments

Cyback Lv 1

This reminds me of BOINC (Berkeley Open Infrastructure for Network Computing ) http://boinc.berkeley.edu/Which uses your computer for science projects when it is idle only this is more interactive which I think makes it more appealing to a lot of people. Still, BOINC does do a lot of great science. Anyway, I plan on spreading the word to my BOINC team to look into playing this as it is fun and does science which is a great combination.