v_mulligan's picture
User offline. Last seen 2 years 13 weeks ago. Offline
Joined: 03/04/2009
Groups: None
Expiry date change

Sorry about that, folks -- I meant to have this expire on the 30th, not the 28th, to space things out a bit with the other puzzles. The expiry date has been updated.

brow42's picture
User offline. Last seen 37 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None
Bridge Stability

In this very small puzzle (I have never satisfied a core filter with such a peptide) won't the bridges be exposed and easily attacked by reducing agents in the blood and CSF? I suppose I can *try* to stuff the bridges in the middle of the core, but again, I probably don't have a core, at least, how the filter defines it.

bkoep's picture
User offline. Last seen 7 hours 54 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Oxidizing environments

The blood and spinal fluid are oxidizing environments, so we don't need to worry about the disulfide bonds being reduced. Any reduced cysteine pairs would quickly oxidize.

brow42's picture
User offline. Last seen 37 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None
Fragment Filter

It seems unlikely that loops will fold in a tiny knot the same way as globular proteins. Perhaps if you are going to make many different peptides in the laboratory, you could compare the effectiveness of the fragment filter on this puzzle. It would be great to turn this off if it is not helping.

bkoep's picture
User offline. Last seen 7 hours 54 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good point

You make a good point that heuristics like the Fragment Filter probably don't apply equally to both large globular proteins and small peptides. Unfortunately, it may be the case that the Fragment Filter is more important here.

In fact, someone in the Baker Lab has recently done an experiment similar to the one you propose. They found that for small disulfide-bonded proteins, fragment quality is actually a powerful predictor of protein stability in the lab.

One possibility is that "bad" (i.e. rarely observed) fragments perhaps represent subtly strained conformations of the backbone. A large protein may be able to compensate for this strain by making a lot of favorable interactions elsewhere. A small protein would simply adopt another conformation with less strained backbone.

User login
Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Search
Only search fold.it
Other Games: Mozak
Recommend Foldit
Topics
Top New Users
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons