puzzle picture
360: Quest to the Native CASP9 Puzzle 3
Status: Closed

Summary

Name: 360: Quest to the Native CASP9 Puzzle 3
Status: Closed
Created: 09/13/2010
Points: 100
Expired: 09/20/2010 - 23:00
Difficulty: Intermediate
Description: We are giving you CASP9 Puzzle 3 again, but this time with the native structure as a guide. Use the alignment tool and try to match the native as much as possible. After threading, make sure to press G to Align the Guide. See the puzzle comments for additional information about this particular protein.
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Comments

beta_helix's picture
User offline. Last seen 6 days 14 hours ago. Offline
Joined: 05/09/2008
Groups: None
More info about this native

The solved native structure for CASP9 Puzzle 3, target T0527, is missing 3 residues in the middle of the protein.

You can see it here:
http://www.rcsb.org/pdb/explore/images.do?structureId=3MR0
in the image on the top left, the green region has a chain break (next to the cyan/blue area).

Because of this, we have used Rosetta to fill in the 3 missing residues so that the guide has a continuous chain (since there aren't that many different places where those 3 residues could go)
These 3 residues are Glycine 47, Histidine 48, & Arginine 49.

Also, as Madde pointed out in the forum:
http://fold.it/portal/node/988108#comment-8844

the C-terminal helix points straight out, even though it has a bunch of hydrophobic residues.

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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