Glycine disallowed at surface on 1313

Case number:845813-2003185
Topic:Game: Tools
Opened by:Susume
Status:Open
Type:Bug
Opened on:Wednesday, December 7, 2016 - 22:31
Last modified:Thursday, December 29, 2016 - 07:18

I used the blueprint tool to put a helix-sheet loop into 1313, then tried to change the green residue to glycine. GLycine was disabled with the message "Cannot place a hydrophobic amino acid as a surface residue". I had to make due with asparagine. Lots of loops have glycine at the surface - it ought to be allowed. Many of the building blocks will not work well if you can't put a glycine in them. This was the first helix-sheet loop in the list, green-blue.

20161026-4422e3a127-win_x86-devprev

(Wed, 12/07/2016 - 22:31  |  4 comments)


bkoep's picture
User offline. Last seen 15 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None

This should not happen. Susume, do you still have this solution? Can you share it using the "Share with Scientists" button?

Susume's picture
User offline. Last seen 1 week 3 days ago. Offline
Joined: 10/02/2011

Shared with scientists as "1313 GLY disabled residue 66". The helix-to-sheet building block is at 65-68, and the one I can't change to GLY is 66. In the sheet-sheet building block at 74-77, GLY is allowed. So it's not consistent.

bkoep's picture
User offline. Last seen 15 hours 50 min ago. Offline
Joined: 11/15/2012
Groups: None

Okay I see the issue. The error message about a "surface hydrophobic" is misleading; this actually has nothing to do with the surface position or "hydrophobicity" of GLY—I'll have to dig a little bit to figure out why that message is output.

GLY in this position actually violates the SS Design filter on this puzzle. The SS Design filter is meant to prohibit certain residue types (ALA, GLY, PRO) in the middle of secondary structures like helices and sheets. Because of the backbone hydrogen bonds at position 66, Foldit (or rather, DSSP) thinks this residue is part of a sheet. I think, if you were to develop this design further, then the backbone H-bond pattern would be disrupted, DSSP would no longer recognize this position as part of a sheet, and GLY would be allowed.

Susume's picture
User offline. Last seen 1 week 3 days ago. Offline
Joined: 10/02/2011

Similar problem with 1321 - glycine is disallowed in a loop where it needs to be. 1st picture - 73G and 74V both have backbone bonds to the helix. Auto structure says 73G is loop, and glycine is allowed. 2nd picture - 73G has lost its backbone bond to the helix but is still green in the rama map. Auto structure says it is now part of the helix, and glycine is now disallowed.

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