puzzle picture
1344: Unsolved De-novo Freestyle 101
Status: Closed

Summary

Name: 1344: Unsolved De-novo Freestyle 101
Status: Closed
Created: 02/20/2017
Points: 100
Expired: 02/27/2017 - 23:00
Difficulty: Intermediate
Description: The structure of this protein is still unknown. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets!

Sequence:
MLQLLLAVFIGGGTGSVARWLLSMRFNPLHQAIPLGTLTANLIGAFIIGIGFAWFSRMTNIDPVWKVLITTGFCGGLTTFSTFSAEVVFLLQEGRFGWALLNVFVNLLGSFAMTALAFWLFSASTAH
Categories: Overall, Prediction

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RankGroupScorePoints
1Anthropic Dreams9,211100
2Beta Folders9,18780
3Void Crushers9,17663
4Go Science9,17149
5Contenders9,12737

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Comments

Joined: 09/24/2012
Groups: Go Science
This protein in oily environment ?

There are so many hydrophobic residues ! Could we suspect that this protein is for oily environment (meaning that orange should be outside and blue inside )?

Like puzzle series 1142-1145-1148 ,
http://fold.it/portal/node/2001287

Then considering adapted score function and bonus for hydrogen bond?

Indeed, the sequence is predicted to have at least 4 transmembrane regions (M = membrane = oily)
##############################################################################
OCTOPUS result file
Generated from http://octopus.cbr.su.se/ at 2017-02-21 16:42:11
Total request time: 20.95 seconds.
##############################################################################

Sequence name: query_sequence
Sequence length: 127 aa.
Sequence:
MLQLLLAVFIGGGTGSVARWLLSMRFNPLHQAIPLGTLTANLIGAFIIGIGFAWFSRMTN
IDPVWKVLITTGFCGGLTTFSTFSAEVVFLLQEGRFGWALLNVFVNLLGSFAMTALAFWL
FSASTAH

OCTOPUS predicted topology:
oMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMooooo
oooooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMo
ooooooo

Then it would be a alpha-helical transmembrane protein and parts of the orange should be outside (the blue ones making hydrogen bonds). BUT the scoring function encourages orange inside isn't it?

bkoep's picture
User offline. Last seen 1 hour 49 min ago. Offline
Joined: 11/15/2012
Groups: None
Yes!

This is believed to be a membrane protein, so the native structure will probably have orange (hydrophobic) residues on the outside with buried blue (polar) residues making internal hydrogen-bond networks. Since we haven't altered the score function to reflect the membrane environment, the native structure will probably not score very well in this puzzle. Expect a follow-up puzzle!

We're also a little curious to see how well Foldit players can bury the excess hydrophobics, i.e. if players can find a stable aqueous model for this sequence.

Joined: 06/06/2013
Groups: Gargleblasters
thanks for note

Bruno
makes me feel like I am not crazy. Plus has a flouride ligand and iron ligand as it matches the second chain.....
Nature or points game?

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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