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1344: Unsolved De-novo Freestyle 101

Closed since about 9 years ago

Intermediate Overall Prediction

Summary

Created
February 20, 2017
Expires
Max points
100
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

Top groups

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    1. Anthropic Dreams
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Comments

Bruno Kestemont Lv 1

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?

Skippysk8s Lv 1

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?

bkoep Staff Lv 1

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.