Wed, 02/22/2017 - 16:54
#2
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.
Tue, 02/21/2017 - 21:46
#3
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?
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?