1996: Unsolved Astrovirus Capsid Multi-Start

Closed since almost 5 years ago

Summary

• Created: May 19, 2021
• Expires: June 03, 2021 at 18:00 UTC
• Max points: 100

Description

Scientists at UC Santa Cruz need your help! They have been unable to solve the structure of the human astrovirus (HAstV) capsid protein, which is involved in host cell receptor binding. They have some experimental data about the protein structure, but have been unable to find a model that explains the experimental data. This is a multi-start puzzle, with 5 different starting structures provided by the Zhang structure prediction server. Reset the puzzle to cycle through the different starting models. We are giving you 2 weeks to try out all 5 starting models.

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Comments

[beta_helix]

https://zhanglab.dcmb.med.umich.edu/I-TASSER/output/S616803/3kg4qm

The above link shows the Predicted Secondary Structure, Predicted Solvent Accessibility, and a ton more information for this protein.

The starting models do not have any assigned secondary structure, because we do not know how accurate the predictions are.

[grogar7]

for a protein of this size and complexity. Especially with multiple starts!

[beta_helix]

We have extended this puzzle by another week :-)

[grogar7]

Thanks to our scientists :)

[Bruno Kestemont]

Secundary structure prediction:

LLLLLLLLLLLLLLLLLLLLLLLLLLLLHHEEEELLLLLLLHHHHHHHLLLEEEELLLEEEEEELLLLEEEEEEEEEEEHHHHHHHHHHHLLLLLLLEELLLLLEEELLLLEEEEEEELLLLLLLLLLLEEEEEELLLLLEEEEEEEEEEEEEEEEELLLLLLLEEEEEELLLLLLEEEELLLLLLLEEEEEEELLLEEEEEEEEEEELLLLLLLLLHHHHHHHHHHHHLLLLLLLLEEEEEEEELLLLLLLLLL

[LociOiling]

The Zhang Lab link has the "Top 5 final models predicted by I-TASSER". You have to scroll down a bit to see them.

A quick check shows they look a lot like the five structures in this multistart puzzle.

The Select Best Start (SBS) recipe is a classic for this type of puzzle: https://fold.it/portal/recipe/22173

SBS tries all the starting structures. It uses the Lua command puzzle.StartOver: https://foldit.fandom.com/wiki/Foldit_Lua_Function_puzzle.StartOver

Each call to StartOver advances to a new starting structure. The same thing happens when you reset the puzzle with control-r. You'll see a quick pop-up telling you which structure loaded.

If you hover over a segment and hit the tab key, the segment information window opens. This also shows which structure is currently loaded.

All the starting structures have features which don't seem quite right. For example, structure 5 starts with long section of loop which wanders from one side of the protein to the other.

The other structures seem to have similar issues.

[beta_helix]

"This is a multi-start puzzle, with 5 different starting structures provided by the Zhang structure prediction server"

Indeed the Zhang models we provided to you are the 5 predictions in the link above.