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1820: Coronavirus ORF8 Prediction

Closed since almost 6 years ago

Intermediate Overall Prediction

Summary

Created
April 01, 2020
Expires
Max points
100
Description

Fold this coronavirus protein! This protein is encoded in the viral genome of SARS-CoV-2, in a region called ORF8, but the protein's structure is still unknown. Evidence suggests this protein triggers a stress signal in the infected cell. If we knew how this protein folds, we might be able to figure out its exact function. The puzzle's starting structure shows SS predictions from PSIPRED, and hints which parts of the protein might fold into helices or sheets. Refold this protein to find high-scoring solutions, which will tell us how this protein is most likely to fold!



Sequence:


MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI

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Comments

bkoep Staff Lv 1 


Conf: 944899999999998844500788826999112899865302025788628998503531
Pred: CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEE
  AA: MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
              10        20        30        40        50        60


Conf: 023105747526877262789757489967899973279888665353013059999771
Pred: EHHHCCCCCCEEEEEECCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEEEEE
  AA: CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
              70        80        90       100       110       120


Conf: 9
Pred: C
  AA: I

jeff101 Lv 1

In this protein's sequence are 7 cysteines.
These could form up to 3 disulfide bonds.
https://fold.it/portal/recipe/43861#comment-28861
says there are 105 different ways to make
3 disulfide bonds from 7 cysteines.
It also says there are 21 different
ways to make 1 disulfide bond from
7 cysteines. I think there are also
105 different ways to make 2 disulfide
bonds from 7 cysteines. This all begs
the question, should any disulfide bonds
form in this protein, and if so, how many?

brow42 Lv 1

Not sure what "stress" means. Should these cysteines be outward facing as part of their function? Does this stress trigger involve competing for and breaking disulfide bonds on the counterpart protein, causing the stress response? Does this protein live in a highly reducing environment, and so, we should consider cysteine to be just a small-sidechain AA?

bkoep Staff Lv 1

It's thought that this protein's function is intracellular. The interior of the cell has a reduction potential that favors free cysteines instead of disulfides, so disulfide bonds rarely form in proteins that remain within the cell.

Serca Lv 1

I have 3 cysteine bridges design that looks pretty nice.
IMHO 1 extra cysteine could be used to move the long helix, switching between 2 protein conformations.

But there is the important note: I know that it may sound a bit stupid but sheet markup by PSIPRED looks wrong. I used different beta-sheets layout.

Steven Pletsch Lv 1

since i really like the psipred data, i decided to spend some time playing with it and figuring out what it can do and what the confidence actually means (0 is low, not 10), I am a visual person when it comes to data, so am sharing these for others that may find them useful.

Google Photos Google Photos