puzzle picture
1820: Coronavirus ORF8 Prediction
Status: Closed

Summary

Name: 1820: Coronavirus ORF8 Prediction
Status: Closed
Created: 04/01/2020
Points: 100
Expired: 04/09/2020 - 23:00
Difficulty: Intermediate
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
Categories: Overall, Prediction

Top Groups

RankGroupScorePoints
1Anthropic Dreams10,812100
2Void Crushers10,61487
3Gargleblasters10,50274
4Go Science10,46064
5Hold My Beer10,45654
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Top Evolvers

RankPlayerGroupScorePoints
1Galaxie 1 2 Anthropic Dreams10,782100
2robgee 15 18 Anthropic Dreams10,646100
3alwen 51 1376 Anthropic Dreams10,64399
4spdenne 51 1376 Void Crushers10,61498
5Mike Cassidy 51 269 Void Crushers10,60197
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Top Soloists

RankPlayerGroupScorePoints
1grogar7 41 58 Anthropic Dreams10,812100
2Galaxie 1 2 Anthropic Dreams10,575100
3Migi 51 1376 Gargleblasters10,49199
4Steven Pletsch 51 391 Hold My Beer10,44498
5steveB 51 1376 Void Crushers10,40497
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Comments

Thu, 04/02/2020 - 00:22
#1
 bkoep 51 368
bkoep's picture
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Joined: 11/15/2012
Groups: Foldit Staff
PSIPRED Predictions 

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
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  • 3
Mon, 04/06/2020 - 06:24
#2
Steven Pletsch 51 391
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User offline. Last seen 4 weeks 2 days ago. Offline
Joined: 05/26/2008
Groups: Hold My Beer
psipred

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.

https://photos.app.goo.gl/QHn6mU5YhxqooVtV9

https://photos.app.goo.gl/npBcwbkQUGiKqeuBA

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  • 1
Fri, 04/03/2020 - 11:59
#3
jeff101 27 75
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Joined: 04/20/2012
Groups: Go Science
Disulfides?

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?

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  • 1
Fri, 04/03/2020 - 17:31
#4
 bkoep 51 368
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Groups: Foldit Staff
No disulfides

We don't expect any disulfide bonds to form in this protein.

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  • 2
Fri, 04/03/2020 - 21:01
#5
Bruno Kestemont 4 5
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Joined: 09/24/2012
Groups: Go Science
how do you

know that ? (if you have time to explain, just curious)

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  • 1
Fri, 04/03/2020 - 22:23
#6
 bkoep 51 368
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Joined: 11/15/2012
Groups: Foldit Staff
Intracellular environment

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.

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  • 4
Sat, 04/04/2020 - 22:13
#7
Serca 51 1376
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Joined: 02/03/2020
Groups: Go Science
What do you mean by 'rarely form'?

Is the cysteine bridge 'strength' reduced in terms of Foldit? How much?

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  • 1
Fri, 04/03/2020 - 21:26
#8
brow42 51 1376
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Joined: 09/19/2011
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Stress function

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?

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  • 1
Sat, 04/04/2020 - 22:32
#9
Serca 51 1376
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User offline. Last seen 2 years 1 week ago. Offline
Joined: 02/03/2020
Groups: Go Science
2 conformations protein?

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.

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  • 0
Wed, 04/08/2020 - 00:41
#10
Serca 51 1376
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User offline. Last seen 2 years 1 week ago. Offline
Joined: 02/03/2020
Groups: Go Science
1820 SS prediction

Here is the structures i've got from my script of 1820 SS prediction:
(helices are red, sheets are green)

link: https://pasteboard.co/J2MjsJ3.png

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  • 2
Wed, 04/08/2020 - 01:13
#11
Serca 51 1376
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Joined: 02/03/2020
Groups: Go Science
Design

Some idea for design for that structures:

https://pasteboard.co/J2MDpsV.png

But it has a lot of exposed hydrophobic segments. So if it is not a membrane protein (but it could be because of the long helix), it doesn't hit the good score.

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  • 2
Wed, 04/08/2020 - 22:38
#12
aofreelancer 51 1376
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Joined: 03/19/2020
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So whats next puzzle?

I do work at this puzzle two, i was able to fold it, but i have no biology science background was kind off thrown away by the complexity of it.

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  • 1
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