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

Top Evolvers

Top Soloists



Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 16 hours 11 min ago. Offline
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
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

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?

bkoep's picture
User offline. Last seen 16 hours 11 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
No disulfides

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

Joined: 09/24/2012
Groups: Go Science
how do you

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

bkoep's picture
User offline. Last seen 16 hours 11 min ago. Offline
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.

Serca's picture
User offline. Last seen 17 weeks 2 days ago. Offline
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?

brow42's picture
User offline. Last seen 29 weeks 3 days ago. Offline
Joined: 09/19/2011
Groups: None
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?

Serca's picture
User offline. Last seen 17 weeks 2 days 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.

Serca's picture
User offline. Last seen 17 weeks 2 days 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

Serca's picture
User offline. Last seen 17 weeks 2 days ago. Offline
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.

Joined: 03/19/2020
Groups: None
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.

User login
Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Search
Only search fold.it
Other Games: Mozak
Recommend Foldit
Topics
Top New Users
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons