puzzle picture
1838: Coronavirus NSP2 Prediction: Tail Domain
Status: Closed

Summary

Name: 1838: Coronavirus NSP2 Prediction: Tail Domain
Status: Closed
Created: 05/14/2020
Points: 100
Expired: 05/21/2020 - 23:00
Difficulty: Intermediate
Description: Fold this coronavirus protein! This is the tail portion of a larger protein encoded in the viral genome of SARS-CoV-2. It is encoded in a region of the genome called NSP2, but the protein's structure and function are still unknown. 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:
KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
Categories: Overall, Prediction

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Comments

bkoep's picture
User offline. Last seen 12 hours 39 min ago. Offline
Joined: 11/15/2012
Groups: None
PSIPRED Predictions

Conf: 957999999864626704466302027828863681589953257786010899999578
Pred: CHHHHHHHHHHHEEEEECCEEEEEECCCEEEEECCCEEEEEECCHHHHHHHCCCCCCCEE
  AA: KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEI
              10        20        30        40        50        60


Conf: 997077015177366799998352433599655788984354699859689998799607
Pred: EEEECCEECEEEECCEEEEEEEEEEECCCCCCCCCCCCCCCCEEEECCEEEEEECCCCEE
  AA: IFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY
              70        80        90       100       110       120


Conf: 7645787245461664299
Pred: EEECCCCCEECCEEEECCC
  AA: CALAPNMMVTNNTFTLKGG
             130
Joined: 05/26/2008
Groups: Hold My Beer
SAM-T08

Do you know what software the SAM-T08 server ran for predictions ? I think a plot like that would be infinitely more helpful with this beautiful disaster.

Joined: 05/09/2008
Groups: None
SAM-T08 is no longer supported :-(

I tried running it on their old site:
https://compbio.soe.ucsc.edu/SAM_T08/T08-query.html
but it is no longer supported :-(

I did love their sequence logos

Joined: 05/26/2008
Groups: Hold My Beer
Sad

I did as well, I really made it a lot easier when deciding when and where to make changes. I have been downloading different software to play with, but have not found anything close to it.

jeff101's picture
User offline. Last seen 4 hours 14 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Cysteines and disulfides

Should we assume no cysteines pair up to make disulfide bonds?
According to https://fold.it/portal/recipe/43861#comment-28861
and https://fold.it/portal/recipe/43861#comment-41453
for 4 cysteines, there is 1 way to form no disulfide bonds,
6 ways to form 1 disulfide bond, and 3 ways to form 2 disulfide bonds.

Joined: 05/09/2008
Groups: None
Predictions:

From http://clavius.bc.edu/~clotelab/DiANNA/:

Disulfide bond scores
Cys position	Distance	  Bond	         Score
10 - 41	        31	KFLALCADSII-GLYRKCVKSRE	0.01039
10 - 105	95	KFLALCADSII-VGTPVCINGLM	0.01126
10 - 121	111	KFLALCADSII-DTEKYCALAPN	0.01654
41 - 105	64	GLYRKCVKSRE-VGTPVCINGLM	0.01708
41 - 121	80	GLYRKCVKSRE-DTEKYCALAPN	0.01426
105 - 121	16	VGTPVCINGLM-DTEKYCALAPN	0.01097
Step 5: Weighted matching
Predicted bonds
10 - 121	KFLALCADSII - DTEKYCALAPN
41 - 105	GLYRKCVKSRE - VGTPVCINGLM
Predicted connectivity
1-4, 2-3


and from http://disulfind.dsi.unifi.it/monitor.php?query=5oIJ1z

                  +------------------------------+                                      
                  |                              |                                      
         .........10........20........30........40........50........60........70........
AA       KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVL
DB_state          1                              1                                      
DB_conf           5                              5                                      

                                  +---------------+                  
                                  |               |                  
         80........90........100.......110.......120.......130.......
AA       KTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG
DB_state                          1               1                  
DB_conf                           6               5                  

DB_bond   bond(10,41)
DB_bond   bond(105,121)

Conn_conf 0.749646

Definitions explained here by jeff101: https://fold.it/portal/node/2009630#comment-41525
Thanks Jeff!
Joined: 09/24/2012
Groups: Go Science
In common language

Does it mean that there is quite good chances of 2 disulfide bonds (10,41 105,121) ?

Joined: 09/21/2011
Groups: Void Crushers
Jpred predictions

I ran the Jpred prediction and something is very strange with this protein. I have never before seen that the 3 engines they use have very different outcomes. One is really different.
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq

Jnet : -HHHHHHHHHHHHHHH---EE------HHHHH-----EEEEEH-HHEEEEE-------EEEEE------EEEEE-EEEEEE----------HHH----EEEEEEEE---EEEEE------E------EEE--EEE---- : Jnet
jhmm : HHHHHHHHHHHHHHHH---EE------EEEE------EEEEEE--EEE----------EEEEE-----EEEEEEEEEEEEEEE---------------EEEEEEEE---EEEEE-----EEE-----EEHHHHHH---- : jhmm
jpssm : -HHHHHHHHHHHHHHHH--------HHHHHHHH----HHHHHHHHHHHHHE--------EEEE------HHHHHHHHHH------H-HHHHHHHH---EEEEEEEE--EEEEEE-------------EEE--EEEE--- : jpssm
As you can see the jpssm prediction has way more helices as the other 2. Can it be that this is a protein with 2 structures, one inside the virus and one when it enters or is inside a cell?

Joined: 09/24/2012
Groups: Go Science
I'm interested in the answer to this question

Can it be that this is a protein with 2 structures, one inside the virus and one when it enters or is inside a cell?

Susume's picture
User offline. Last seen 2 hours 7 min ago. Offline
Joined: 10/02/2011
Suggests low sequence identity

My guess is there are very few known proteins with similar sequences. If the algorithm bases its prediction on proteins that are slightly similar but not really related, it can come up with wildly varying SS predictions.

I think this protein only exists inside the host cell - it is probably not packaged into the capsid when the virus exits the cell to travel to a new host. Instead, when outside the cell, it is carried as instructions in the RNA.

jeff101's picture
User offline. Last seen 4 hours 14 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Reformated version of Timo's post above:
          0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111
          0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333
          1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq
PsiPred : -HHHHHHHHHHHEEEEE--EEEEEE---EEEEE---EEEEEE--HHHHHHH-------EEEEEE--EE-EEEE--EEEEEEEEEEE----------------EEEE--EEEEEE----EEEEE-----EE--EEEE--- : PsiPred 
   Jnet : -HHHHHHHHHHHHHHH---EE------HHHHH-----EEEEEH-HHEEEEE-------EEEEE------EEEEE-EEEEEE----------HHH----EEEEEEEE---EEEEE------E------EEE--EEE---- : Jnet
   jhmm : HHHHHHHHHHHHHHHH---EE------EEEE------EEEEEE--EEE----------EEEEE-----EEEEEEEEEEEEEEE---------------EEEEEEEE---EEEEE-----EEE-----EEHHHHHH---- : jhmm
  jpssm : -HHHHHHHHHHHHHHHH--------HHHHHHHH----HHHHHHHHHHHHHE--------EEEE------HHHHHHHHHH------H-HHHHHHHH---EEEEEEEE--EEEEEE-------------EEE--EEEE--- : jpssm 
Joined: 09/24/2012
Groups: Go Science
Reformated version of jeff101's post above:

0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111
0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
OrigSeq : KLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG : OrigSeq
PsiPred : LHHHHHHHHHHHEEEEELLEEEEEELLLEEEEELLLEEEEEELLHHHHHHHLLLLLLLEEEEEELLEELEEEELLEEEEEEEEEEELLLLLLLLLLLLLLLLEEEELLEEEEEELLLLEEEEELLLLLEELLEEEELLL : PsiPred
Jnet : LHHHHHHHHHHHHHHHLLLEELLLLLLHHHHHLLLLLEEEEEHLHHEEEEELLLLLLLEEEEELLLLLLEEEEELEEEEEELLLLLLLLLLHHHLLLLEEEEEEEELLLEEEEELLLLLLELLLLLLEEELLEEELLLL : Jnet
jhmm : HHHHHHHHHHHHHHHHLLLEELLLLLLEEEELLLLLLEEEEEELLEEELLLLLLLLLLEEEEELLLLLEEEEEEEEEEEEEEELLLLLLLLLLLLLLLEEEEEEEELLLEEEEELLLLLEEELLLLLEEHHHHHHLLLL : jhmm
jpssm : LHHHHHHHHHHHHHHHHLLLLLLLLHHHHHHHHLLLLHHHHHHHHHHHHHELLLLLLLLEEEELLLLLLHHHHHHHHHHLLLLLLHLHHHHHHHHLLLEEEEEEEELLEEEEEELLLLLLLLLLLLLEEELLEEEELLL : jpssm

Joined: 01/05/2019
Groups: None
problems

I can't seem to open the puzzle, my game crashes every time I try to open it. I know there have been issues in the past with Macs, so I don't know if that's the problem (since I am using a Mac) but I just thought I would mention it.

Susume's picture
User offline. Last seen 2 hours 7 min ago. Offline
Joined: 10/02/2011
64 bit game required

If 1837 is the puzzle that is crashing for you, open menu, options, and see what the build ID starts with. If it does not start with 20200409, you are running an old version of the game, probably the 32-bit version, which can't handle the new BUNS filter in 1837. If so, you will have to reinstall to get the 64 bit version. Make sure to copy the all.macro and options.txt file out of your game directory before re-installing. Better yet, rename your entire game directory before reinstalling, so you can go get your history (puzzles you have played) out of it later if you want. Reinstalling removes your history.

Joined: 09/24/2012
Groups: Go Science
Warning

Better to keep the old version on you Mac, by renaming it.
I tried to re-install (64b) on an old Mac and it didn't work at all. Impossible to come back to the old version of foldit. Since then, I'm running Devprev on the same mac: fortunately I had the old version there. This works very fine but it's impossible to play this BUNS puzzle there, and it doesn't recognise filter or symmetric commands in recent recipes.

An alternative could be to install Linux (Ubuntu) on this Mac, but Linux has it's own problems with Foldit. I've an old PC with linux, but I can only run one client (it was 7 under windows in old times). It's not clear to me if these problems are linked to old computer (defective mastercard) or to system.

Joined: 01/05/2019
Groups: None
Oops

wrong puzzle

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