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1911: Revisiting Puzzle 140: Rosetta Decoy 4
Status: Closed

Summary

Name: 1911: Revisiting Puzzle 140: Rosetta Decoy 4
Status: Closed
Created: 10/29/2020
Points: 100
Expired: 11/06/2020 - 18:00
Difficulty: Novice
Description: This is a throwback puzzle to the early days of Foldit. This protein helps to regulate oxidation in the cell; the starting structure is a model produced by Rosetta. This protein contains four cysteine residues, but in this state only two of them are expected to oxidize to form a single disulfide bond. We are revisiting old Foldit puzzles so we can see how useful the recent additions to the game have been and to provide newer players with puzzles that are still scientifically relevant.

Sequence:
MPVNQIQETISDNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDLLEYGNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQCYL
Categories: Overall, Prediction

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Comments

APPAAP's picture
User offline. Last seen 23 hours 38 min ago. Offline
Joined: 04/25/2020
Groups: None
Secondary Stracture Prediction

psipred

MPVNQIQETISDNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDLLEYGNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQCYL

1
CCHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCCCC
MPVNQIQETISDNCVVIFSKTSCSYCTMAKKLFHDMNVNYKVVELDLLEY

51
CHHHHHHHHHHHCCCCCCEEEECCEEECCHHHHHHHHHCCCHHHHHHHCC
GNQFQDALYKMTGERTVPRIFVNGTFIGGATDTHRLHKEGKLLPLVHQCY

101
C
L

Who knows what this regulate oxidation in the cell means?

APPAAP's picture
User offline. Last seen 23 hours 38 min ago. Offline
Joined: 04/25/2020
Groups: None
human glutaredoxin-2

This protein is solved as far I learned by now
https://foldit.fandom.com/wiki/Revisiting_puzzle/140:_Rosetta_Decoy_4
provides more about this

APPAAP's picture
User offline. Last seen 23 hours 38 min ago. Offline
Joined: 04/25/2020
Groups: None
UniProtKB - Q9NS18 (GLRX2_HUMAN)

see also
https://www.uniprot.org/uniprot/Q9NS18 as I can see there exist all the data to test validity with foldit puzzle!!

APPAAP's picture
User offline. Last seen 23 hours 38 min ago. Offline
Joined: 04/25/2020
Groups: None
Importance of Recipes in 2C groups

There is more to it in order to get extra bonus you need to form the 2C (Cysteine) bonds in the 2Fe-2C.
This is hard to be achieved manually and now it comes to the importance of recipes.
You all can download Bridge Wiggle v 1.2.1 - Brow42 recipe from foldit recipes ID 37416 or
you can go to the recipe pages in https://fold.it/portal/recipe/37416 and read the information provided.
There exist a nice explanation by foldit user JeniferRM.
One thing I noticed with recipes is that one learns to use the recipe for the specific job.
More to this is to understand the script which is a little bit of programming in lua with foldit functions.
The reason that I do not mostly use recipes is that one has to understand first.
Personally I prefer to work alone but also have in the back of my mind the powerfull techniques of groups and recipes
in automation and time saving.
Good luck to anyone with this puzzle but I do not have the time to get involved online, may I will check it in my rest time in stand alone mode. I mostly concerned about SARS CoV-2.

Joined: 09/29/2016
Groups: Gargleblasters
Alternatively.......

You can do it the easy way by banding from CYS tip to CYS tip, type in for Length: 1.95 and Strength: 10.0 (that's Ten point Zero).

If they are already close enough, simply Wiggle Sidechains to create the bond.
If they are close, but just outside the range of WiggleSC, then you can either:
----Grab ("Pull" with mouse) the structure that one of the CYS is on and gently move it a tiny it. The Band should take care of the rest.
----Perform a "Local Wiggle" on one of the structures a CYS is on. The band will take care of the rest.
After they've made their Disulfide Bond, disable the band. IF there are minor clashes, do a WiggleSC first. Then do a Global Wiggle.

Easy peasy, lemon squeezy!

I used Brow's recipe originally, but found that most of the time it would end up causing the protein to bounce around and break the CYS bonds. where I'd end up having to do the above anyways (or CTRL+Z to get back the bands it made, then do the rest manually) just to re-forge their bonds.

LociOiling's picture
User offline. Last seen 6 hours 28 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
a little late

The wiki has a page for each of the revisiting puzzles. These pages include the matching PDB entries and show the known locations of any disulfide bridges.

This information can be helpful, but some of the revisiting puzzles don't like to fall in line with the PDB.

Just for reference, the page for this puzzle is: https://foldit.fandom.com/wiki/Revisiting_puzzle/140:_Rosetta_Decoy_4

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