puzzle picture
1848: Revisiting Puzzle 126: Ethanolamine Utilization
Status: Closed

Summary

Name: 1848: Revisiting Puzzle 126: Ethanolamine Utilization
Status: Closed
Created: 06/05/2020
Points: 100
Expired: 06/12/2020 - 18:00
Difficulty: Novice
Description: This is a throwback puzzle to the early days of Foldit. This protein allows bacteria to metabolize ethanolamine and use it in constructing cell walls and cell membranes. The protein is modeled here in reduced form, so no disulfides are expected to form. 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:
MKLAVVTGQIVCTVRHHGLAHDKLLMVEMIDPQGNPDGQCAVAIDNIGAGTGEWVLLVSGSSARQAHKSETSPVDLCVIGIVDEVVSGGQVIFHK
Categories: Overall, Prediction

Top Groups

RankGroupScorePoints
1Beta Folders10,920100
2Anthropic Dreams10,78376
3Contenders10,72156
4Go Science10,68741
5Void Crushers10,53429

Top Evolvers

Top Soloists



Need this puzzle? Log in to download.  

Comments

marsfan's picture
User offline. Last seen 20 weeks 3 days ago. Offline
Joined: 12/18/2015
Groups: None
Regarding starting pattern

These puzzles start out with a preliminary fold performed. Is that just a general guideline, or is it known that this protein folds to somewhere around that shape?

LociOiling's picture
User offline. Last seen 5 hours 2 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
it depends...

Sometimes the revisiting puzzles are close to the native state, but sometimes they are farther away.

All the revisiting puzzles have at least one published solution, and some have a long list of solutions. You can always compare the starting pose to the published solution, as described below.

For the close ones, small differences can matter. For example, I think on the last ice binding revisit, puzzle 1845, the key to success may have been the "omega" backbone angle between segments 38 and 39. You can get close to the native if they're in the normal "trans" configuration, but I suspect they should be "cis" instead, with both sidechains more or less on the same side.

For other revisits, the starting pose may be farther away, and you can have major differences like sheets being out of order. There's a a whole series of "Rosetta decoy" revisits which mostly fall into this category. (For some reason, the Rosetta decoy puzzles were skipped in the last revisiting cycle.)

There are also some revisiting puzzles where the best Foldit results seem to be far from the published native protein. Not clear what's going on with those, but some of the smaller puzzles are like that.

Here's the scoop on this week's puzzle:

https://foldit.fandom.com/wiki/Revisiting_puzzle/126:_Ethanolamine_Utilization

The protein in this puzzle matches two PDB entries. You can look at the solutions at rcsb.org, which includes an online protein viewer that's somewhat similar to Foldit. The matching entries are 2HD3 and 2Z9H, and both have multiple copies of the protein, which complicates viewing a little. For Foldit, we're working with a single copy of the protein, which in theory should fold into its native shape, and then bond to another copy of itself.

Susume's picture
User offline. Last seen 2 hours 43 min ago. Offline
Joined: 10/02/2011
How to make cis bond in foldit?

Is there a way to purposely make a cis bond in foldit? One could cut both sides of an amino acid and roll it 180 degrees around its backbone axis - but that risks making both ends of it cis, and wiggle is likely to fight with it as you try to stabilize. I suppose one could try very strong bands to space to try and force the sidechain to the other side of the backbone. Is there a better way?

jeff101's picture
User offline. Last seen 11 hours 18 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
You could use bands
https://www3.nd.edu/~aseriann/ctpep.html
gives bond angles and lengths for cis & trans
peptide bonds. You could use these diagrams
and some trigonometry, like the law of sines 
https://www.calculatorsoup.com/calculators/geometry-plane/triangle-law-of-sines.php
or the law of cosines
https://www.calculatorsoup.com/calculators/geometry-plane/triangle-law-of-cosines.php
to find distances between certain atoms 
(like between 2 adjacent alpha-carbons), 
and then use bands to enforce these distances.
Some of my notes give Ca-Ca distances of
3.79 A for trans & 2.91 A for cis. 

Perhaps a more thorough google image search
would find a figure with more distances on it.
spmm's picture
User offline. Last seen 2 days 21 hours ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Pymol education version

https://pymol.org/edu/?q=educational - this is a free version of Pymol for educational purposes so you have to register. Other sites may also have versions.
The last one I had stopped working on the Mac when Apple moved to 64 bit - not sure if they have updated the edu version yet.

Why bother? Pymol allows you to display side chains which as you can see from Loci’s comment above, can be very important in strand orientation and points for the revisiting puzzles. You can also view a single chain in an assembly. Pymol is a professional tool and can take a bit of getting used to.

IMol viewer lite works well on an iPad - just type the PDB number in and it will display - limited choice of display options but quite useful. Side chains can be viewed as well.
There may be more recent tools of course for all platforms.

jeff101's picture
User offline. Last seen 11 hours 18 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Do any viewers show hydrogen bonds?

Can Pymol or some other pdb viewer show hydrogen bonds?

Mikisp's picture
User offline. Last seen 22 weeks 2 days ago. Offline
Joined: 04/01/2020
Groups: None
Hydrogen bonds

VMD is also a very good professional tool to construct and view all proteins and show hydrogen bonds, of course. But it isn't very easy to use. Perse is an other viewer for Ipad.

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