puzzle picture
813: Unsolved Electron Density: Hand-folding Round
Status: Closed

Summary

Name: 813: Unsolved Electron Density: Hand-folding Round
Status: Closed
Created: 11/22/2013
Points: 100
Expired: 12/01/2013 - 09:00
Difficulty: Advanced
Description: The Baker Lab and its collaborators have been unable to solve the crystal structure of this protein. The automated methods have been able to generate a model that fits part of the density, but we need your help to get the rest of the structure to fit the remaining density. We're posting this one in 2 rounds, only GUI scripts are allowed and sharing has been disabled for this round. You'll be able to load in your solutions from this puzzle and use scripting and sharing in the next round. Please help us solve the structure of this protein!
Categories: Electron Density, Hand-Folding, Overall, Prediction

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1Go Science8,330100
2Anthropic Dreams8,29485
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4Beta Folders8,19761
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Comments

beta_helix's picture
User offline. Last seen 9 hours 59 min ago. Offline
Joined: 05/09/2008
Groups: None
Here are the secondary structure predictions!

Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Leucines at residues 71 & 76 are highly predicted to be part of a helix. However, the Leucines at residues 93 & 186 are not.

The above predictions are already on the starting model (based on the horizontal lines in the above figure).

Susume's picture
User offline. Last seen 3 hours 50 min ago. Offline
Joined: 10/02/2011
degree of certainty?

Do you have some measure of how certain you are that the given portion is correctly matched?

mimh's picture
User offline. Last seen 5 years 50 weeks ago. Offline
Joined: 05/30/2012
Groups: None
Hi

We are pretty certain about the overall placement of the model. However, there is still a lot of uncertainty and side chain ambiguity in the modeled portion. Registry shifts might be one of them.

Susume's picture
User offline. Last seen 3 hours 50 min ago. Offline
Joined: 10/02/2011
symmetry?

Given that residues 3-93 are identical to residues 6-186, is it safe to assume that the first half of the protein will fold the same and have the same contacts as the second half?

mimh's picture
User offline. Last seen 5 years 50 weeks ago. Offline
Joined: 05/30/2012
Groups: None
Hi Susume,

This is a designed protein and it basically was built in two different steps - The first one was building the helices, which indeed included symmetry!
The second step in designing this protein involved the design of loops to connect the helices, which might have broken perfect symmetry though.
So one would hope that residues 3-93 and 96-186 will fold up the same way... but you never know with proteins!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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