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670: 30 Residue Symmetric Dimer of Dimers Freestyle Retry
Status: Closed


Name: 670: 30 Residue Symmetric Dimer of Dimers Freestyle Retry
Status: Closed
Created: 01/11/2013
Points: 100
Expired: 02/05/2013 - 12:00
Difficulty: Intermediate
Description: Puzzle 670 is a small (30 residue) symmetric tetramer design puzzle. In other words you will be working with a protein that is made up of 4 symmetric chains. Symmetry becomes complicated when you are working with more than 3 chains. Tetramers, which we learned have 4 chains, can be arranged in a ring (called "C4" symmetry). Or, they can be arranged as a dimer of dimers ("D2" or "two-by-two" symmetry - 2 dimers put together forming a total of 4 symmetric sub-units). The dimer of dimers arrangement is much more common in nature. Keep in mind that symmetric proteins rely on more than just how well-folded each chain is. They also rely on how well the chains interface together. This protein has two fundamentally different interfaces: the interface between chains A and B, and the interface between dimer AB and its partner, CD.
Categories: Design, Overall, Symmetry

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tamirh's picture
User offline. Last seen 8 years 32 weeks ago. Offline
Joined: 05/11/2012
More info here:

This puzzle will have two filters enabled, the Residue IE and the Layer Score filter. If you look under your score, there will be a message similar to "No bonuses, 1 penalty acquired, all conditions met". If you click on the > arrow you will get more information about these filters.

The Layer Score filter is a new filter designed to ensure proteins fold up into desirable shapes. It will categorize each backbone residue as either 'core', 'surface', or 'boundary'. If you think of the protein as being suspended in a liquid, the 'surface' residues are those most exposed to the liquid. Subsequently, the 'core' residues are those that are most protected and the 'boundary' residues are the ones that lie between the 'core' and the 'surface'. Most residues are categorized as either 'core' or 'surface'.

In this puzzle, the filter requires 30% of your protein residues to be in the 'core'. If you do not meet this criteria, you will lose points. If you are losing points, you can click the 'Show' button in the filters dropdown below the score and it will highlight all of the residues that are on the surface and how many you still need to move into the 'core'.

tamirh's picture
User offline. Last seen 8 years 32 weeks ago. Offline
Joined: 05/11/2012

You will need the updated client (released 01/16) to play this puzzle.

There is a bug where using 'Show expected residue burial' will cause instability with this puzzle.

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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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