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Symmetry puzzle

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Irc 202811 1322780540 S2 CH Granier

A Symmetric Dimer puzzle. The main chain is shown in green on the bottom, the shadow copy is shown in gray on top.

Most Symmetry puzzles are a type of design puzzle.

In a symmetry puzzle, there are multiple copies of the same protein. Players can work on one copy of the protein, called the "monomer" or "main chain", in the usual way. The monomer is colored normally, while the other copies of the protein are normally gray.

Changes made to the monomer are automatically reflected in the copies.

The first goal of a symmetry puzzle is to produce a well-folded monomer, just as in a standard design puzzle. The next goal is to assemble the monomer and the copies into a "oligomer", or what Foldit usually calls a "complex". The area where the copies connect to each other is called the "interface".

The design goals for a oligomer are generally similar to those for a monomer. For example, the oligomer complex should be tightly packed, ideally with few voids between the monomer and the copies.

Many symmetry puzzles call for the complex to have its own hydrophobic core. This is a tricky requirement, since the hydrophobic residues that go into the the complex's core must be on the surface of the monomer. The exposed residues lead to a worse "hiding" score for the monomer.

To get around the hiding issue, symmetry puzzles often include a filter which awards a bonus for creating a complex with a hydrophobic core. (And, there's usually a penalty for missing the goal.)

Types of symmetryEdit

There are two main aspects to symmetry in Foldit. The first is the degree of symmetry, or the number of copies of the protein. The puzzle's degree of symmetry is identified in the the title using the somewhat obscure terms listed below.

The other aspect of symmetry involves the geometry of the relation between the copies of the protein. The geometry normally isn't discussed in detail in puzzle descriptions.

Symmetry puzzle geometryEdit

The Foldit symmetry category mentions rotational and translational symmetry, but doesn't explain what these terms mean. There are also occasional references to things like "D2 symmetry" or "C4 symmetry" in puzzle descriptions, but again with little explanation of what these terms mean.

In practical terms, the puzzle's geometry affects what happens when you rotate or move the main chain. Do the other chains rotate in the same way, or in the opposite direction? Can you move the main chain past the copies, or do the ends of the chains stay together? Different symmetry puzzles have different answers to these questions.

See the wikipedia articles molecular symmetry and character tables for 3D point groups for more background on the geometry of symmetry. These articles help to explain why there isn't more discussion of geometry in symmetry: this stuff's complicated!

See symmetry file format for details on how Foldit defines symmetry puzzle geometry.

Degree of symmetryEdit

Just to make things even more confusing, the number of copies of the protein is described using terms derived from the language of ancient Greece. To quote Homer: "D'oh!". Here's a quick translation for all these -mers:

  1. monomer - one copy of the protein
  2. dimer - two copies
  3. trimer - three copies
  4. tetramer - four copies
  5. pentamer - five copies
  6. hexamer - six copies.
  7. heptamer - seven copies

While there have been hexamer puzzles in Foldit, so far no heptamers. But who knows, we may see an octamer some day.

There are a few more -mers that serve to stun and amaze:

  • oligmer - a few copies of a chemical unit bonded together (just as oligarchy means "rule by the few")
  • polymer - many copies of a chemical unit bonded together (just as polymorphous means "having many forms")
  • homomer - something made of multiple exact copies of one thing
  • heteromer - something made of units which are similar, but not the same

So while Foldit symmetry puzzles involve oligomers made up of a few copies of a monomer, the each monomer itself is a polymer (made up of many similar chemical units known as amino acids). So the monomer is a polymer that's really a heteromer, while the symmetry puzzle oligomer is a homomer. Are we confused yet? D'oh!

Symmetry puzzle examplesEdit

Symmetric DimerEdit

A symmetry puzzle with a monomer and one copy, for a total of two units.

Irc 202811 1322780540 S2 CH Granier

Symmetric Dimer puzzle.


Symmetric TrimerEdit

A symmetry puzzle with a monomer and two copies, for a total of three units.

Foldit 1323441184

Symmetric Trimer puzzle.


Symmetric Dimer of DimersEdit

A symmetry puzzle with a monomer and three copies, for a total of four units. The main chain and one copy form a unit, which then interfaces to the other two copies. See Puzzle 670 for a description of "dimer of dimers" symmetry.

Foldit 1323441653

Symmetric Dimer of Dimers puzzle.


StrategiesEdit

Editors note: this section needs work(!).

Usually taking the shape of a helix. They can be contorted into many different shapes.

We will investigate the theoretical structures of the basic helix and how they interact.

When a helix forms it likes to twist into a right hand twist. A helix with a left hand twist is not a happy helix. When joined together freely into a bundle they will all twist together with a slight left hand twist. This is the same in the making of ropes and twine. This slight counter twist helps the strand hold together and not unravel. Now there can be exceptions, like being restrained by the loops on the ends, that may force the helix to deflect.

Being constructed of helices, it is best to keep them fairly straight and close together. If they become knotted or move far apart it is probably not a good thing.

Tweeking is important in getting the helix aligned properly. Orange in blue out.

Followed by lots of wiggles, shakes, and mutate.

Puzzle HistoryEdit

The Baker Lab tests Foldit player-designed proteinsEdit

The Baker Lab tests Foldit player-designed proteins

External LinksEdit

Wikipedia articles:

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