Selenocysteine, pyrrolysine and ambiguous amino acids

Case number:699969-990285
Topic:General
Opened by:Parclytaxel
Status:Open
Type:Suggestion
Opened on:Tuesday, August 30, 2011 - 09:10
Last modified:Tuesday, August 30, 2011 - 17:04

Normal puzzles have 20 different types of amino acids, the ones every folder is familiar with.

Alanine (A)
Cysteine (C)
Aspartic acid (D)
Glutamic acid (E)
Phenylalanine (F)
Glycine (G)
Histidine (H)
Isoleucine (I)
Lysine (K)
Leucine (L)
Methionine (M)
Asparagine (N)
Proline (P)
Glutamine (Q)
Arginine (R)
Serine (S)
Threonine (T)
Valine (V)
Tryptophan (W)
Tyrosine (Y)

Design puzzles have a 21st "type" of amino acid, which actually represents any of the standard 20. It is abbreviated by the letter X. These are the only types of segments currently implementable in Foldit. However, these are not enough.

Overriding stop codons allows for two more amino acids:

Pyrrolysine (O), a lysine with a pyrroline ring attached to the end of its sidechain.
More information: http://en.wikipedia.org/wiki/Pyrrolysine
Selenocysteine (U), cysteine with the sulfur atom replaced with selenium.
More information: http://en.wikipedia.org/wiki/Selenocysteine

In addition, some techniques that can determine primary structure cannot distinguish two similar but different amino acids. Placeholders for these pairs are:

B for asparagine/aspartic acid
J for leucine/isoleucine
Z for glutamine/glutamic acid

Using a combination of techniques to resolve the amino acid pairs is a waste of resources. Pyrrolysine and selenocysteine are common enough to be recognised by the IUPAC and IUBMB, and can be found in certain enzymes in the human body. It is therefore a disadvantage that Foldit cannot implement these segments. To implement them, let the amino acid pairs be initially set as asparagine for B, leucine for J and glutamine for Z, and let them change into the other amino acid if clicked on in Design Mode, and vice versa. Also, the number of choices on the pie menu shown when mutating segments should expand from 20 to 22. Any comments?

Reshiram For The Win

Freywa

(Tue, 08/30/2011 - 09:10  |  1 comment)


infjamc's picture
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This represents a major technical challenge as Foldit runs on the Rosetta 3.x engine, which only supports the 20 standard amino acids by default.

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