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Primary Structure

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6-1 Basic Threading Alignment Panel

The primary structure of a protein, shown as uppercase letters in the Alignment Panel in Foldit.

The primary structure of a protein is the sequence of amino acids that make up the protein. The primary structure is also called the primary sequence, amino acid sequence or AA sequence.

The primary structure of the protein is what makes a protein unique. For natural proteins, a given sequence of amino acids is expected to fold up into one specific shape. Changing even one amino acid changes the shape of protein, and might even cause the protein not to fold up.

In Foldit, it's common to see the sequence listed as a string of one-character lowercase amino acid codes, for example:

rkeeivkriekyykehsngdqnryehvrqrieelsksngdesvevrggkhhrirvqdgdeidlqd

Strings like these are the basis of FASTA format, which is commonly used in the Protein Data Bank (PDB) and other scientific tools.

The Foldit functions structure.GetAminoAcid and structure.SetAminoAcid use lowercase amino acid codes.

In Foldit puzzles which offer the Alignment Tool, the Alignment Panel shows sequences using uppercase letters.

Outside of Foldit, both upper- and lowercase may be used for the amino acid codes.

See amino acids for a complete list of amino acid codes.

There's an assumption in biochemistry called Anfinsen's dogma which states that a protein's shape is determined by its primary structure. This may not be a valid assumption for all proteins. There is a growing body of research into intrinsically disordered proteins which may assume different shapes in different biological contexts.

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