Sunday, February 21, 2010

Short notations for α-amino acids and peptides based on three-letter code (3LC)

α-Amino acids are the building blocks of biomolecules such as peptides and proteins as well as supramolecular structures that are of interest in materials science and nanotechnology. Abbreviations and short notations are frequently used for the “standard” and other amino acids. For the 22 proteinogenic amino acids, which include the 20 standard amino acids plus pyrrolysine and selenocysteine, three-letter codes (3LCs) are in common use. These 3LCs are applied to encode peptides as linear notations. For example, the notation for the synthetic pentapeptide pentigetide [1],
indicates that the molecule consists of a sequence of the L-enantiomers of the α-amino acids aspartic acid (Asp), serine (Ser), aspartic acid (Asp), proline (Pro) and arginine (Arg). The four hyphens in the notation “symbolize” peptide bonds that each connect the carboxylic group of the left-side amino acid residue to the amino group at the Cα-atom of the right-side amino acid residue. The Chemical Abstract name for pentigetide is [1]:
Pentigetide is an oligopeptide. Many biomolecules, polypeptides and other biopolymers contain more than five amino acid units and the efficiency of the 3LC is immediately appreciated when encoding their molecular structure.

[1] Entry 7086 on page 1130 in The Merck Index, Eleventh Edition, Merck & Co. Inc., Rahway, NJ, U.S.A., 1989.
[2] Bibliography and links: Notations for amino acids.

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