Amino acids, abbreviated names

Most of three-letter abbreviations are taken from the first three letters of the name of the corresponding amino acid and are pronounced as written (alanine-Ala, cysteine-Cys). The one-letter symbol for the amino acids is usually the first letter of the amino acid s name and is often used when comparing the amino acids sequences of several similar proteins. 

Amino acid Abbreviation Structure Common name of side chain Md Pi... 

Full name of mycosporine-like amino acid Abbreviation (nm) (dm mole cm ) Species Reference m 9... 

With the exception of the C-terminal amino acid, the names of all the other amino acids in a peptide end with yl. For example, a tripeptide consisting of alanine at the N-terminal, glycine, and serine at the C-terminal is named as one word alanylglycylserine. For convenience, the order of amino acids in the peptide is often written as the sequence of three-letter or one-letter abbreviations. 

Residue name - one of the standard amino acids (lliree-letler abbreviations are used), nucleic acids (one- or two-lctter abbreviations), or the non-standard group designation as dc ncd in lire HHT dictionary 23-26 Residue sequence nuniber,... 

The Chains and Averages of Polymers Table 1.3 Name, Abbreviation, and R Group for Some Common Amino Acids ... 

The 20 different side chains that occur in proteins are shown in Panel 1.1 (pp. 6-7). Their names are abbreviated with both a three-letter and a one-letter code, which are also given in the panel. The one-letter codes are worth memorizing, as they are widely used in the literature. A mnemonic device for linking the one-letter code to the names of the amino acids is given in Panel 1.1. 

Table 26.1 The 20 Common Amino Acids in Proteins (continued) Name Abbreviations MW Stricture...

The long, repetitive sequence of —N—CH-CO- atoms that make up a continuous chain is called the protein s backbone. By convention, peptides are written with the N-terminal amino acid (the one with the free -NH3 1 group) on the left and the C-terminal amino acid (the one with the free -C02 group) on the right. The name of the peptide is indicated by using the abbreviations listed in Table 26.1 for each amino add. Thus, alanylserine is abbreviated Ala-Ser or A-S, and serylalanine is abbreviated Ser-Ala or S-A. Needless to say, the one-letter abbreviations are more convenient than the older three-letter abbreviations. 

The Common a-Amino Acids (names and abbreviations below structures)... 

WW domains (named after the one letter abbreviation for the amino acid tryptophan) are small regions of around 30 residues, which, like SH3 domains, bind to polyproline sequences. These sequences often contain the consensus sequence PPXY or PPLP. Examples of proteins that contain WW domains include Nedd4 E3 ubiquitin ligase (Fig. 1) and IQGAP1. 

A nomenclature was proposed by Seebach for the description of / -amino acids according to their substitution pattern, and for naming the resulting / -peptides [66, 67]. Enantiomerically pure / -amino acid derivatives with substituents in the 2-or 3-position are thus defined as - and / -amino acids, respectively (abbreviated to H-/ -HXaa-OH and H-/ -HXaa-OH). The corresponding /S-peptides built from these monomers will be named ff - and / -peptides. Similarly, /S -peptides consist of / -amino acid residues with substituents in both the 2- and 3-positions. Finally, peptides built from geminally disubsituted amino acids are referred to as and / -peptides (Fig. 2.6). 

Of the 20 amino acids, 11 have polar side chains (color screened), and 9 have nonpolar side chains. One, proline, has a unique ring structure. Under the name of each amino acid is its three-letter abbreviation. 

Biochemists represent each amino acid with a three-letter abbreviation. These abbreviations appear under the names of the amino acids in Figure 13-32. For example, the abbreviation for glycine is Gly. 

Table 6.1 Abbreviations BAN, BANYULS bHLH, basic helix-loop-helix CHS, chalcone synthase CHI, chalcone isomerase DFR, dihydroflavonol reductase F3H, flavonol 3-hydroxylase F3 H, flavonoid 3 -hydroxylase FLS, flavonol synthase icx, increased chalcone synthase expression LDOX, leucoanthocyanidin dioxygenase LCR, leucoanthocyanidin reductase MATE, multidrug and toxic compound extrusion NR, not yet reported tt, transparent testa ttg, transparent testa glabrous the WD40 and WRKY transcription factors are named for conserved amino acid sequences within these proteins. PC = personal communication.

The amino acid components of peptides and proteins are linked together by amide bonds (see p. 60) between a-carboxyl and a-amino groups. This type of bonding is therefore also known as peptide bonding. In the dipeptide shown here, the serine residue has a free ammonium group, while the carboxylate group in alanine is free. Since the amino acid with the free NHs group is named first, the peptide is known as seryl alanine, or in abbreviated form Ser-Ala or SA. 

There are two generally accepted systems of abbreviation for trivial names, using either one or three letters. The choice of form to use is generally determined by circumstances. Normally, three-letter symbols are used, and one-letter symbols are reserved for long sequences of amino acids. A list of such symbols is shown in Table 7.1. 

Table 7.1 Names and their abbreviations and symbols for amino acids. ...

Each amino acid name has an associated three-letter abbreviation and a one-letter symbol (Figure 1.7). The one-letter codes are determined by the following rules ... 

The structures and names of some particularly important a-amino acids are shown in Table 25-1. You will notice that the names in common use for amino acids are not descriptive of their structural formulas but at least they have the advantage of being shorter than the systematic names. The abbreviations Gly, Glu, and so on, that are listed in Table 25-1 are particularly useful in designating the sequences of amino acids in proteins and peptides, as will become evident later in the chapter. 

Notice that in the conventions used for names and abbreviated formulas the amino acid with the free amino group the N-terminal amino acid) always is written on the left. The amino acid with the free carboxyl group (the C-termi-... 

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