Amino acid standard abbreviations

The structures of the 20 amino acids that are commonly found in proteins are shown in Figure 5.2. These amino acids are referred to as standard amino acids. Common abbreviations for the standard amino acids are listed in Table 5.1. Note that 19 of the standard amino acids have the same general structure (Figure 5.3. These molecules contain a central carbon atom (the a-carbon) to which an amino group, a carboxylate group, a hydrogen atom, and an R (side chain) group are attached. 

FIGURE 24.4 PTH amino acid standards run on a Procise instmment see Tabie 24.1 for amino acid abbreviations. Peaks marked dmptu (dimethylphenyithiourea) and dptu (diphenyithiourea) represent side-reaction products of the Edman degradation. (Copyright 2012 ufe Technology Corporation. 

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,... 

Standard one-letter amino acid abbreviation (see list of Abbreviations and Acronyms). 

Fig. 2a-d. Multiple alignment of primary structures from 36 PHA synthases. A comparison of amino acid sequences derived from PH A synthase genes is shown. Amino acids are specified by the standard one-letter abbreviations. The consensus sequence represents amino acid residues (shaded) which are present in at least 50% of the PHA synthases. Highly conserved amino acids, which are present in at least 70% of the PHA synthases, are additionally underlined in the consensus sequence and the eight amino acid residues, which are present in all PHA synthases, are indicated as bold letters. See Table 1 for references... 

Scheme 4 u-Amanitin. Standard three letter abbreviations are used for the amino acids... 

Amino acids in proteins Standard abbreviation Molecular mass ... 

AMINO ACIDS, PEPTIDES AND PROTEINS Table 13.1 Amino acids structures and standard abbreviations... 

The tripeptide formed from L-alanine, L-phenylala-nine and L-serine by two condensation reactions is alanyl-phenylalanyl-serine, considering each additional amino acid residue as a substituent on the previous. This would be more commonly represented as Ala-Phe-Ser, using the standard three-letter abbreviations for amino acids shown in Table 13.1. 

The cosmopolitan cyanobacterium Microcystis aeruginosa is frequently the major component of freshwater cyanobacterial blooms. These blooms can cause serious water management problems and are occasionally associated with animal poisoning. The aeruginosa toxins are potent lethal peptides which contain three invariant D-amino acids (Ala, erythro-3-methyl Asp, and Glu), two variant L-amino acids, N-methyl dehydroalanine, and a 3 amino acid (1-3). Multiple toxins have been purified from clonal isolates (1,4). The toxic peptide described in this chapter is denoted toxin-LR using the standard one-letter abbreviations for its two variant amino acids, leucine and arginine. 

Three-letter symbols and standard group abbreviations are used to designate amino acids functionalised on -COOH or substituted on -NH2. Modifications are indicated by hyphens in abbreviations. 

Figure 1. Amino acid sequence of human ACTH (6). a-MSH is [Ac-Ser", Val-NHjSjACTH-d-IS). The underlined sequence is ACTH-(4-10). Standard abbreviations are used for amino acids lUPAC-lUB Commission on Biochemical Nomenclature, Eur. J. Biochem. 1975, 53, 1-14 1972, 27, 201-7.

Fig. 6 Typical ion-exchange separation of amino acids followed by postcolumn reaction with ninhydrin. Separation was achieved employing Beckman 6300 amino acid analyzer with cation-exchange column. Three sodium buffers were used with a stepwise elution scheme as supplied/recommended by the manufacturer. Detection was the sum of 440-nm and 570-nm absorbance. Standard three-letter abbreviations for amino acids are used also, CA = cysteic acid, tau = taurine, and nle = norleucine. Data was supplied by Stephen D. Smith, Ross Products Division of Abbott Laboratories, Columbus, OH.

Fig. 7 Typical reversed-pbase separation of amino acids. Precolumn derivatization of a standard amino acid mixture was achieved employing FMOC. Resolution was achieved by gradient elution with acetonitrile, methanol, and acetate buffer (pH 4.2) on a C,8 column. Standard three-letter abbreviations for amino acids are used also, CySO H = cysteic acid. (From Ref. 164. Copyright 1983 Elsevier Science.)...

The table shows a lis names, which can be called Ala or simpl of the 20 standard amino acids and the abbreviations of their a 3-letter code or a single letter. For example, alanine can be IT A. ... 

Amino acid abbreviations are the standard one- and three-letter ones... 

Twenty standard amino acids commonly occur in nature. They differ in the structure of the side chain that is attached to the a-carbon (the R group in the previous structure). Table 26.1 shows the structures of the standard amino acids at pFI 7, along with their names and abbreviations. 

The standard amino acids are 20 common a-amino acids that are found in nearly all proteins. The standard amino acids differ from each other in the structure of the side chains bonded to their a carbon atoms. All the standard amino acids are L-amino acids. Table 24-2 shows the 20 standard amino acids, grouped according to the chemical properties of their side chains. Each amino acid is given a three-letter abbreviation and a one-letter symbol (green) for use in writing protein structures. 

Figure 2. Chromatographic separation of amino acids after derivatization with phenylisothiocyanate (PITC) A. Separation of 200 picomole standard amino acid mix H containing 18 amino acids. B. Separation of an extended amino acid mix containing 28 amino acids. The standard one-letter abbreviations are used for the usual amino acids. Nonstandard amino acids are Sp, phosphoserine Hp, hydroxyproline Citr, citrulline Tau, taurine aAba, a-amino butyric acid HKl HK2, hyi oxylysines Om, ornithine , artifacts from reagents.

A convenient way of representing peptide structures by use of standard abbreviations (see Table 36.1) is illustrated here. According to convention, the N-terminal amino acid residue (having the free amino group) is written at the left end, and the C-terminal amino acid residue (having the free carboxyl group) at the right end. 

The primary structure of a protein is the order in which the individual amino acids are sequenced. This tells us little about the shape that the protein will assume in solution, although the primary stmcture naturally determines the secondary, tertiary and even quaternary forms. These amino acid building blocks (Table 11.2) give the key to stmcture and behaviour. The standard three-letter (Glu, Arg, Trp, etc.) and one-letter (E, R, W, etc.) abbreviations for amino acids are also listed their use makes stmctural descriptions more accessible. 

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