Nomenclature amino acids

Although other systems of nomenclature have been used in the past— e.g., the C-terminal amino acid nomenclature (apo-Gln-I, etc.) (F21), and Fractions III, IV, V, etc. (S4)—the A, B, C system developed initially by Gustafson et al. (G34, G35) then Alaupovic et al. (A6) has become universally accepted. 

At the incentive of Chibnall (4), the editorial boards of the Journal of the Chemical Society of London and the Biochemical Journal worked out a first project, after consulting numerous biochemists of Great Britain and of other countries. This first text (14) made it possible for Sir Charles Harington to submit a project on amino acid nomenclature to the commission in July 1947 at the conference of London. At the same time, the commission considered a second project, worked out by the commission for nomenclature of the American Chemical Society and the editorial board of the Journal of Biological Chemistry (12). 

American Chemical Society Committee on Amino Acid Nomenclature, Chem. Eng. News 30, 4522 (1952). 

Scheme 1 Low-energy structures for the complex of and Trp. Structures can be classified as salt-bridge (SB interaction between the positive metal ion and the negative carboxylate of the zwitterionic amino acid) or charge solvation (CS interaction of the metal ion with Lewis-basic sites of the canonical amino acid). Nomenclature of the various structures further includes the main binding sites of the amino acid...

As in the names of the sugars (Section 24-1), an older amino acid nomenclature uses the prefixes d and l, which relate all the L-amino acids to (S)-2,3-dihydroxypropanal (l-glyceraldehyde). As emphasized in the discussion of the natural d sugars, a molecule belonging to the L family is not necessarily levorotatory. For example, both valine ([a] = +13.9) and isoleucine ([ajn = +11.9) are dextrorotatory. 

The same nomenclature has been adopted for amino-acids, the configurational family to which the a-carbon atom belongs being denoted by the prefixes d- and L-. 

The latter nomenclature is always used for amino acids with trivial names. 

Figure 1.2 Proteins are built up by amino acids that are linked by peptide bonds to form a polypeptide chain, (a) Schematic diagram of an amino acid. Illustrating the nomenclature used in this book. A central carbon atom (Ca) is attached to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a side chain (R). (b) In a polypeptide chain the carboxyl group of amino acid n has formed a peptide bond, C-N, to the amino group of amino acid + 1. One water molecule is eliminated in this process. The repeating units, which are called residues, are divided into main-chain atoms and side chains. The main-chain part, which is identical in all residues, contains a central Ca atom attached to an NH group, a C =0 group, and an H atom. The side chain R, which is different for different residues, is bound to the Ca atom.

Peptidases are enzymes that catalyse the hydrolysis of peptide bonds - the bonds between amino acids that are found in peptides and proteins. The terms protease , proteinase and proteolytic enzyme are synonymous, but strictly speaking can only be applied to peptidases that hydrolase bonds in proteins. Because there are many peptidases that act only on peptides, the term peptidase is recommended. Peptidases are included in subclass 3.4 of enzyme nomenclature [1,5]. 

Protein phosphatases are classified according to their activity toward phospho-amino acids they act on (Fig. 1). Nomenclature is independent of regulation simply because stimuli were unknown. Protein phosphatases hydrolyzing O-phospho-monoesters are currently subdivided into two major classes (i) phosphatases acting on phosphoserine (pSer) and phosphothreonine (pThr), and (ii) the second class... 

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). 

Fig. 2.34 The two conformations free of destabilizing syn-pentane interaction [215, 216] in 2,4-disubstituted y-amino acid derivatives with like and unlike configuration. According to the nomenclature proposed by Balaram...

FIGURE 3.5 Alignment of the TM2 amino acid sequences. The nomenclature of the rings is based on the a7 sequence. Selectivity indicates the charge of the permeant ions. Mutl and Mut2 are site-directed mutants (indicated by the asterisks) of the a7 subunit (see text). 

It was earlier considered that all the amino acid-activating synthetases were derived from a single primeval synthetase , so that all synthetases would have similar structures. Surprisingly, however, this is not the case. When the primary sequences, and in part the secondary and tertiary structures, of all the synthetases had been determined, clear differences in their construction became obvious. The aminoacyl-tRNA synthetases consist either of one single polypeptide chain (a) or of two or four identical polypeptides (ot2 or 04). In addition, there are heterogeneously constructed species with two sets of two identical polypeptide chains (OC2P2). This nomenclature indicates that, for each synthetase, a or P refers to a primary structure. The number of amino acids can vary from 334 to more than 1,000. 

In nomenclature for amino acids as ligands, the atoms in the R group are labeled with Greek letters starting with (5 for the first atom attached to the a carbon followed by y and 8 and e. The common bioinorganic ligands histidine, cysteine, and aspartic acid have their atoms labeled in the manner shown in Figure 2.5. The... 

Figure 6.4. Fragmentation spectrum of a tryptic peptide obtained from bovine serum albumin. Peptide sequence LGEYGFQNALIVR, monoisotopic [M + H]+ = 1479.796, monoisotopic [M+2H]2+ =740.402. Upper panel full scan MS spectrum. Lower panel MS/MS spectrum of a doubly-charged ion at 740.7 m/z with a ladder of y ions, the distances between which correspond to amino acid residues (upper row of letters). A shorter series of b ions is also seen (lower row of letters). See Fig. 6.5 for description of nomenclature. Note the often observed phenomenon where multiply-charged ions lose the charge during fragmentation process and, therefore, have higher m/z values than the original parent ion.

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