The Nomenclature of Amino Acids

International Union of Pure and Applied Chemistry, /. Am. Chem. Soc. 82, 5575-84 (I960) Definitive rules for the nomenclature of amino acids, steroids, vitamins, and carotenoids (lUPAC). 

The work methods used by the commission for the determination of the nomenclature of amino acids have, certainly, been slow, but the purpose was to avoid hasty decisions which would run the risk of not being accepted. This is effective, for experience has shown that rules which had been established too rapidly had great difficulties in being accepted later on. 

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). 

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. 

The molecules of amino acids have two functional groups with different properties, the basic amino group and the acidic carboxyl group. Because the amino group can be bound to different carbon atoms on the hydrocarbon chain, the names of these compounds are derived from the position of this functional group. However, for this class of compounds, the traditional nomenclature in which the C-atoms are labeled not by numbers, but by letters of the Greek alphabet is still in use. In addition, the letter a does not correspond to the carbon atom labeled with number 1, but to the atom with the number 2. In this nomenclature there are a, p, y amino acids, etc. 

This chapter will present the most fundamental concepts for structure, nomenclature, and chemical reactions of amines. Biological applications will focus on the characteristics, formation, and reactions of amino acids. The use of amino acids in proteins and relatively simple reactions that form peptides will be discussed. In addition, several chemical reactions that lead to controlled degradation of peptides and proteins will be introduced. 

B. Pullman I would like to make a comment about nomenclature which may avoid some misunderstandings. For the majority of people dealing with the conformation of amino acid residues of proteins, and in particularly those interested in theoretical computations, the term dipeptide (tripeptide etc.) refer to neutral species of the type... 

The nomenclature of penicillins requires special comment. Compound (2) can be named as follows (a) penicillin G (b) benzylpenicillin (note that the term penicillin may refer to the compound class (1), to the structural fragment (3) or, especially in the medical literature, to compound (2) itself) (c) 6/3-phenylacetamidopenicillanic acid (d) 2,2-dimethyl-6/3-phenylacetamidopenam-3a -carboxylic acid (e) (2S,5i ,6i )-3,3-di-methyl-7-oxo-6-(2-phenylacetamido)-4-thia-l-azabicyclo[3.2.0]heptane-2-carboxylic acid and (f) [2S-(2a,5a,6/3)]-3,3-dimethyl-7-oxo-6-[(phenylacetyl)amino]-4-thia-l-azabicyclo-[3.2.0]heptane-2-carboxylic acid. The numbered system shown in (2) is the one most commonly used in the penicillin literature and will be used in this chapter note that different number is used when (2) is named according to (e) and (f) above. 

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]. 

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). 

FIGURE 1.1 Chemical and stereochemical nature of amino acids. Substituents in (a) and (b) are on opposite sides of the plane N-Ca-C, the bold bond being above the plane. Interchange of any two substituents in (a) changes the configuration. For the Cahn-Ingold-Prelog system of nomenclature, the order of preference NH2 > COOH > R2 relative to H is anticlockwise in (a) = (S) and clockwise in (c) = (R). 

Fig. 3. Amino acid sequence of several somatic human histone HI proteins to illustrate the microheterogeneity of linker histones. The sequences for human histone HI variants (H1.1-H1.4) were obtained from Ref [373] and Hl-5 was from Ref [412]. The nomenclature followed for the designation of these histone variants was Doenecke (e.g., see Ref. [412]). The nomenclature of Parseghian et at. [373] is shown in parentheses. The regions corresponding to the trypsin-resistant (winged helix motif [96]) which is characteristic of the protein members of the histone HI family are indicated by a boxed inset.

Fig. 6. Post-translational modifications of core and linker histones. The sites of acetylation, phosphorylation, poly-ADP ribosylation, methylation, and ubiquitination are incficated by numbers that correspond to the amino acid position from the N-termini of the molecules. The nomenclature of histone HI variants is as in Fig. 3. The length of C- and N-terminal tails is in relative scale between core histones to illustrate primary structural differences between these proteins.

Scheme 1 The Expected Fragmentation Pattern of Protonated Peptide Ions and the Nomenclature of the Amino Acid Sequence Fragment Ions for Determining Amino Acid Sequences...

The nomenclature of the peptoid monomers that have the same side chain as a corresponding amino acids, consist of an N prefix followed by the three-letter code of the amino acid in small letters. Thus, for example, the peptoid isomer of His is Nhis. 

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