Protein amino acids nomenclature

Nomenclature for the protein amino acids , alias the coded amino acids ... 

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... 

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.

AMINO ACIDS, PEPTIDES PROTEINS Recommended nomenclature and symbolism for amino acids and peptides J. Biol Chem. (1985) 260, 14-42 Biochemistry (1975) 14, 449-462 Abbreviations and symbols for the description of the conformation of polypeptide chains /. Biol Chem. (1970) 245, 6489-6497 Nomenclature of iron-sulfur proteins Eur. J. Biochem. (1979) 93, 427-430 Corrections Eur. J. Biochem. (1979) 102, 315 Nomenclature of peptide hormones J. Biol Chem. (1975) 250, 3215-3216 Nomenclature of human immunoglobulins Eur. J. Biochem. (1974) 45, 5-6 Recommended nomenclature of glycoproteins, glyco-peptides, and peptidoglycans /. Biol Chem. (1987) 262, 13-18 Recommended nomenclature of electron-transfer proteins... 

AMINO ACID RACEMASE Amino adds, peptides proteins, BIOCHEMICAL NOMENCLATURE AMINO ACID TURNOVER KINETICS AMINOACYLASE AMINOACYL-tRNA HYDROLASE Aminoacyl-tRNA synthetase,... 

Summary Reactions of Amino Acids 1172 24-8 Structure and Nomenclature of Peptides and Proteins 1173... 

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