Proteogenic amino acid

Due to the absence of a hydrogen atom on the a-carbon, the a-fluoroalkyl amino acids (except, of course, the fluoroalanines, vide supra) cannot undergo an elimination of HR Consequently, they are more stable than fluoroalanines and other jS-fluoro amino acids previously described. On the other hand, similar to proteogenic amino acids, jS-fluoro amino acids and a-fluoroalkyl amino acids are generally substrates of pyridoxal phosphate depending on enzymes such as racemases and decarboxylases. When an amino acid is a substrate of such enzymes, the enzyme induces the development of a negative charge on the a-carbon, which can initiate a /(-elimination process. This reaction affords an electrophilic species (Michael acceptor type), which is able to add a nucleophilic residue of the enzyme. This notion of mechanism-based inhibitor is detailed in Chapter 7. 

A variety of experimental setups were developed for structure analysis of proteins, based on the excitation of the tryptophan moiety (the most brightly fluorescent proteogenic amino acid residue), that produces an intrinsic fluorescence emission of a folded protein. Tryptophane residues excited at wavelength values around 280-290 nm emit at a characteristic wavelength range (330-350 nm) thus reporting on how much this residue is buried within the protein. Techniques such... 

Proline (18) is a nonessential proteogenic amino acid that plays important and unique roles in protein structure because of its conformational rigidity. In proteins, it is commonly found at the beginning of an a-helix, in turns, and it disrupts secondary... 

Not only proteogenic amino acids are useful catalyst to promote the aldol, but also other cycUc amino acids served as catalysts for this reaction (Fig. 4.29). For instance, cycUc azetidine derivative 153 (10 mol%) catalyzed the reaction between acetone (3a, 27.2 equiv.) and aldehyde 2b giving the expected aldol compound 4b with 62% yield and 59% ee [237]. Also, moderated results were obtained when 6-aminopenicillanic acid (6-APA, 154,10 mol%) was used in the reaction between cyclohexanone and aromatic aldehydes affording mainly the yn-isomer (43-86% yield, 2-14% de, 18-23% ee) [238]. 

Amber codon, nonsense codon the sequence UAG in mRNA. It does not code for any of the 20 proteogenic amino acids, and it results in the termination of protein synthesis (premature termination when UAG is produced by mutation of a sense codon). Potential precursors for the production of UAG by mutation are UCG (serine), UAU and UAC (tyrosine) and CAG (glutamine). 

Table 1. Proteogenic amino acids. The three-letter abbreviations are universally accepted and are routinely used for depicting protein and peptide sequences (see Peptides). One-letter notations (recommended by the llJPAC-lUB Commission on Biochemical Nomenclature [Eur. J.Biochem. 5 (1968) 151-153] should not be used for the publication of sequences, but are intended to facilitate storage of sequence information and sequence comparison by computer.

At higher temperatures, the deamination reaction occurs spontaneously. This pathway, which exists only for aspartate and for no other proteogenic amino acid, is lacking in vertebrates. Bacterial A. (M,... 

L-Cysteine, Cys, L-2-amino-3-mercaptopropionic acid- HS-CH2-CH(NH2)-C00H, a sulfur-containing, proteogenic amino acid, M, 121.2, m.p. 240 C (d.X [o]p +6.5 (c = 2 in 5M HCl). Cys occupies a pivot position in intermediary Sulfur metabolism (see) (Fig. 1), and is an important component of redox reactions in living cells. In neutral or alkaline solution, Cys is oxidized in the air to L-cystine. The SH-groups of Cys residues and the disuifide groups (-S-S-) of cystine residues are important for the tertiary structure and/or enzymatic activity of proteins. 

G. are also known that arise from proteogenic amino acids after homologization (Fig. 3), which consists of a series of type reactions already well known in... 

L-Glutamine, Gin, Glu-NH a proteogenic amino acid, the 5-amide of L-glutamic acid, M, 146.15, m.p. 185-186°C (d,), [a]gt-9.2° fc = 2 in water) or -t 46.5 °(c = 2in5M HCI). In boiling, neutral aqueous solutions or in weak acid. Gin rapidly cyclizes to the ammonium salt of pyrrolidone carboxylic acid (see Glutamic acid). 

L-Histidine, His, imidazolyInUmitu a weakly glu-coplastic, proteogenic amino acid, M, 155.2. It is a component of the catalytic centers of many enzymes. 

L-Phenylalanine, Phe L-a-amino-P-phenylpropio-nic acid, an aromatic proteogenic amino acid, Af, 165.2. Phe is essential in the animal diet, and it is both glucogenic and ketogenic The first stage in the catabolism of Phe is hydroxylation to L-tyrosine, which is the precursor of Melanin (see), the neurotransmitter Dopamine (see), the hormones Adrenalin, Noradrenalin and Thyroxin (see separate entries), and other compounds. Tliis first step is catalysed by Phe hydroxylase (a monooxygenase), EC 1.14.16.1. Excess L-tyrosine is broken down to fumarate and acetoacetate (Fig. 1). 

L-Tyrosine, Tyn L-a-amino-P-(p-hydroxyphenyl)-propionic acid, an aromatic, ketogenic, proteogenic amino acid, M, 181.2, m.p. 342-344°C (d.), [0] ... 

L-Valine, VaL L-a-aminoisovaleric acid, (CHj)2CH-CH(NH2)-C00H, an aliphatic, neutral, essential, glucogenic, proteogenic amino acid. For biosynthesis, see L-lsoleucine. For degradation, see Leucine. The intact molecule of Val is incorporated in the biosynthesis of Penicillin. 

Amino acids are ubiquitous in nature, most prominently as the building blocks of proteins [2, 11]. Naturally occurring amino acids can be classified into three categories (1) the 20 primary proteogenic amino acids specifically coded for in the process of translation, (2) those that are the products of post-ribosomal modifications [14], and (3) non-proteogenic amino acids, of which well over 700 had been reported by 1985 [4], Glycine (1) and leucine (2) were the first of the 20 primary amino acids to be described, by Braconnet in 1820, and threonine (3) was the last to be isolated in 1925 [2, 14]. 

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