Trivial amino acids

In summary, cyclosporin A is a cyclic undecapeptide composed of ten trivial amino acids and the unique MeBmt as the eleventh building block. All chiral amino acids belong to the L-series, with the exception of one D-alanine unit. Another striking feature is the A-methylation of seven amino acids responsible... 

Compound name(s) systematic and trivial Amino-acid sequence for peptides Chemical formula Author name... 

For amino acids having trivial names ending in -ine, the suffix -amide is added after the name of the acid (with elision of e for monoamides). For example, HjN—CHj—CO—NHj is glycin-amide. 

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

Parvalbumin is a muscle protein with a single polypeptide chain of 109 amino acids. Its function is uncertain, but calcium binding to this protein probably plays a role in muscle relaxation. The helix-loop-helix motif appears three times in this structure, in two of the cases there is a calcium-binding site. Figure 2.13 shows this motif which is called an EF hand because the fifth and sixth helices from the amino terminus in the structure of parvalbumin, which were labeled E and F, are the parts of the structure that were originally used to illustrate calcium binding by this motif. Despite this trivial origin, the name has remained in the literature. 

One of the most useful applications of chiral derivatization chromatography is the quantification of free amino acid enantiomers. Using this indirect method, it is possible to quantify very small amounts of enantiomeric amino acids in parallel and in highly complex natural matrices. While direct determination of free amino acids is in itself not trivial, direct methods often fail completely when the enantiomeric ratio of amino acid from protein hydrolysis must be monitored in complex matrices. 

Compound 593A (109 Scheme 11.16) was isolated from Streptomyces griseoluteus by a group at Merck, Sharp, and Dohme in 1970 [167]. Its structure was proposed in 1973 [168] and confirmed by X-ray crystallography in 1976 [169, 170], The trivial name streptolutine was proposed for the amino acid 110, so 109 would conse-... 

The yellow analogues, the betaxanthins, are composed of betalamic acid with amino acids or amines, respectively, amounting to 26 structures known to occur naturally. " Structures unambiguously assigned by NMR spectroscopy usually carry trivial names derived from the plant material from which they have been first isolated. The substitution patterns of betalyanins and betaxanthins hitherto reported together with their particular plant sources are listed in Table 4.4.1 and 4.4.2, respectively. 

Interesting as it is, the study of transporters for amino acids and other nitrogenous nutrients in Saccharomyces cerevisiae is a tricky field. Many difficulties must be circumvented to avoid trivial errors. These practical problems are linked with several features of eukaryotic uptake systems, the first being the multiplicity of permeases which transport a given substrate. In relation to this, a major point is to make certain that one is not studying more than one uptake system at a time, and this can hardly be done without genetics. Once individual uptake systems have been identified and separated with the help of genetics, a second difficulty arises, which... 

Resonance energy transfer between the aromatic amino acids proceeds by very weak coupling between the donor and acceptor.151,52) Very weak coupling implies that the interaction between the donor and acceptor wave functions is small enough so as not to perturb measurably the individual molecular spectra. This transfer process, which is distinct from the trivial process of absorption of an emitted photon, involves radiationless deexcitation of an excited-state donor molecule with concomitant excitation of a ground-... 

Systematic substitutive nomenclature may be used to name all organic molecules. However, those that are of animal or vegetable origin have often received trivial names, such as cholesterol, oxytocin and glucose. Biochemical nomenclature is based upon such trivial names, which are either substitutively modified in accordance with the principles, rules and conventions described in Chapter 4, Section 4.5 (p. 70), or transformed and simplified into names of stereoparent hydrides, i.e. parent hydrides of a specific stereochemistry. These names are then modified by the rules of substitutive nomenclature. Three classes of compound will be discussed here to illustrate the basic approach carbohydrates amino acids and peptides and lipids. For details, see Biochemical Nomenclature and Related Documents, 2nd Edition, Portland Press, London (1992). 

Amino acids are represented in two ways either as H2N-CHR-COOH or as the zwitterionic form H3N-CHR-COO . Although the second of these forms is overwhelmingly predominant in the crystal and in solution, it is generally more convenient to name them and their derivatives from the first form. They are normal organic compounds and are treated as such as far as numbering and naming are concerned, although trivial names are retained for all natural amino acids. 

There are two generally accepted systems of abbreviation for trivial names, using either one or three letters. The choice of form to use is generally determined by circumstances. Normally, three-letter symbols are used, and one-letter symbols are reserved for long sequences of amino acids. A list of such symbols is shown in Table 7.1. 

Great care has to be taken in the analytical characterization of synthetic cyclic peptides.[73] The major side reactions during cyclization are epimerization of the C-terminal amino acid residue and cyclodimerization. Cyclodimers can be detected by mass spectrometry, although the analysis is not trivial, because artifacts do occur in some ionization techniques such as ES-MS as a result of aggregation.1 1 Ll 121 Real dimers can be detected as double-charged particles with mlz values identical to the cyclic monomers, but with a mass difference of 0.5 amu in the resolved isotope signals. The mass difference of the corresponding monomer is 1 amu. The cyclodimerization has received some attention as a direct method for the synthesis of C2-symmetrical cyclic peptides.[62 67 94113 115]... 

Here Vij denotes the distance between atoms i and j and g(i) the type of the amino acid i. The Leonard-Jones parameters Vij,Rij for potential depths and equilibrium distance) depend on the type of the atom pair and were adjusted to satisfy constraints derived from as a set of 138 proteins of the PDB database [18, 17, 19]. The non-trivial electrostatic interactions in proteins are represented via group-specific dielectric constants ig(i),g(j) depending on the amino-acid to which atom i belongs). The partial charges qi and the dielectric constants were derived in a potential-of-mean-force approach [20]. Interactions with the solvent were first fit in a minimal solvent accessible surface model [21] parameterized by free energies per unit area (7j to reproduce the enthalpies of solvation of the Gly-X-Gly family of peptides [22]. Ai corresponds to the area of atom i that is in contact with a ficticious solvent. Hydrogen bonds are described via dipole-dipole interactions included in the electrostatic terms... 

Despite its efficiency in numerous cases optical resolution is by no means a trivial operation. In each case the optimum method has to be found by laborious trial and error procedures the optical purity of the material has to be secured and its absolute configuration has to be established before the compound can be used in a synthetic sequence. These drawbacks of optical resolution led chemists to start their syntheses from optically active natural products (the so-called chiral carbon pool ). A variety of suitable ex-chiral-pool compounds including carbohydrates, amino acids, hydroxy acids, and terpenoids are shown. 

Pencharz, P.B. Ball, R.O. (2003) Different approaches to define individual amino acid requirements. Annu. Rev. Nutr. 23, 101-116. Determination of which amino acids are essential in the human diet is not a trivial problem, as this review relates. 

The presence of two or more carboxyl groups in a carbon chain gives rise to dicarboxylic, tricarboxylic, etc., acids many of these acids are designated by universally recognised and accepted trivial names (see Table 10.20). Unsaturated acids are considered in Section 5.18.3, p. 804 other functionally substituted acids (e.g. hydroxy acids, amino acids, etc.) are considered in Section 5.14. 

The naturally occurring a-amino acids have universally recognised trivial names (see Table 10.36). 

Aconitase is the trivial name for citrate dehydratase cw-aconitate hydratase (EC 4.2.1.3). It catalyzes the reversible isomerization reaction of citrate into isocitrate via the intermediate cA-aconitate (Figure 2). It is a water-soluble, monomeric protein. In eukaryotic cells aconitase is located in the mitochondrial matrix. In prokaryotes the enzyme occurs in the cytoplasma. The pig heart enzyme consists of 754 amino-acid residues, providing a molecular mass of 83 kDa [27], Aconitase from other sources has similar size. The porcine protein is synthesized with a mitochondrial targeting sequence. The mature, functional protein can be (over)expressed in Escherichia coli [28],... 

Available compounds with a 1,2-relationship include many simple ones 78-90 whose trivial names may help you find them in suppliers catalogues. The amino acids 83 are the constituents of proteins and are available with R = alkyl, aryl, and various functionalised groups.14... 

Amino acids are normally known by their trivial names (Table 1.1). In peptide and protein structures their structures are indicated by either three letter groups or single letters (Table 1.1, and Figure 1.7). Amino acids such as ornithine and citrulline, which are not found in naturally occuring peptides and proteins, do not have an allocated three or single letter code (Figure 1.3). 

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