Amino acids generic

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

Amino acid abbreviations aa, generic amino acid Ala, L-alanine Aib, 2-aminoisobutyric acid Cys, L-cysteine Asp, L-aspartic acid Glu, L-glutamic acid Gly, glycine Lys, L-ly-sine Ser, L-serine Trp, L-tryptophan Ser, 2-amino-3-(5-methyl-2,4-dioxo-3,4-dihydro-2H-... 

The discovery of this lead compound as a potent PDF inhibitor was a result of an integrated combinatorial and medicinal chemistry approach based on the proposed generic PDF inhibitor structure. This focused chemical library was designed by Chen et al. [79], and was prepared using solid-phase parallel synthesis in which 22 amines and 24 amino acids were used as building blocks, as outlined in Scheme 23. 

Some generic structures of /3-amino acids are shown in Fig. 6.40. Since, in /3-amino acids, two C-atoms separate the amino and carboxylate groups, there are two possible locations for attachment of a single side chain (i.e., /32 and /33), or even two or more side chains (e.g., /32,3 and /32,2,3, respectively). In a /3-peptide, these symbols can be used as prefixes, e.g., the /33/32-dipeptide in Fig. 6.40 becomes /33-HAla- /32-HVal for R=Me and R = i-Pr. The stereodescriptors (R) and (S) should be used to specify the absolute configuration at the stereogenic centers. The same rules apply to y-amino acids and y-peptides. 

Fig. 6.40. Examples of generic structures of /3-amino acids, /3-peptides, and y-amino acids with the superscripts) indicating the location of the side chain(s)...

Aspartame is the generic name for IV-ai-aspartyl-L-phenylalanine methyl ester. It is composed of two amino acids, L-aspartic acid and L-phenylalanine, joined by a methyl ester link. It was discovered in 1965 by J. Schlatter at the G.D. Searle Laboratories. It is a white crystalline product and its solubility in water is 10 g/1 at 20°C this figure increases at elevated temperatures and in acidic conditions (Ajinomoto Aspartame Technical Bulletin, 2003). It is sparingly soluble in other solvents. 

The convention has over the last three decades proved to be adaptable, versatile and universal.9 It should be pointed out, however, that with amino acids (Section 5.14.4, p. 746), and hence in peptide and protein chemistry, and with carbohydrates (Section 5.10), the d/l convention is still the more convenient, mainly because it is used specifically to designate generic relationships between an enormous number of compounds of closely related structure. 

Amino acids Amino acid oxidase (generic) specific amino acid oxidase Milk, fruits, teas Quality of the product, nutritive value, aging... 

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