Peptides abbreviated names

Our reviewer felt the molecule builder was easy to use. It is set up for organic molecules. Specialized building modes are available for peptides, nucleotides, and carbohydrates. It is also possible to impose constraints on the molecular geometry. Functions are accessed via a separate window with buttons labeled with abbreviated names. This layout is convenient to use, but not completely self-explanatory. The program is capable of good-quality rendering. At the time of this book s publication, a new three-dimensional graphic user interface called Maestro was under development. 

Given the one- or three-letter abbreviated name for a peptide, write its structure. 

The amino acid sequence in the abbreviated name shows that alanine should be written at the left with a free HgN— group, glycine should be written at the right with a free —COOH group, and both should be connected to serine by peptide bonds ... 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

The long, repetitive sequence of —N—CH-CO- atoms that make up a continuous chain is called the protein s backbone. By convention, peptides are written with the N-terminal amino acid (the one with the free -NH3 1 group) on the left and the C-terminal amino acid (the one with the free -C02 group) on the right. The name of the peptide is indicated by using the abbreviations listed in Table 26.1 for each amino add. Thus, alanylserine is abbreviated Ala-Ser or A-S, and serylalanine is abbreviated Ser-Ala or S-A. Needless to say, the one-letter abbreviations are more convenient than the older three-letter abbreviations. 

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). 

The amino acid components of peptides and proteins are linked together by amide bonds (see p. 60) between a-carboxyl and a-amino groups. This type of bonding is therefore also known as peptide bonding. In the dipeptide shown here, the serine residue has a free ammonium group, while the carboxylate group in alanine is free. Since the amino acid with the free NHs group is named first, the peptide is known as seryl alanine, or in abbreviated form Ser-Ala or SA. 

The structures and names of some particularly important a-amino acids are shown in Table 25-1. You will notice that the names in common use for amino acids are not descriptive of their structural formulas but at least they have the advantage of being shorter than the systematic names. The abbreviations Gly, Glu, and so on, that are listed in Table 25-1 are particularly useful in designating the sequences of amino acids in proteins and peptides, as will become evident later in the chapter. 

The names and structures of the twenty natural amino acids are given in Table 1.13. The International Union of Pure and Applied Chemistry (IUPAC) uses the three-letter abbreviations shown in the second column of Table 1.13 to describe amino acids. These are widely used in biological circles as well but are inappropriate when long peptide or protein sequences need to be described. For example, when proinsulin is cleaved, it forms the biologically important peptide insulin and another peptide usually called C-peptide. The human peptide consists of a linear chain of 31 amino acids that have the sequence, from amino to carboxyl, H2N-Glu-Ala-Glu-Asp-Leu-Gln-Val-Glu-Gln-Glu-Leu-Gly-Gly-Gly-Pro-Gly-Ala-Gly-Ser-Leu-Gln-Pro-Leu-Ala-Leu-Glu-Gly-Ser-Leu-Gln-OH. This is readily comprehensible to most chemists because the abbreviations are typically the first three letters of the amino acid. Thus, alanine is Ala and arginine is Arg. Aspartic acid and asparagine cannot both be named Asp so the latter is distinguished as Asn. 

Proteins are natural polymers composed of a-amino acids linked by amide (peptide) bonds. Except for glycine (aminoacetic acid), protein-derived amino acids are chiral and have the L configuration. Table 17.1 lists the names, one- and three-letter abbreviations, and structures of the 20 common amino acids. Of these, eight (the essential amino acids) cannot be synthesized in the bodies of adult humans and must be ingested in food. 

Problem 28.14 Name each peptide using both the one-ietter and the three-ietter abbreviations for the names of the component amino acids. 

The most important of the peptidic phosphatase inhibitors are the microcystins and nodularin. Mycrocystins are heptapeptides characterised by the sequence cyclo(D-Ala-X-D-e/7t/i/ o-P-methylisoAsp-Y-Adda-D-isoGlu-iV-methyldehydroAla), where X and Y are different L-aminoacids, and Adda is the abbreviation of the P-aminoacid [25,35,85,95]-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4(E),6(E)-dienoic acid. In the most common microcystin, namely microcystin-LR, X is Leu and Y is Arg. This kind of compounds was considered to be the highly hepatotoxic principle of the cyanobacteria genera Microcystis, Artabaena and Oscillatoria. Apart Jfrom the variations represented by X and Y, other differences arising jfrom the demethylation of aminoacids, lead to the existence to more than fifty microcystins. The rare acid Adda is also... 

To keep names of amino acids and peptides to manageable proportions, there are agreed conventions for nomenclature (see the footnotes to Table 1.1). The simplest a-amino acid, glycine, would be depicted H—Gly—OH in the standard three-letter system, the H— and —OH representing the H20 that is expelled when this amino acid undergoes condensation to form a peptide (Figure 1.2). The three-letter abbreviations therefore represent the amino-acid residues that make up peptides and proteins. 

Peptide motifs. Proteins with certain homologous sequences are rapidly degraded. For example, proteins that have extended sequences containing proline, glutamate, serine, and threonine have half-lives of less than 2 hours. (PEST sequences are named for the one-letter abbreviations for these amino acids. See Table 5.1.) The cyclin destruction box is a set of homologous nine-residue sequences near the N-terminus of cyclins that ensures rapid ubiquination. 

Oligonucleotide analogues have commonly been considered as nucleic acids even in the absence of an acidic group, e.g., methyl phosphon-ates. In a formal sense, peptide nucleic acids are neither peptides nor composed of nucleic acids, nor should they be confused with peptide/protein oligonucleotide conjugates as described in the previous section. The PNA monomeric unit contains features of both amino acids and nucleosides. The four common base portions of nucleosides—adenyl, cytosyl, guanidyl, and thymidyl—are tethered to the PNA backbone, which carries the functionality of common amino acids. Amide bonds then consecutively link these monomer units. The term polyamide is more chemically appropriate thus an alternative name is polyamide nucleoside analogue, which is still abbreviated PNA. 

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