Continued from 2-Carb-37
Note The recommendations presented here are a modified version of the published 1980 recommendations .
2-Carb-38.1. General considerations
Oligosaccharide and polysaccharide structures occur not only in free form but often as parts of glycopeptides or glycoproteins  or of glycolipids . It can be cumbersome to designate their structures by using the recommendations of 2-Carb-37. The use of three-letter symbols for monosaccharide residues is therefore recommended. With appropriate locants and anomeric descriptors, long sequences can thus be adequately described in abbreviated form.
Symbols for the common monosaccharide residues and derivatives are listed in Table 2. They are generally derived from the corresponding trivial names. Abbreviations for substituents (see 2-Carb-1.16.2), preceded by locants, follow the monosaccharide abbreviations directly.
Table 2. Symbols for monosaccharide residues and derivatives in oligosaccharide chains
|Glucosamine||GlcN||Ribulose||Ribulo (or Rul)|
|Ethyl glucopyranuronate||GlcpA6Et||Xylulose||Xylulo (or Xul)|
2-Carb-38.2. Representations of sugar chains
For writing the structure of an oligo- or poly-saccharide chain, the glycose residue [the 'reducing group', i.e. the residue with the free hemiacetal group or modification thereof (e.g. alditol, aldonic acid, glycoside)] should be at the right-hand end. Also, when there is a glycosyl linkage to a non-carbohydrate moiety (e.g. protein, peptide or lipid) the glycosyl residue involved should appear at the right.
Numbering of monosaccharide units, if desired, should proceed from right to left.
2-Carb-38.3. The extended form
This is the form employed by the carbohydrate databank CarbBank, and is preferred for most purposes. Each symbol for a monosaccharide unit is preceded by the anomeric descriptor and the configuration symbol. The ring size is indicated by an italic f for furanose or p for pyranose, etc. The locants of the linkage are given in parentheses between the symbols; a double-headed arrow indicates a linkage between two anomeric positions. In CarbBank, omission of α/β, D/L, or f/p means that this structural detail is not known.
α-D-Galp-(16)-αL-Glcp-(12)-β-D-Fruf for raffinose (see 2-Carb-37.1)
β-D-Glcp-(14)-β-D-Glcp-(14)-D-Glc for cellotriose (see 2-Carb-37.2)
Branches are written on a second line, or in brackets on the same line.
(see , 2-Carb-37.3)
The hyphens may be omitted, except that separating the configurational symbol and the three-letter symbol for the monosaccharide.
2-Carb-38.4. The condensed form
In the condensed form, the configurational symbol and the letter denoting ring size are omitted. It is understood that the configuration is D (with the exception of fucose and iduronic acid which are usually L) and that the rings are in pyranose form unless otherwise specified. The anomeric descriptor is written in the parentheses with the locants.
For most purposes, the short form (2-Carb-38.5) is preferred when abbreviation of the extended form is desirable.
2-Carb-38.5. The short form
For longer sequences, it is desirable to shorten the notation even further by omitting (i) locants of anomeric carbon atoms, (ii) the parentheses around the locants of the linkage and (iii) hyphens (if desired). Branches can be indicated on the same line by using appropriate enclosing marks (parentheses, square brackets etc.). Whenever necessary, configuration symbols and ring size designators etc. may be included, to make the notation more specific.
The following examples show all three representations of the same structure:
(a) extended form
(b) condensed form in two lines
or in one line
(c) short form
This last version is recommended as the most explicit representation of branching using the short form.
Note. These representations do not follow the recommendations for choice of main chain given in 2-Carb-37.3. Such deviations are common in depicting series of naturally occurring oligosaccharides where it is desirable to show homomorphic relationships.
6. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), Abbreviated terminology of oligosaccharide chains (Recommendations 1980), J. Biol. Chem., 257, 3347-3351 (1982); Eur. J. Biochem., 126, 433-437 (1982); Pure Appl. Chem., 54, 1517-1522 (1982); Arch. Biochem. Biophys., 220, 325-329 (1983); ref. 2, pp. 169-173.
11. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), Nomenclature of glycoproteins, glycopeptides and peptidoglycans, Eur. J. Biochem., 159, 1-6 (1986); Glycoconjugate J., 3, 123-124 (1986); J. Biol. Chem., 262, 13-18 (1987); Pure Appl. Chem., 60, 1389-1394 (1988); Royal Society of Chemistry Specialist Periodical Report, 'Amino Acids and Peptides', vol. 21, p. 329 (1990); ref. 2, pp. 84-89.
21. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), The nomenclature of lipids (Recommendations 1976), Eur. J. Biochem., 79, 11-21 (1977); Hoppe-Seyler's Z. Physiol. Chem., 358, 617-631 (1977); Lipids, 12, 455-468 (1977); Mol. Cell. Biochem., 17, 157-171 (1977); Chem. Phys. Lipids, 21, 159-173 (1978); J. Lipid Res., 19, 114-40728 (1978); Biochem. J., 171, 21-35 (1978); ref. 2, pp. 180-191.
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