The aim of this revision and extension is to bring up-to-date the existing Carbohydrate document in the light of the enormous progress made in the areas of glycoscience, biotechnology and bio-informatics in the past 20 years.
The nomenclature of carbohydrates as described in the IUPAC/IUBMB document of 1996 (Pure Appl. Chem., 1996, Vol. 68, No. 10, pp. 1919-2008; https://dx.doi.org/10.1351/pac199668101919) has served as an immense help for authors and editors to name the compounds unambiguously. Since 1996, the number of compounds that have been discovered and/or synthesized has grown enormously. The number of constituting monomers and substituents has increased, i.e. due to study of carbohydrates and glycoconjugates in a larger range of organisms in the animal and plant kingdoms and to the progress in analytical and synthetic methods.
The current document requires a profound up-date to be applicable to the newly identified compounds and to the recent developments in the area of chemical and systems biology of carbohydrates and glycoconjugates. Abbreviations and trivial names need to be extended.
Furthermore, the explosion of data stemming from glycomics and glycoproteomics, necessitates the connection with databases for presenting adequately carbohydrate structure and sequence information. There exist a number of databases, each covering different collections of data. Developing guidelines for harmonizing these data are within the goals to be achieved. Another aspect deals with the correction of some names.
The task group met following the JCNB meeting in Killarney, Ireland on May 9-11, 2017.
The discussion on the revision of 2-Carb was finished. Important decisions were taken on cyclocarbohydrates in terms of numbering the rings and positions in the rings in case of one or more substituents. The possibility of hetero-oligomers was also considered. On this basis of the extensive discussions:
– One of entries of 2-Carb viz. glycoconjugates was singled out and treated separately, in view of recent developments.
– Glycoconjugates are defined as compounds consisting of one or more carbohydrate moieties covalently attached to a non-carbohydrate constituent. This class comprises natural and synthetic compounds.
– The compounds described in the “Glycoprotein” document and in the “Glycolipid” document are now arranged under the item Glycoconjugates.
– The glycoprotein/glycopeptide recommendations were revised and extended. A systematic classification according to the type of linkage to the protein or peptide as introduced. New are the linkages via C or S.
– Glycosaminoglycans are now defined in the carbohydrate document, since they consist of carbohydrate, only.
– Further definitions are given of Proteoglycans, Peptidoglycans and of the products arising from glycation. Glycation is conceived as the non-enzymatic reaction between carbohydrate and protein, starting with a Maillard type of reaction followed by an Amadori rearrangement, ultimately, further conversions may take place.
– The glycolipid document was reconsidered. Although a large part can be kept as is, many items need a careful up-date because of new developments and uniform type of presentation in the whole carbohydrate document.
– Lipopolysaccharides are still waiting for details to be described, properly.
– For the nomenclature of Glycodendrimers the dendrimer document is leading.
– Glyconanoparticles still need further definition.
– As to the graphical representation of carbohydrate structures we adhere to the recommendations in SNFG. The group members Martin Frank and Thomas Lütteke contributed significantly to arrive at well-defined symbols for the common monosaccharides.
– A second draft of the glycoinformatics was discussed; it turned out that changes and additions are necessary to bring carbohydrate chemistry and informatics further on the same wave-length.
In summary: a draft 3-Carb containing all items can be prepared. Many further corrections and suggestions can be taken care of by e-mail correspondence. To finalize the document, a meeting in person will be essential.
July 2019 update – The task group met last June in Braunschweig, Germany, and carefully screened draft 3-Carb part I, item by item. Many small textual corrections were discussed and finally approved. The text of the first part of 3-Carb, which mainly concerns carbohydrates as such, is now finished except for the fine-tuning of all figures in ChemDraw. As to part II dealing with glycoconjugates the text of the glycoprotein document was finished. The figures have to re-drawn in another format. The glycolipids division needs further fine-tuning and the figures need to be extended with more examples.
For glycoconjugates consisting of a carbohydrate moiety and dendrimers, fullerenes or comparable entities nomenclature has still to be developed.
As to the part III on glycoinformatics it was decided to adopt the proposal of Martin Frank. Needed is only a rewriting of the paper in a format that is in-line with the remainder of 3-Carb. It is concluded that this proposal fits the approach of International Protein database. It is relevant that this part gets soon International confirmation to avoid the confusion that could arise by circulation of different systems.
Last update 23 July 2019