Glycosidic Linkage definition

October 27, 2016
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Disac3DB is an annotated information base which contains the 3D structural information of about 120 entries of disaccharides. These disaccharides constitute molecules in their own legal rights and additionally they constitute the inspiration associated with the the greater part of oligosaccharides, complex carbohydrates such as for instance “glycan determinants” (bloodstream group antigens, core structures, fucosylated oligosaccharides, sialylated oligosaccharides, Lewis antigens, GPI-anchors, N-linked oligosaccharides, globosides, ….), glycosaminoglycans, plants and algal polysaccharides and some microbial polysaccharides. The dining table summarizes the 125 disaccharides which have been considered currently (March 2013).

Result of the anomeric OH group (hemiacetal OH) of a monosaccharide A with an OH band of monosaccharide B causes the synthesis of an acetal A-B and water. The formed glycoside is a disaccharide, and also the acetal linkage amongst the two monosaccharides is called the glycosidic linkage. And so the glycosidic linkage describes the coupling of the anomeric carbon (C1) via an oxygen connection (O1) with a carbon atom at place x of another residue. The glycosidic linkage can occur in α or β setup. As for the nomenclature, discover an all-natural extension of that useful for the monosaccharide database (monobank.cermav.cnrs.fr), as reference to the residue letter Name, the character and area of substitutents the anomeric configuration, additionally the band conformation (anytime several conformations will likely take place).
The assumption is the D or L configuration associated with the monosaccharide at the glycosidic linkage is known.

Ex: Fuca1-4 GlcNAc; Gal[3S6S] b1-4 GlcNAc[6S]; Gal a1-6 Gal (gg); Neu5Ac a2-8 Neu5Ac; IdoA[2S](1C4) a1-4 GlcNS[6S]

The relative direction of two contiguous monosaccharide connected by a glycosidic relationship in a disaccharide is characterized by the Φ and Ψ torsion sides. In the so called “Heavy Atom Definition” commonly used in crystallography Φ is the torsion angle Φ= O5-C1-O-Cx and Ψ may be the torsion perspective Ψ=C1-O1-Cx-Cx+1, where x could be the number of the carbon atom for the second monosaccharide with that your 1→ x glycosidic relationship is created. An alternative definition, of use in NMR spectroscopy, is the hydrogen atoms about the glycosidic bond in a way such as :ΦH = H1-C1-O-Cx and ΨH = C1-O-Cx-Hx. For just two monosaccharides connected by a 1 → 6 linkage, another parameter (ω) is required described the orientation towards exo-cyclic relationship C5-C6. Its positioning is customarily described by the torsion perspectives O5-C5-C6-O6 and C4-C5-C6-O6, which combo defines the so named gauche-trans (gt), gauche-gauche (gg) and trans-gauche (tg) conformations.

Source: glyco3d.cermav.cnrs.fr
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