Disac3DB is an annotated data base that contains the 3D structural information of about 120 entries of disaccharides. These disaccharides constitute molecules in their own rights and they constitute the building blocks of the vast majority of oligosaccharides, complex carbohydrates such as “glycan determinants” (blood group antigens, core structures, fucosylated oligosaccharides, sialylated oligosaccharides, Lewis antigens, GPI-anchors, N-linked oligosaccharides, globosides, ….), glycosaminoglycans, plants and algal polysaccharides and some bacterial polysaccharides. The table summarizes the 125 disaccharides which have been considered at this time (March 2013).
Reaction of the anomeric OH group (hemiacetal OH) of a monosaccharide A
with an OH group of monosaccharide B results in the formation of
an acetal A-B and water. The formed glycoside is a disaccharide,
and the acetal linkage between the two monosaccharides is called
the glycosidic linkage. Therefore the glycosidic linkage describes
the coupling of the anomeric carbon (C1) via an oxygen bridge (O1)
with a carbon atom at position x of another residue. The glycosidic linkage
can exist in α or β configuration. As for the nomenclature, there is
a natural extension of that used for the monosaccharide database
(monobank.cermav.cnrs.fr),
as regard to the residue letter Name, the nature and location of substitutents
the anomeric configuration, and the ring conformation (whenever several conformations
are likely to occur).
It is assumed that the D or L configuration of 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 orientation of two contiguous monosaccharide linked by a glycosidic bond in a disaccharide is characterized by the Φ and Ψ torsion angles. In the so called “Heavy Atom Definition” commonly used in crystallography Φ is the torsion angle Φ= O5-C1-O-Cx and Ψ is the torsion angle Ψ=C1-O1-Cx-Cx+1, where x is the number of the carbon atom of the second monosaccharide with which the 1→ x glycosidic bond is formed. An alternate definition, of use in NMR spectroscopy, refers to the hydrogen atoms about the glycosidic bond in a way such as :ΦH = H1-C1-O-Cx and ΨH = C1-O-Cx-Hx. For two monosaccharides linked by a 1 → 6 linkage, another parameter (ω) is required described the orientation about the exo-cyclic bond C5-C6. Its orientation is customarily described by the torsion angles O5-C5-C6-O6 and C4-C5-C6-O6, which combination defines the so called gauche-trans (gt), gauche-gauche (gg) and trans-gauche (tg) conformations.
For each disaccharide, an exhaustive search was performed using the MM3 molecular mechanics force-field. It gave a complete sampling of the conformational space, yielding the construction of a relaxed adiabatic energy map, which is represented as a function of Φ and Ψ torsion angles. In the case of 1→6 linkages relaxed adiabatic maps can be established for the three low energy orientation of the torsion angle ω. Typically, the exploration of each such energy maps indicated the occurrence of 2 to 5 energy minima.
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Both the Simple Search and the Advanced Search options are equipped with an “auto-complete” function, which guides the user while querying the database. It comprises two parts; (i) a single filed of entered text: (ii) the auto-prompt when the data is entered, through which the desired hit in the data base can be selected either by scrolling down with the mouse, or by using the arrow keys on the keyboard