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WELCOME TO THE GLYCaNS SERVER HELP |  |
The glycans server makes use of CNS (Crystallography and X-ray Systems) to build up glycans from the glycans_uu_1.0 topology developped at Utrecht University by M. Krzeminski and A.M.J.J. Bonvin. This page will drive you through the use of this server.
Three steps are required to build your glycans:
| 1. | Defining the monosaccharides |
| 2. | Specifying how to link them |
| 3. | Providing some information to retrieve the result |
For further questions, you can report to the FAQ |
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Defining monosaccharides
GlyCaNS proposes a large panel of basic monosaccharides that can be modified with patches and linked with linkages patches. Monosaccharides are distinguihable from the length of their straight chain:
| • Trioses | 3 Carbons | Glyceraldehyde, Dihydroxyacetone |
| • Tetroses | 4 Carbons | Erythrose, Threose, Erythrulose |
| • Pentoses | 5 Carbons | Ribose, Arabinose, Xylose, Lyxose, Ribulose, Xylulose |
| • Hexoses | 6 Carbons | Allose, Altrose, Glucose, Mannose, Gulose, Idose, Galactose, Talose, Psicose, Fructose, Sorbose, Tagatose |
| • Heptoses | 7 Carbons | Sedoheptulose, Mannoheptulose |
The server offers to generate glycans from the most represented monosaccharides in nature: pentoses and hexoses. A common way to display them in their linear form is the Fisher projection. In this representation, the links along horizontal lines get out of the plane, toward you:
In nature, pentoses and hexoses tend to circle, upon hemi-acetylation of the aldehyde or keton group, and leads to the formation of furanoses or pyranoses, as following:
GlyCaNS generates built up in the same conformation, i.e. envelop for furanoses, with the C1 out the plane that contains the four other atoms, and chair for pyranoses, with C1 and C4 below and above the medium plane formed by the four other atoms of the ring, respectively (considering C2 and C3 in front and on the left side of C1).
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GlyCaNS abandons the notion of alpha/beta for the anomery of C1 and R/S absolute configuration for other carbons. We prefer, to generalize a notation common to all monosaccharides that will not depends on the neibourhood, the notion of L/R, which indicates whether the hydroxyl group is on the left (L) or right (R) side in the Fisher projection.
Consequently, C1 of the beta-D-Glucose depicted above is L.
Modifying the topology of monosaccharides
Patches proposed by GlyCaNS are numerous and aplliable on the conformation of the ring and generally on hydroxyl groups when it deals with substituents. You can reverse the chair conformation of a furanose, or transform it into a boat conformation. As for substituents, GlyCaNS gives the possibility to invert OH and H, replace the hydroxyl group by an N-acetyl or carboxyl one.
The following table summarizes the different patches proposed by GlyCaNS:
| Type | CNS Code | Short explanation |
|---|---|---|
| Conformation of the ring | RCHP | Reversing the chair conformation of a pyranose |
| UD1F, UD2F, UD3F, UD4F, UD4O | Reversion of the envelope form (Up to Down) in Furanoses | |
| CB1, CB2, CB3 CB4, CB5, CBO | From chair to boat conformation. The last letter indicates the carbon which suffers of the flip. This patch can be combined with the "reversion of the envelope" one | |
| E1E2, E1E3 E1E4, E1O4 | From initial envelope form (C1 above the plan formed by the four other atoms of the ring) to the other types of envelope forms in furanoses | |
| Substituents | L1RF, R1LF L1RP, R1LP | Mutarotation (isomerization of C1) when the OH group is in L or R position. This patch is available for Furanoses (F) and Pyranoses (P) |
| L2R, R2L L3R, R3L L4RP, R4LP, L4RF, R4LF L5RP, R5LP | Isomerization of carbons by reversing the position of their substituents (From Left to Right or vice versa). The middle figure indicates the carbon number | |
| OH1P, OH1F OH2H, OH3H, OH4H OH6H | Dehydroxylation of C1 (in Furanoses or Pyranoses), C2 to C4 and C6 | |
| OH56, OH5H | Dehydroxylation of C5 when it is out of the ring, in both cases where it is followed by C6 (OH56) or not (OH5) | |
| NOC6 | Replacement of the C6H2OH group by an H | |
| N1LP, N1RP, N1LF, N1LF N2L, N2R N3L, N3R N4L, N4R N5LP, N5RP, N5F N6 | Substitution of a hydroxyl group by an N-acetyl one. The figure specifies the hydroxyl group number, L/R the position of the hydroxyl group and P/F if it is applicable only for pyranoses or furanoses |
FAQ
Why are there some patches for reversing the chirality of carbons 4? Would not it be easier to choose Galactose instead of Glucose?
The database of GlyCaNS will be extended in the future. The patches that aim at reversing the chirality of saccharides are essential in case of more complicated saccharides. For instance, consider reversing the hydroxyl group and the hydrogen in position 3 of the neuraminic acid.