Pentasaccharide

Using a simple illustration show how the completed pentasaccharide subunits of xanthan are assembled into tile finished polymer. 

Fondaparinux, the factor Xa-binding pentasaccharide (Arixtra, MW 1,728 Da), is prepared synthetically, unlike UFH, LMWH and danaparoid, which are obtained from animal sources. Despite only inactivating free factor Xa, clinical trials indicate that fondaparinux is an effective antithrombotic agent, both for venous thromboembolism prophylaxis and treatment, as well as for acute coronary syndrome and ST elevation myocardial infarction [4]. 

Penicillin Binding Protein Pentasaccharide Peptide Mass Fingerprint Peptide YY Peptidoglycans Peptidyl Transferase Center Peptidyl-Dipeptidase PERI... 

Three welan helices pass through the unit cell, as shown in Fig. 37b. Two of them, I and II, at (2A A0) and ( A2A0), are antiparallel as in gellan. A third helix, III, at (000) is new and parallel to the first. They are equilaterally 12.0 A apart from each other, 2.9 A farther than in 41. The unit cell contains a total of nine pentasaccharides surrounded by ordered guest molecules, which are accounted by six calcium ions and 75 water molecules. The two up and down helices interact via side chains, calcium ions, and/or water molecules. Specifically, helices I and II are linked only by side chain side chain hydrogen bonds... 

D-Mannose is common, but L-mannose has only been found in a small group of extracellular polysaccharides of related structures, one of which is elaborated by Alcaligenes ATCC 31555. In these polysaccharides, it is a-linked and partially replaces an a-L-rhamnopyranosyl residue in the pentasaccharide repeating-unit. It seems possible that these sugar residues are scrambled, but the other possibility, that there are two populations of polysaccharides, has not yet been excluded. 

Figure 47-4. Structures of the major types of asparagine-linked oligosaccharides. The boxed area encloses the pentasaccharide core common to all N-linked glycoproteins. (Reproduced, with permission, from Kornfeld R, Kornfeld S Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 1985 54 631.)...

Figure 47-5. Schematic diagram of the pentasaccharide core common to all N-linked glycoproteins and to which various outer chains of oligosaccharides may be attached. The sites of action of endoglycosidases F and H are also indicated.

In the present study the pentasaccharide fragment related to the backbone structure of rhamnogalacturonan I, together with its rudimentary galactan side-chain, has been subjected to further exhaustive modelling study using the MM3(92) [5] and CICADA protocols [6],... 

In Fig. 3 all conformers are plotted within 3 kcal/mol above, the global minimum found by CICADA for each of the glycosidic torsions, superimposed on the corresponding disaccharide relaxed map. Fig. 4 clearly indicates that most of the local minima present in the corresponding disaccharide fragments are also explored along the PES of the pentasaccharide by CICADA... 

Fig. 3. Projections on the (<1>, maps of the CICADA conformational search of the pentasaccharide. The dots indicate the values of all the optimized conformations determined by CICADA at each glycosidic linkange in 8 kcal/mol energy window For comparison, the isocontours, drawn in 1 Kcal/mol steps with an outer limit of 8 kcal/mol, represent the energy level of each disaccharide and calculated with the relaxed grid search approach. Dashed regions represent the locations of the low energy conformation of the pentasaccharide plotted on the potential energy surfaces of the constituting disaccharide segments...

From the complete ensembles of conformations found by the CICADA analysis of the pentasaccharide, H- H distances have been calculated.These distances (not shown here) can be compared to the interesidual H- H distances estimated from the NOE build-up rates of the corresponding cross-peaks in the 2D NOESY spectra, to be made un future experiments. 

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