The pathogenic encapsulated fungus causes serious illness in immunosuppressed hosts. The capsule is normally primarily made up of a glucuronoxylomannan polysaccharide (GXM, around 90%); further minimal components certainly are a galactomannan polysaccharide (GXMGal, 10%) and mannoproteins ( 1%) . is classified into two types referred to as and  currently. A couple of three serotypes of var. var. and groupings include various types and they are seen as types complexes  currently. The serotype classifications for are based on antigenic differences due to structural variants in GXM . Light scattering and hydronamic research claim that GXM can be a branched polymer composed of an serotype, the Bis-NH2-PEG2 GXM framework has a main triad and a number of minor triads. For serotype A, the dominant triad is a six-residue RU with two serotypes. Serotype A (var. var. capsule . In addition, the mechanisms through which the GXM polysaccharides (and other capsule molecules) assemble into a capsule remain largely undiscovered , although there are indications that GXM molecules self-aggregate, possibly mediated by divalent cations [22,23,24]. In the absence of experimental evidence on secondary structure (which is extremely challenging to obtain for flexible polysaccharides), molecular modelling has been demonstrated to provide insights into molecular conformation, biophysical dynamics and interactions that can usefully inform vaccine development . In this work we employ molecular dynamics simulations on an array of oligosaccharides (Figure 2) to establish the conformation of GXM in serotype A and D, aiming to investigate the following questions. Open in a separate window Figure 2 The array of GXM oligosaccharides simulated in this work, shown with the SNFG symbols [13,14] for the sugar residues. Six RUs of an unsubstituted backbone (cnX); the main repeat motifs in serogroup D (cnD) serogroup A (cnA) and 6-time series and corresponding histograms for (a) cnX, (b) cnD, (c) cnA and (d) cnA. Here we define for all 6-RU GXM chains as the distance from Bis-NH2-PEG2 O3 in the second linkage in the mannose chain to the O3 in the second last linkage, thereby excluding the more flexible two terminal residues on either end of the chain (labeled on the cnA molecule in Figure 3, right). The (Figure 3 right column) are tight and skewed to the right (larger values), with all the four saccharides having a narrow peak at the median chain length of 54 ?. The mannan Bis-NH2-PEG2 backbone is thus remarkably inflexible, as there are no short distances indicating bends that bring the ends of the chain into close proximity; although transient elbow bends do occur occasionally, they do not persist. Further, comparison of the plots shows a trend of decreasing chain flexibility with increasing chain substitution: the unsubstituted cnX backbone is the most flexible with the broadest spread in (= 2.8); this flexibility is decreased in cnA (= 2.3) and the most substituted cnA is markedly the least flexible, with the narrowest range of (= 1.6). Open in a separate window Figure 3 End-to-end distance, is defined to exclude the two terminal residues on either end of the chain, as the distance from O3 in the second linkage to O3 in the 16th linkage in the 18-mannose backbonelabelled for cnA in the image on the right. The residues and substitutions are coloured as follows: and histogram (see Figure A3). In addition, the prevalence of this primary conformation increases in the order cnX (51%) cnD (55%) cnA (57%) cnA (69%)A further indication that in GXM the chain flexibility TLR3 decreases with increasing chain substitution. In all conformations, the backbone is extended, as is most apparent in the unsubstituted cnX conformation (Figure 5a), but can be very clear for cnD (Shape 5b), cnA (Shape 5c) and cnA (Shape 5d). The backbone twists from flatter ribbon-like conformations to prolonged helical conformations dynamically, but its behaviour is unaffected from the Bis-NH2-PEG2 presence or lack of side-chain substitutions relatively.