| Literature DB >> 27412370 |
Po-Hung Hsieh1, David F Thieker2, Marco Guerrini3, Robert J Woods2, Jian Liu1.
Abstract
The L-iduronic acid (IdoA) residue is a critically important structural component in heparan sulphate polysaccharide for the biological functions. The pyranose ring of IdoA is present in (1)C4-chair, (2)SO-skew boat, and less frequently, in (4)C1-chair conformations. Here, we analyzed the conformation of IdoA residue in eight hexasaccharides by NMR. The data demonstrate a correlation between the conformation of IdoA and sulphations in the surrounding saccharide residues. For the 2-O-sulpho IdoA residue, a high degree of sulphation on neighboring residues drives ring dynamics towards the (2)SO-skew boat conformer. In contrast, the nonsulphated IdoA residue is pushed towards the (1)C4-chair conformer when the neighboring residues are highly sulphated. Our data suggest that the conformation of IdoA is regulated by the sulphation pattern of nearby saccharides that is genetically controlled by the heparan sulphate biosynthetic pathway.Entities:
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Year: 2016 PMID: 27412370 PMCID: PMC4944151 DOI: 10.1038/srep29602
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Figure 1Chemical structures of hexasaccharides used in this study.
Structures of hexasaccharides synthesized in this study. Both IdoA2S (in 1 to 4) and IdoA (5 to 8) residues are colored in blue.
Figure 23-D Images of the NOE cross-peaks of H2-H5 and H4-H5 signals from representative hexasaccharides.
The images of NOE cross-peak signals of H2-H5 and H4-H5 from compound 1, 4, 5 and 8 are presented. Cpd 1 and 4 are IdoA2S-containing hexasaccharides, and cpd 5 and cpd 8 are IdoA-containing hexasaccharides. The structures of three different conformers for IdoA or IdoA2S are presented on top of the figure, where R represents –H or –SO3H. The calculated distance between H2 and H5, as well as H4 and H5 and displayed in lines with doubled arrows.
Measurement of the population of conformers for IdoA2S and IdoA residues in hexasaccharides.
| Hexasaccharides | Measured | Population of conformers | Sum of square difference | NOE signals for measuring | |||||
|---|---|---|---|---|---|---|---|---|---|
| H2-H5/H4-H5 | |||||||||
| 2.2 (2.7) | 4.3 (4.1) | 3.2 (3.0) | 2.2 (2.1) | 68% | 32% | – | 0.34 | 0.19 | |
| 2.2 (2.7) | 4.3 (4.1) | 3.2 (3.0) | 2.3 (2.2) | 68% | 32% | – | 0.34 | 0.21 | |
| 3.0 (3.6) | 5.8 (5.5) | 3.6 (3.6) | 2.7 (2.5) | 47% | 53% | – | 0.49 | 0.26 | |
| 3.7 (4.5) | 7.4 (6.9) | 4.0 (4.2) | 3.1 (2.8) | 25% | 75% | – | 1.02 | 0.34 | |
| 3.0 (3.3) | 5.2 (5.1) | 3.5 (3.4) | 2.7 (2.4) | 53% | 47% | – | 0.20 | 0.34 | |
| 3.1 (3.4) | 5.3 (5.2) | 3.5 (3.5) | 2.7 (2.4) | 51% | 49% | – | 0.19 | 0.35 | |
| 2.3 (2.8) | 4.3 (4.1) | 3.4 (3.2) | 2.4 (2.2) | 68% | 29% | 3% | 0.37 | 0.22 | |
| 2.3 (2.7) | 3.9 (3.8) | 3.5 (3.2) | 2.2 (2.2) | 73% | 19% | 8% | 0.26 | 0.19 | |
aCalculated J values using Amber 14 with GLYCAM06 parameter39 for C conformer are 1.35 (J), 2.04 (J), 2.19 (J) and 1.69 Hz (J), respectively.
bCalculated J values using Amber 14 with GLYCAM06 parameter39 for S conformer are 5.55 (J), 8.48 (J), 4.82 (J) and 3.14 Hz (J), respectively.
cCalculated J values using Amber 14 with GLYCAM06 parameter39 for C conformer are 7.85 (J), 8.03 (J), 8.5 (J) and 5.08 Hz (J), respectively.
dObtained by least sum of square difference analysis of the calculated and experimental values.
eThe residual sum of squares (RSS) was used to determine how well the calculated population ratios fit the experimental data42.
fThe calculated ratio of NOE H2-H5 signal and H4-H5 signal for pure S, C and C conformer is 0.53, 0.05, and 0.03 respectively39.
Figure 3Images of IdoA2S or IdoA and hexasaccharides from the MD simulations.
Atomic distances are indicated by dashed lines. The C, S, and C conformations of IdoA2S are colored orange, green, and purple, respectively. Panel A shows the IdoA2S residue in the C and S conformations (from a representative snapshot of the simulations of 4). Panel B displays the GlcNS(3S,6S) and IdoA residues from a representative frame of the simulation of 8 in the S conformation. Panel C contains a superimposition of the ring atoms in oligosaccharides from simulations of 4 in each of the three IdoA ring conformations. The sulfur atom of the IdoA2S residue is also displayed in yellow for each conformation. The RMSD of the ring atoms of the ligands with IdoA in the C and C conformation are 0.9 Å and 0.7 Å, respectively, relative to the molecule containing IdoA in the S conformation. Each model is the snapshot most similar to the average structure during the MD simulations.
Figure 4Inhibition curve of Xa activity by compound 4 and 8.
Different concentrations of compound 4 and 8 were incubated with antithrombin and Xa. The activity of Xa was then measured using a chromogenic substrate.
Figure 5Biosynthetic pathway of HS and relevant to the hexasaccharide model compounds.
HS biosynthesis is initiated from the polysaccharide containing -GlcA-GlcNAc- repeating units, followed by the modifications of N-deacetylase/N-sulphotransferase, C5-epimerase, 2-O-sulphotransferase, 6-O-sulphotransferase and 3-O-sulphotransferase. The 2-O-sulphotransferase modification can be incomplete, resulting the polysaccharide product consists of IdoA2S-containing domain and IdoA-containing domain. Hexasaccharide 2 and 6 represent these two domain structures. Hexasaccharide 3 and 7 represent the domain structures after 6-O-sulphotransferase modification, and hexasaccharide 4 and 8 represent the structures after 3-O-sulphotransferase modification. The wavy lines represent the linker between domains in HS polysaccharide with unknown structures.