In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism

Abstract

GAGs exhibit a high level of conformational and configurational diversity, which remains untapped in terms of the recognition and modulation of proteins. Although GAGs are suggested to bind to more than 800 biologically important proteins, very few therapeutics have been designed or discovered so far. A key challenge is the inability to identify, understand and predict distinct topologies accessed by GAGs, which may help design novel protein-binding GAG sequences. Recent studies on chondroitin sulfate (CS), a key member of the GAG family, pinpointing its role in multiple biological functions led us to study the conformational dynamism of CS building blocks using molecular dynamics (MD). In the present study, we used the all-atom GLYCAM06 force field for the first time to explore the conformational space of all possible CS building blocks. Each of the 16 disaccharides was solvated in a TIP3P water box with an appropriate number of counter ions followed by equilibration and a production run. We analyzed the MD trajectories for torsional space, inter- and intra-molecular H-bonding, bridging water, conformational spread and energy landscapes. An in-house phi and psi probability density analysis showed that 1→3-linked sequences were more flexible than 1→4-linked sequences. More specifically, phi and psi regions for 1→4-linked sequences were held within a narrower range because of intra-molecular H-bonding between the GalNAc O5 atom and GlcA O3 atom, irrespective of sulfation pattern. In contrast, no such intra-molecular interaction arose for 1→3-linked sequences. Further, the stability of 1→4-linked sequences also arose from inter-molecular interactions involving bridged water molecules. The energy landscape for both classes of CS disaccharides demonstrated increased ruggedness as the level of sulfation increased. The results show that CS building blocks present distinct conformational dynamism that offers the high possibility of unique electrostatic surfaces for protein recognition. The fundamental results presented here will support the development of algorithms that help to design longer CS chains for protein recognition.

Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface

“…Thus, the output secondary structure looks similar. In [ 46 ], there is, however, a lack of the second region on the angles, observed in our case with the positive values of angles.…”

“…Numerically derived histograms have various numbers of maxima, but these local maxima may be wider or narrower, which is essential in the entropy calculated here. Therefore, our work builds upon [ 46 ], which focuses on a sole CS6 and shows that a smaller number of regions are preferred to occupy by ( , ) angles than our work that shows a larger number where HSA was added to the solution.…”

“…This can be the reason for the differences in the ( , ) distribution plot. The greater probability cluster, which contains the maximum, is placed in the range of angles obtained lately in [ 46 ] for similar computer simulations of various kinds of chondroitin sulfate in water solution without any protein contribution. Thus, it can be clearly seen that the vicinity of HSA changed this crucial angle distribution, making them more disordered but still in a specific way.…”

“…In the case of angles ( , ) for CS6, we can see quite different plots than the ones for ( , ) (see Figure 3 bottom line, and Figure S1 in Supplementary Materials ). According to [ 46 ], the differences were expected because, for angles 1–3, the most probable occupancy should be in the region of – ( ) and – ( ). In our results, the shadow (slightly visible red color on the plot) of those angles can be seen, especially in the case of Na and Mg , where the maximum is placed within this range (cf.…”

“…A common pattern on the maps presented in Figure 4 and the ones presented in Figure 2 in [ 31 ] indicates that the proximity of the HSA protein does not prevent the HA chain from taking the shape of a helix (cf., Figure 5 in [ 31 ]). In the case of CS6, positions of preferred ( , ) angles regions have been recently reported in [ 46 ]. The location of the angles presented in this study for HSA-CS6 complexes overlaps with those for the HA chain in [ 31 ].…”