Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

Abstract

<p>The conformational flexibility of the glycosaminoglycans (GAGs) are known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucoronate and iduronate. These calculations indicate that in some cases, an excess of 15 microseconds are required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for eleven monosaccharides found in GAGs; this includes to our knowledge the first simulation study of sulfation effects on GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the <sup>1</sup>C<sub>4</sub> ring conformation; this observation may have implications for understanding the structural basis of the biological function of GalNAc-containing glycosaminoglycans such as dermatan sulfate.</p>

Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics

“…Importantly, none of the 1 C 4 , 2 S O , or 4 C 1 puckers introduced a kink in the polymer chain, so we would not expect variations in the relative proportions of these ring puckers to alter overall polymer backbone conformations. IdoA also sampled other boat and skew-boat conformations in 20-mer MD simulations, specifically B 1,4 , 5 S 1 , 2,5 B, B 3,O , 1 S 3 , 1,4 B, and 1 S 5 ( Figure 9 b and Table S2 ), which is in agreement with results from MD simulations of IdoA monosaccharides [ 107 , 126 ]. Another force field study showed that 2,5 B and B 3,O IdoA conformers are also feasible interpretations of existing NMR data [ 127 ].…”

“…GalNAc monosaccharide ring C-P parameters ( Figure 9 a) show mostly 4 C 1 conformations, as well-established by X-ray diffraction [ 49 , 106 , 118 ], NMR [ 47 , 119 ], and force field [ 33 , 47 , 49 , 107 ] data. Biased MD simulations of β-GalNAc monosaccharides showed that nonsulfated β-GalNAc sampled boat and skew-boat conformations, namely B 3,O , 1 S 3 , and 1,4 B, with relatively high free energies [ 107 ]. In line with this study, our simulations showed very few boat and skew-boat puckers, namely 1 S 3 , 1,4 B, 1 S 5 ( Figure 4 a; -3GalNAcβ1- endocyclic ring and linker oxygen atoms were identical to those of -3GlcNAcβ1-), and B 2,5 , on the microsecond timescale.…”

“…IdoA monosaccharide rings in 20-mer MD sampled a majority of 1 C 4 and, to a lesser degree, 2 S O and 4 C 1 puckers ( Figure 9 b and Table S2 ), as observed in NMR and force field studies [ 29 , 45 , 47 , 51 , 107 , 120 , 121 , 122 , 123 , 124 , 125 ]. Literature reports of the relative proportions of these three ring puckers in nonsulfated IdoA vary, which may be explained by differences in the structure of neighboring residues (or lack thereof) [ 45 , 120 , 123 , 124 ] and differences in ion concentrations [ 123 ].…”

“…C-P analysis of GlcA monosaccharide rings in the hyaluronan 20-mer showed that GlcA is found mostly in 4 C 1 chair conformations ( Figure 3 b), as seen in crystal structures [ 92 , 93 , 94 , 95 ] and NMR and force field studies [ 51 , 67 , 101 , 102 , 107 , 109 , 110 ], with some boat and skew-boat conformations, including 3 S 1 , B 1,4 , 5 S 1 , 2,5 B, 2 S O , 1 S 3 , 1,4 B, and 1 S 5 ( Figure 3 b and Figure 4 b,c), which were also observed in GlcA rings in unbiased MD simulations of nonsulfated chondroitin 20-mers [ 33 ]. Some of these conformations were also sampled rarely in unbiased MD simulations of GlcA monosaccharides [ 51 , 107 ]. The slight differences between boat/skew-boat conformations in our simulations and monosaccharide simulations may have arisen from intramolecular interactions in the hyaluronan 20-mer.…”

“…For example, one GlcNAc ring in the crystal structure of a hyaluronan tetramer in complex with hyaluronidase was found in the 1,4 B boat conformation [ 95 ]. Additionally, GlcNAc boat/skew-boat conformations have been sampled in biased MD [ 107 ], 1-µs unbiased MD [ 108 ], and 10-µs unbiased MD simulations of GlcNAc monosaccharides [ 100 ]. One NMR and force field study suggested that these conformations were important for GAG-protein interactions [ 100 ].…”