The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations

A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility

“…The ring conformation may, in some cases, affect the glycosidic conformation (Plazinski and Drach, ; Plazinski et al ., ,b). To investigate this, the free energy map of xylobiose was decomposed into four parts, each one corresponding to a different combination of ring conformations (Figure ).…”

“…At present, there are no published studies that mention this, and further investigations into this matter are probably called for. The ring conformation may, in some cases, affect the glycosidic conformation (Plazinski and Drach, 2015;Plazinski et al, 2016a,b). To investigate this, the free energy map of xylobiose was decomposed into four parts, each one corresponding to a different combination of ring conformations ( Figure 6).…”

Revision of the GROMOS 56A6CARBO force field: Improving the description of ring‐conformational equilibria in hexopyranose‐based carbohydrates chains

“…Interestingly, the least populated rotamer is precisely the one with a potential for intramolecular hydrogen‐bonding between the hydroxymethyl group and the hydroxyl group at C 4 . This suggests that the formation of such a hydrogen‐bond is not a major conformational driving force in water (see also A. Lonardi, P. Oborsky, P. H. Hünenberger, manuscript in preparation). The J ‐values calculated based on the simulations typically deviate by about 1 Hz or less from the experimental estimates (up to 1.5 Hz for J R in the Gal derivatives).…”

“…This is expected considering that the patch does not alter parameters having a direct influence on the glycosidic‐linkage properties (no change in the trans ‐glycosidic torsions or nonbonded interactions). However, each FEM represents a weighted average of FEMs corresponding to different conformers of the two rings, predominantly the 4 C 1 and 1 C 4 chairs, and may thus be indirectly affected by the corresponding ring‐conformational equilibria . The correlation between glycosidic‐linkage FEM and single‐ring FEPs can be deconvoluted more specifically by analyses of the FEPs at fixed glycosidic‐linkage conformation or of the FEMs at fixed ring conformations (A. Lonardi, unpublished results).…”

“…[8][9][10][11] Second, there is lack of direct experimental data against which to perform the parametrization, at least beyond the monosaccharide level. [12][13][14][15][16][17][18] Although it is known that the 4 C 1 chair conformation is the most stable one for nearly all unfunctionalized hexopyranoses of the D-series in water, [12,18] D-idose being an exception, [16] the conformational equilibrium of the six-membered ring may be affected by many environmental factors, e.g., functionalization of the exocyclic groups, [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37] neighbouring residues within an oligosaccharide chain, [38] surrounding aminoacids in an enzyme active site, [39][40][41][42][43] consideration of a nonaqueous solvent [35,36,44] or of a crystal/fiber environment, [45] or pulling forces in an atomic force microscopy (AFM) experiment. [46]…”