Toward an accurate conformational modeling of iduronic acid.

Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of 1C4, 4C1 and 2SO conformations of α-l-IdoA-OMe and α-l-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1–4 interaction) were tested. It was found that scaling (reduction) of 1–4 electrostatic interactions significantly changes conformational preferences toward the 4C1 conformation. More interestingly, scaling of 1–4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1–4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments.