title: Toward an accurate conformational modeling of iduronic acid.
abstract: 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 (1)C(4), (4)C(1) and (2)S(O) 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 (4)C(1) 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.
authors.affiliation: Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 3, Prague 6 166 28, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Oborský
authors.forename: Igor
authors.initials: I
authors.lastname: Tvaroška
authors.forename: Blanka
authors.initials: B
authors.lastname: Králová
authors.forename: Vojtěch
authors.initials: V
authors.lastname: Spiwok
mesh_terms: D002236:Carbohydrate Conformation; D007067:Iduronic Acid / Q000737:chemistry*; D008958:Models, Molecular
chemical_list: D007067:Iduronic Acid