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Toward an accurate conformational modeling of iduronic acid.
- Source :
-
The journal of physical chemistry. B [J Phys Chem B] 2013 Jan 31; Vol. 117 (4), pp. 1003-9. Date of Electronic Publication: 2013 Jan 15. - Publication Year :
- 2013
-
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.
- Subjects :
- Carbohydrate Conformation
Models, Molecular
Iduronic Acid chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1520-5207
- Volume :
- 117
- Issue :
- 4
- Database :
- MEDLINE
- Journal :
- The journal of physical chemistry. B
- Publication Type :
- Academic Journal
- Accession number :
- 23286518
- Full Text :
- https://doi.org/10.1021/jp3100552