Toward an Accurate Conformational Modeling of Iduronic Acid

详细信息    查看全文

• 作者：Pavel Oborsk媒 ; Igor Tvaro拧ka ; Blanka Kr谩lov谩 ; Vojt臎ch Spiwok
• 刊名：The Journal of Physical Chemistry B
• 出版年：2013
• 出版时间：January 31, 2013
• 年：2013
• 卷：117
• 期：4
• 页码：1003-1009
• 全文大小：360K
• 年卷期：v.117,no.4(January 31, 2013)
• ISSN：1520-5207

文摘

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 ²S_O conformations of 伪-l-IdoA-OMe and 伪-l-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1鈥? interaction) were tested. It was found that scaling (reduction) of 1鈥? electrostatic interactions significantly changes conformational preferences toward the ⁴C₁ conformation. More interestingly, scaling of 1鈥? van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1鈥? interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments.