Toward an accurate conformational modeling of iduronic acid.
Toward an accurate conformational modeling of iduronic acid.
复制标题
建立艾杜糖醛酸的准确构象模型。
DOI：
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发表时间：
2013
影响因子：
3.3
通讯作者：
V. Spiwok
中科院分区：
文献类型：
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作者：
Pavel Oborský;I. Tvaroška;B. Králová;V. Spiwok
与大多数其他单糖不同，艾杜糖醛酸（IdoA）可以采用不同的环构象，这取决于分子结构的背景。准确建模的这种积木是必不可少的了解糖胺聚糖和其他糖缀合物的作用。在这里，我们使用元动力学来预测α-L-IdoA-OMe和α-L-IdoA 2S-OMe的（1）C（4）、（4）C（1）和（2）S（O）构象的平衡。测试了由三个键（1-4相互作用）分离的原子的不同标度方案。结果发现，1-4静电相互作用的缩放（减少）显着改变构象偏好（4）C（1）构象。更有趣的是，1-4货车德瓦尔斯相互作用的缩放有利于斜船构象。这表明，非共价1-4相互作用参数的微小修改可以提供来自模拟和实验的艾杜糖醛酸在水中的构象体群体之间的良好一致性。
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.