Principles of carbopeptoid folding: a molecular dynamics simulation study
Principles of carbopeptoid folding: a molecular dynamics simulation study
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DOI：
10.1002/psc.597
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发表时间：
2005-02-01
影响因子：
2.1
通讯作者：
Van Gunsteren, WF
中科院分区：
文献类型：
--
作者：
Baron, R;Bakowies, D;Van Gunsteren, WF
通过9个分子动力学模拟，研究了五种四氢呋喃类碳肽在氯仿和二甲基过氧二甲酯中的构象空间。在核磁共振实验的推动下，显示了一些但不是所有这些碳肽的稳定折叠，研究了它们的折叠行为作为立体化学、链长和溶剂的函数。从氢键的出现、主链扭角分布、构象簇集和溶质构象熵等方面分析了这些分子的构象分布。虽然四氢呋喃环上的顺式连接有利于右旋螺旋结构，但反式连接导致更大的构象可变性。溶质内氢键随着链长的增加和溶剂极性的增加而降低。溶质构型熵证实了所获得的图景：对于顺式连接的多肽，它们小于反式连接的多肽；对于作为溶剂的氯仿，它们小于作为溶剂的二甲基亚砜；对于较短的多肽链，它们是较小的。模拟提供了分子构象可变性的原子图，这与现有的实验数据一致。版权所有(C)2004欧洲肽协会和John Wiley Sons，Ltd.
The conformational spaces of five oligomers of tetrahydrofuran-based carbopeptoids in chloroform and dimethyl suffoxide were investigated through nine molecular dynamics simulations. Prompted by nuclear magnetic resonance experiments that indicated various stable folds for some but not all of these carbopeptoids, their folding behaviour was investigated as a function of stereochemistry, chain length and solvent. The conformational distributions of these molecules were analysed in terms of occurrence of hydrogen bonds, backbone torsional-angle distributions, conformational clustering and solute configurational entropy. While a cis-linkage across the tetrahydrofuran ring favours right-handed helical structures, a trans-linkage results in a larger conformational variability. Intra-solute hydrogen bonding is reduced with increasing chain length and with increasing solvent polarity. Solute configurational entropies confirm the picture obtained: they are smaller for cis- than for trans-linked peptides, for chloroform than for dimethyl sulfoxide as solvent and for Shorter peptide chains. The simulations provide an atomic picture of molecular conformational variability that is consistent with the available experimental data. Copyright (C) 2004 European Peptide Society and John Wiley Sons, Ltd.