• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文学位 >Molecular dynamics studies on the folding dynamics of poly-phenylacetylene, a non-biological polymer with a helical, folded state.
【24h】

Molecular dynamics studies on the folding dynamics of poly-phenylacetylene, a non-biological polymer with a helical, folded state.

机译：分子动力学研究聚苯乙炔（一种具有螺旋折叠状态的非生物聚合物）的折叠动力学。

获取原文
获取原文并翻译 | 示例
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Molecular Dynamics simulations of all-atom models of polymeric systems provide a unique perspective into the molecular folding dynamics at the bulk ensemble level as well as the investigation of single molecule events. We have created several theoretical models of a non biological oligomer, poly-phenylacetylene (pPA), with a unique, stable helical native state incorporating increasing levels of molecular complexity. This class of Foldamers, also known as phenylene ethynylene oligomers, folds via non-exponential kinetics expressed in the cumulative folding time distribution; observed independently via molecular dynamics simulations and also experimentally using laser temperature jump fluorescence methods.; We outline computational methods to probe the kinetic behavior of pPA oligomers of different lengths, specifically 12-mers and 20-mers, each from an ensemble of folding trajectories in implicit solvent. The length dependent folding mechanism is extracted from a non-linear fit to a minimalist kinetic model derived from the Law of Mass Action. We find that the pPA 12-mer folds via a three-state process in which the fully extended chain collapses to an intermediate kinetic state with partially helical intermediate structures and topologically diverse conformations including beta-like strands and also knots. Quantitative agreement between the experimentally observable rate constant and the rate measured from our simulations serves to validate the theoretical model for its predictive value.; The kinetic mechanism by which the pPA 20-mer chains fold is also extracted from a fit to a 4-state kinetic model derived from the Law of Mass Action. One important and striking difference observed in the 20-mer chains compared to the 12-mers is the appearance of a trapped kinetic phase in the cumulative folding time distribution. We present structural evidence implicating a very topologically diverse set of non-native conformations contributing to the trapped kinetic phase. Topologically similar structures to those observed in the 12-mer chains are also found in the 20-mer chains, including longer beta-like strands and more entangled knots, in addition to other structures not observed in the 12-mer data set.; A more complex computational model of poly-phenylacetylene is used to study the folding mechanism of the model 12-mer chains in explicit solvent. We model the folding of these pPA 12-mer chains in a broad range of solvents, specifically acetonitrile, chloroform, methanol, and water. We observed folding propensities consistent with experiments, in which chloroform acts as a denaturant preventing the pPA chains from folding. Water, on the other hand is a very poor solvent and promotes aggregation, which is consistent with what we observe in our simulations. Acetonitrile and methanol are intermediate between these two extremes and are found to be optimal (theta) solvents to promote the folding of the pPA chains.
机译：聚合物系统全原子模型的分子动力学模拟为整体集成水平的分子折叠动力学以及对单分子事件的研究提供了独特的视角。我们已经创建了非生物低聚物聚苯乙炔（pPA）的几种理论模型，其具有独特，稳定的螺旋天然状态，并结合了不断增加的分子复杂性水平。这类Foldamers，也称为亚苯基乙炔低聚物，通过累积时间分布中表示的非指数动力学折叠。通过分子动力学模拟独立观察到，也通过实验使用激光温度跳跃荧光法观察到。我们概述了计算方法，以探测不同长度的pPA低聚物的动力学行为，特别是12聚体和20聚体，每种均来自隐式溶剂中的折叠轨迹系。长度相关的折叠机制是从非线性拟合中提取的，该非线性拟合是根据质量作用定律得出的极简动力学模型。我们发现，pPA 12-mer通过三态过程折叠，其中完全延伸的链折叠成具有部分螺旋状中间结构和拓扑多样的构象（包括β样链和结）的中间动力学状态。实验上可观察到的速率常数与我们的模拟测得的速率之间的定量一致性有助于验证理论模型的预测价值。 pPA 20-mer链折叠所通过的动力学机制也从对质量作用定律的四态动力学模型的拟合中提取。与12聚体相比，在20聚体链中观察到的一个重要的显着差异是累积折叠时间分布中出现了捕获的动力学相。我们目前的结构证据暗示一组非常多样的非天然构象构成了被困的动力学阶段。除了在12-mer数据集中未观察到的其他结构外，在20-mer链中还发现了与12-mer链中观察到的结构相似的拓扑结构，包括更长的β样链和更多纠缠的结。使用更复杂的聚苯乙炔计算模型来研究模型12-聚体链在明确溶剂中的折叠机理。我们对这些pPA 12-mer链在多种溶剂（尤其是乙腈，氯仿，甲醇和水）中的折叠进行建模。我们观察到与实验一致的折叠倾向，其中氯仿充当变性剂，防止pPA链折叠。另一方面，水是一种非常差的溶剂，会促进聚集，这与我们在模拟中观察到的一致。乙腈和甲醇介于这两个极端之间，被发现是促进pPA链折叠的最佳（θ）溶剂。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号