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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Molecular Dynamics Simulation for the Dynamics and Kinetics of Folding Peptides in the Gas Phase
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Molecular Dynamics Simulation for the Dynamics and Kinetics of Folding Peptides in the Gas Phase

机译：气相折叠肽动力学和动力学的分子动力学模拟

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摘要

The conformations of flexible molecular species, such as oligomers and oligopeptides, and their interconversion in the gas phase have been probed by ion mobility spectrometry measurements. The ion motion is interpreted through the calculation of effective cross sections in the case of stable conformations of the macromolecules. However, when the molecular structures transform to each other as the ions collide with gas atoms during their flight through the drift tube, the introduction of an average cross section is required. To provide a direct way for the reproduction of the ion motion, we employ a nonequilibrium molecular dynamics simulation method and consider a molecular model that consists of two connected stiff cylindrical bodies interacting through an intramolecular model potential. With this procedure we have calculated the ion mobility as a function of temperature for a prototype peptide that converts between a helical and an extended globular form. The results are in good agreement with ion mobility spectrometry data confirming that an angular vibration coordinate can be used for the interpretation of the shifting of the drift-time distributions at high temperatures. The approach produces mean kinetic energies as well as various combined distributions of the ion degrees of freedom. It is easily applied to flexible macromolecular ions and can be extended to include additional degrees of freedom.
机译：柔性分子种类的构象，例如低聚物和寡肽，以及它们在气相中的相互转化已经通过离子迁移谱测量法进行了探测。在大分子稳定构型的情况下，通过计算有效截面来解释离子运动。但是，当离子在通过漂移管的飞行过程中离子与气体原子碰撞时，分子结构相互转换时，需要引入平均横截面。为了提供直接的离子运动再现方法，我们采用了非平衡分子动力学模拟方法，并考虑了一个分子模型，该模型由两个连接的刚性圆柱体组成，这些圆柱体通过分子内模型势相互作用。通过此过程，我们已经计算出了在螺旋形和扩展球形之间转换的原型肽的离子迁移率随温度的函数。结果与离子迁移谱数据高度吻合，证实了角振动坐标可用于解释高温下漂移时间分布的变化。该方法产生平均动能以及离子自由度的各种组合分布。它很容易应用于柔性大分子离子，并且可以扩展为包括其他自由度。

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