a Department of Chemistry , Isfahan University of Technology , Isfahan , 84156-83111 , Iran.
J Biomol Struct Dyn. 2019 Feb;37(3):691-701. doi: 10.1080/07391102.2018.1436090. Epub 2018 Feb 12.
In this work, the transport behaviors of the enantiomers of lactic acid (LA) in two cyclic peptide nanotubes (CPNTs) with different diameters were studied using steered molecular dynamic (SMD) simulation to investigate the effect of the diameter of CPNT on the discrimination of the enantiomers of LA. For this purpose, two cyclic peptides with two different sizes ([Ala--Ala-] and [Ala--Ala-]) were used for constructing two CPNTs so that each CPNT was composed of eight cyclic peptide units. The docking calculations were performed to obtain the appropriate position of each enantiomer at the lumen of each CPNT. The variation of the pulling force versus time, exerted on the enantiomers moving in the CPNTs was calculated using the SMD simulations with two different strategies (positional and directional).The obtained results showed that the diameter of CPNT has considerable effect on the discrimination of the LA enantiomers so that the increase of the diameter of CPNT, increased the velocity difference between two enantiomers and improved the performance of CPNT for the chirality discrimination. The SMD simulations indicated that the velocity of S-enantiomer became more than R-enantiomer and its motion became more comfortable than R-enantiomer when the diameter of CNPT increased. The RDFs of the H and O atoms of the LA enantiomers relative to the O atoms of CPNT were calculated and it was found that the increase of the diameter of CPNT creates the significant changes in the RDFs of H1, H2 and H3 atoms of the enantiomers.
在这项工作中，使用导向分子动力学（SMD）模拟研究了两种具有不同直径的环肽纳米管（CPNT）中乳酸（LA）对映体的传输行为，以研究 CPNT 直径对 LA 对映体选择性的影响。为此，使用两种具有两种不同尺寸的环肽 ([Ala--Ala-] 和 [Ala--Ala-]) 构建了两个 CPNT，使得每个 CPNT 由八个环肽单元组成。进行对接计算以获得每个 CPNT 管腔中每个对映体的适当位置。使用 SMD 模拟通过两种不同策略（位置和方向）计算作用在 CPNTs 中移动的对映体上的随时间变化的拉力。结果表明，CPNT 的直径对 LA 对映体的选择性有很大影响，CPNT 直径的增加增加了两种对映体之间的速度差异，提高了 CPNT 用于手性选择性的性能。SMD 模拟表明，当 CPNT 的直径增加时，S-对映体的速度超过 R-对映体，其运动比 R-对映体更舒适。计算了 LA 对映体的 H 和 O 原子相对于 CPNT 的 O 原子的 RDF，并发现 CPNT 直径的增加导致对映体的 H1、H2 和 H3 原子的 RDF 发生显著变化。
