Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
Soft Matter. 2020 Jun 7;16(21):5071-5080. doi: 10.1039/d0sm00090f. Epub 2020 May 26.
This work reports on the chiral structure fluctuations of peptide clusters at the early stages of aggregation in a coarse-grained peptide model. Our model reproduces a variety of aggregate structures, from disordered to crystal-like, that are observed experimentally. Unexpectedly, our molecular dynamics simulations showed that the small peptide cluster undergoes chiral structure fluctuations although the underlying implicit solvent model does not assume the chirality of peptides. The chiral fluctuations are quantified through a cluster twist parameter. A simple model is presented where the twist parameter undergoes a stochastic diffusion on a 1D potential surface. The shape of the potential surface changes with the cluster size. The model shows semi-quantitative agreement with the simulations. We hypothesize that the chiral fluctuations at the early stages of peptide aggregation can contribute to the selection of the final fibril structures.
本工作报道了在粗粒肽模型中聚集早期肽簇的手性结构波动。我们的模型再现了各种实验观察到的聚集结构，从无规到类似晶体。出乎意料的是，尽管基础隐溶剂模型不假设肽的手性，但我们的分子动力学模拟表明，小肽簇经历手性结构波动。通过簇扭转参数来量化手性波动。提出了一个简单的模型，其中扭转参数在一维势能表面上经历随机扩散。势能表面的形状随簇尺寸而变化。该模型与模拟结果具有半定量的一致性。我们假设肽聚集早期的手性波动可以有助于最终纤维结构的选择。
