Nicolaï Adrien, Rath Aniket, Delarue Patrice, Senet Patrick
Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France.
Nanoscale. 2020 Nov 19;12(44):22743-22753. doi: 10.1039/d0nr05185c.
Solid-state nanopores have emerged as one of the most versatile tools for single-biomolecule detection and characterization. Nanopore sensing is based on the measurement of variations in ionic current as charged biomolecules immersed in an electrolyte translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. The passage of a biomolecule through a pore yields information about its structure and chemical properties, as demonstrated experimentally with sub-microsecond temporal resolution. However, extracting the sequence of a biomolecule without the information about its position remains challenging due to the fact there is a large variability of sensing events recorded. In this paper, we performed microsecond time scale all-atom non-equilibrium Molecular Dynamics (MD) simulations of peptide translocation (motifs of alpha-synuclein, associated with Parkinson's disease) through single-layer MoS2 nanopores. First, we present an analysis based on the current threshold to extract and characterize meaningful sensing events from ionic current time series computed from MD. Second, a mechanism of translocation is established, for which side chains of each amino acid are oriented parallel to the electric field when they are translocating through the pore and perpendicular otherwise. Third, a new procedure based on the permutation entropy (PE) algorithm is detailed to identify protein sequence motifs related to ionic current drop speed. PE is a technique used to quantify the complexity of a given time series and it allows the detection of regular patterns. Here, PE patterns were associated with protein sequence motifs composed of 1, 2 or 3 amino acids. Finally, we demonstrate that this very promising procedure allows the detection of biological mutations and could be tested experimentally, despite the fact that reconstructing the sequence information remains unachievable at this time.
固态纳米孔已成为用于单生物分子检测和表征的最通用工具之一。纳米孔传感基于测量离子电流的变化，当浸入电解质中的带电生物分子响应施加在膜上的外部电压而通过纳米尺寸的通道时，就会产生这种变化。生物分子通过孔的过程会产生有关其结构和化学性质的信息，实验已证明其具有亚微秒级的时间分辨率。然而，由于记录的传感事件存在很大的变异性，在没有生物分子位置信息的情况下提取其序列仍然具有挑战性。在本文中，我们对肽（与帕金森病相关的α-突触核蛋白基序）通过单层二硫化钼纳米孔的转运进行了微秒时间尺度的全原子非平衡分子动力学（MD）模拟。首先，我们基于电流阈值进行分析，以从MD计算的离子电流时间序列中提取和表征有意义的传感事件。其次，建立了一种转运机制，即每个氨基酸的侧链在通过孔时与电场平行，否则与电场垂直。第三，详细介绍了一种基于排列熵（PE）算法的新程序，以识别与离子电流下降速度相关的蛋白质序列基序。PE是一种用于量化给定时间序列复杂性的技术，它可以检测规则模式。在这里，PE模式与由1、2或3个氨基酸组成的蛋白质序列基序相关。最后，我们证明了这个非常有前景的程序能够检测生物突变，并且尽管目前重建序列信息仍然无法实现，但仍可以进行实验测试。
