Laboratoire Interdisciplinaire Carnot de Bourgogne , UMR 6303 CNRS-Univ. Bourgogne Franche-Comté , 9 Av. A. Savary, BP 47 870 , F-21078 Dijon Cedex , France.
Department of Physics, Applied Physics, and Astronomy , Rensselaer Polytechnic Institute , 110 Eighth Street , Troy , New York 12180 , United States.
J Phys Chem B. 2019 Mar 14;123(10):2342-2353. doi: 10.1021/acs.jpcb.8b10634. Epub 2019 Mar 1.
Solid-state nanopores (SSN) made of two-dimensional materials such as molybdenum disulfide (MoS) have emerged as candidate devices for biomolecules sequencing. SSN sequencing is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. Although several experiments on DNA translocation through SSNs have been performed in the past decade, translocation of proteins has been less studied, partly due to small protein size and detection limits. Moreover, the threading of proteins through nanopore channels is challenging, because proteins can exhibit neutral global charge and not be sensitive to the electric field. In this paper, we investigate the translocation of lysine residues and a model protein with polylysine tags through MoS nanoporous membranes using molecular dynamics simulations. Adding lysine tags to biological peptides is the method proposed here to promote the entrance of proteins through SSN. Specifically, we study the relationship existing between the translocation events and the ionic conductance signal drops. We show that individual lysine residues translocate easily through MoS nanopores, but the translocation speed is extremely fast, which leads to indiscernible ionic conductance drops. To reduce the translocation speed, we demonstrate that increasing the thickness of the membrane from single-layer to bilayer MoS reveals a stepwise process of translocation with discernible conductance drops that could be measured experimentally. Finally, a study of the threading of proteins with polylysine tags through MoS nanopores is presented. The addition of the positively charged tag to the neutral protein allows the threading and full translocation of the protein through the pore (at least two lysine residues are necessary in this case to observe translocation) and a similar sequence of translocation events is detected, independently of the tag length.
基于二维材料（如二硫化钼 (MoS)）的固态纳米孔 (SSN) 已成为生物分子测序的候选设备。SSN 测序基于测量带电荷的生物分子在响应跨膜施加的外部电压穿过纳米级通道时，离子电导率的变化。尽管过去十年已经进行了几项关于 DNA 通过 SSN 迁移的实验，但对蛋白质的迁移研究较少，部分原因是蛋白质尺寸较小且检测限较低。此外，由于蛋白质可以表现出中性整体电荷并且对电场不敏感，因此蛋白质穿过纳米孔通道的穿线具有挑战性。在本文中，我们使用分子动力学模拟研究了赖氨酸残基和带有聚赖氨酸标签的模型蛋白通过 MoS 纳米多孔膜的迁移。向生物肽中添加赖氨酸标签是本文提出的促进蛋白质通过 SSN 进入的方法。具体来说，我们研究了迁移事件与离子电导信号下降之间存在的关系。我们表明，单个赖氨酸残基很容易通过 MoS 纳米孔迁移，但迁移速度极快，导致离子电导下降难以察觉。为了降低迁移速度，我们证明从单层到双层 MoS 增加膜的厚度会显示出具有可辨电导下降的逐步迁移过程，这可以通过实验测量。最后，提出了带有聚赖氨酸标签的蛋白质通过 MoS 纳米孔的穿线研究。向中性蛋白质添加带正电荷的标签允许蛋白质通过孔穿线和完全迁移（在这种情况下，至少需要两个赖氨酸残基才能观察到迁移），并检测到类似的迁移事件序列，而与标签长度无关。
