IBM Research Australia, 204 Lygon Street, 3053 Carlton, Victoria, Australia.
Nanotechnology. 2014 Apr 18;25(15):155502. doi: 10.1088/0957-4484/25/15/155502. Epub 2014 Mar 20.
Solid-state nanopores have been shown to be suitable for single molecule detection. While numerous modeling investigations exist for DNA within nanopores, there are few simulations of protein translocations. In this paper, we use atomistic molecular dynamics to investigate the translocation of proteins through a silicon nitride nanopore. The nanopore dimensions and profile are representative of experimental systems. We are able to calculate the change in blockade current and friction coefficient for different positions of the protein within the pore. The change in ionic current is found to be negligible until the protein is fully within the pore and the current is lowest when the protein is in the pore center. Using a simple theory that gives good quantitative agreement with the simulation results we are able to show that the variation in current with position is a function of the pore shape. In simulations that guide the protein through the nanopore we identify the effect that confinement has on the friction coefficient of the protein. This integrated view of translocation at the nanoscale provides useful insights that can be used to guide the design of future devices.
固态纳米孔已被证明适合用于单分子检测。虽然有许多针对纳米孔内 DNA 的建模研究，但对蛋白质转运的模拟却很少。在本文中，我们使用原子分子动力学来研究蛋白质通过氮化硅纳米孔的转运。纳米孔的尺寸和轮廓与实验系统具有代表性。我们能够计算出蛋白质在孔内不同位置的阻断电流和摩擦系数的变化。当蛋白质完全在孔内时，离子电流的变化可以忽略不计，当蛋白质在孔中心时，电流最低。我们使用一种简单的理论，该理论与模拟结果具有很好的定量一致性，能够表明电流随位置的变化是孔形状的函数。在引导蛋白质通过纳米孔的模拟中，我们确定了限制对蛋白质摩擦系数的影响。这种纳米尺度转运的综合观点提供了有用的见解，可用于指导未来器件的设计。
