School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China.
Small. 2019 Apr;15(14):e1900036. doi: 10.1002/smll.201900036. Epub 2019 Mar 8.
The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.
蛋白质的功能取决于氨基酸的组成，这对蛋白质组学至关重要。然而，由于蛋白质的不规则电荷状态及其高级结构，蛋白质测序仍然具有挑战性。在这里，使用分子动力学模拟对原子力显微镜集成石墨烯纳米孔进行蛋白质测序能力进行了原理验证研究。结果发现，纳米孔可以以单残基分辨率区分蛋白质序列甚至其质子化状态。发现蛋白质残基渗透引起的拉力和电流阻断都与氨基酸的类型高度相关，这使得残基可以识别。还发现，除了尺寸之外，残基的构象和电荷状态也会显著影响其在纳米孔中渗透时的力和电流信号。特别是，由于电渗流效应，双质子化组氨酸的阻断电流略小于单质子化组氨酸的阻断电流，这使得区分氨基酸的不同质子化状态成为可能。这里报道的结果提出了一种使用石墨烯纳米孔结合纳米操作技术进行新型蛋白质测序的方案。
