Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via del Politecnico 1, 00133, Roma, Italy.
Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Università di Roma "La Sapienza", Via A. Scarpa 14-16, 00161, Rome, Italy.
Sci Rep. 2019 Apr 23;9(1):6440. doi: 10.1038/s41598-019-42867-7.
Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.
单分子蛋白质测序将是蛋白质组学研究中的一个突破性进展，具有重要的生物医学影响。由于在 DNA 测序方面的成功，基于纳米孔的设备最近被提议作为测序肽链的可能工具。纳米孔蛋白质测序中的一个悬而未决的问题是，这些设备是否能够为所有 20 种标准氨基酸提供不同的信号。在这里，我们使用平衡全原子分子动力学模拟，估计了与 20 种不同的同聚肽相关的α-溶血素纳米孔的孔堵塞，每种同聚肽对应一种标准氨基酸。我们的结果表明，孔堵塞受氨基酸体积、疏水性和净电荷的影响。对于选定的同聚肽，通过非平衡运行来计算电流阻断，也支持了平衡估计。最后，我们讨论了修饰α-溶血素纳米孔的可能性，即在靠近 trans 侧的桶区部分切割，以减少虚假信号，从而提高纳米孔的灵敏度。
