Liu Jingqian, Aksimentiev Aleksei
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
ACS Nanosci Au. 2023 Nov 14;4(1):21-29. doi: 10.1021/acsnanoscienceau.3c00046. eCollection 2024 Feb 21.
The nanopore sensing method holds the promise of delivering a single molecule technology for identification of biological proteins, direct detection of post-translational modifications, and perhaps de novo determination of a protein's amino acid sequence. The key quantity measured in such nanopore sensing experiments is the magnitude of the ionic current passing through a nanopore blocked by a polypeptide chain. Establishing a relationship between the amino acid sequence of a peptide fragment confined within a nanopore and the blockade current flowing through the nanopore remains a major challenge for realizing the nanopore protein sequencing. Using the results of all-atom molecular dynamics simulations, here we compare nanopore sequencing of DNA with nanopore sequencing of proteins. We then delineate the factors affecting the blockade current modulation by the peptide sequence, showing that the current can be determined by (i) the steric footprint of an amino acid, (ii) its interactions with the pore wall, (iii) the local stretching of a polypeptide chain, and (iv) the local enhancement of the ion concentration at the nanopore constriction. We conclude with a brief discussion of the prospects for purely computational prediction of the blockade currents.
纳米孔传感方法有望提供一种单分子技术，用于生物蛋白质的鉴定、翻译后修饰的直接检测，甚至可能用于从头确定蛋白质的氨基酸序列。在这种纳米孔传感实验中测量的关键量是通过被多肽链阻断的纳米孔的离子电流大小。在纳米孔内的肽片段的氨基酸序列与流过纳米孔的阻断电流之间建立关系仍然是实现纳米孔蛋白质测序的主要挑战。利用全原子分子动力学模拟的结果，我们在此比较了DNA的纳米孔测序和蛋白质的纳米孔测序。然后，我们描述了影响肽序列对阻断电流调制的因素，表明电流可以由以下因素决定：（i）氨基酸的空间占用，（ii）其与孔壁的相互作用，（iii）多肽链的局部拉伸，以及（iv）纳米孔收缩处离子浓度的局部增强。最后，我们简要讨论了阻断电流纯计算预测的前景。
