Cardoch Sebastian, Timneanu Nicusor, Caleman Carl, Scheicher Ralph H
Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
ACS Nanosci Au. 2021 Dec 28;2(2):119-127. doi: 10.1021/acsnanoscienceau.1c00022. eCollection 2022 Apr 20.
A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.
纳米孔是单分子传感生物技术中的一种工具，可实现无标记的高通量识别。纳米孔已成功应用于DNA测序，并在蛋白质研究中显示出潜力。然而，由于蛋白质的大小、电荷和折叠存在很大差异，该任务仍然具有挑战性。微型蛋白质具有少量残基、有限的二级结构和稳定的三级结构，这可以提供一种降低复杂性的系统方法。在这项计算工作中，我们从理论上评估了使用氮化硅纳米孔对人体中发现的两种微型蛋白质进行传感的情况。我们采用分子动力学方法来计算占据孔的离子电流大小，并通过电子结构计算来获得孔壁与微型蛋白质之间的相互作用强度。根据相互作用强度，我们使用组合数学和数值解的混合方法推导出驻留时间。后一种方法规避了使用分子动力学模拟转运事件所需的典型计算需求。我们关注两种由于各向同性几何形状、相似的残基数量和总体可比结构而可能难以区分的微型蛋白质。我们发现占据孔的电流大小没有显著变化，但它们的驻留时间相差1个数量级。总之，这些结果表明了一种针对相似微型蛋白质的成功识别方案。
