Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Nanoscale. 2016 Jun 16;8(24):12143-51. doi: 10.1039/c6nr00410e.
An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable "unfoldon" motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.
一系列的生物过程，如蛋白质降解和蛋白质跨膜运输，都依赖于纳米孔界面介导的蛋白质展开事件。在这项工作中，我们利用基于 CNT 的人工纳米孔的全原子模拟来研究泛素展开的性质。通过对蛋白质的一端施加外力，我们观察到非典型的展开行为，当泛素被拉过孔口时。二级结构元件依次从蛋白质上脱离并穿过纳米管，有趣的是，剩余部分保持类似天然的特征。纳米孔界面的限制因此促进了在纳米管孔径上方形成稳定的“展开结构”，即使没有与其他二级结构的特定天然接触也能存在。这些展开结构的破坏会在我们的模拟中产生明显的力峰，为我们研究串联展开事件的动力学提供了一个敏感的探针。我们对纳米孔介导的蛋白质展开事件的详细分析不仅提供了对相关过程在细胞中可能如何进行的深入了解，也加深了我们对形成蛋白质构象稳定性基础的结构排列的理解。
