Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy
Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy
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DOI：
10.1021/jacs.9b06776
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发表时间：
2019-09-18
影响因子：
15
通讯作者：
Nash, Michael A.
中科院分区：
文献类型：
--
作者：
Bernardi, Rafael C.;Durner, Ellis;Nash, Michael A.
分子动力学模拟能预测蛋白质复合物的力学行为吗？模拟能破译大分子复合物中未知功能的蛋白质结构域的作用吗？在这里，我们采用了广泛的采样计算方法来证明，分子动力学模拟，当仔细执行，并结合单分子原子力光谱实验，可以预测和解释的行为高度机械稳定的蛋白质复合物。作为一个测试案例，我们研究了一个以前未报道的同源物，从瘤胃球菌flavefaciens称为X-模块-Dockerin（XDoc）结合到它的合作伙伴Cohesin（Coh）。通过在破裂事件附近执行数十个短模拟副本，并分析动态网络波动，我们能够生成大量模拟统计数据，并将其与实验直接进行比较，以揭示机械稳定性所涉及的机制。我们的单分子力谱实验表明，XDoc-Coh同系物复合物在10（5）pN/s的加载速率下承受高达1 nN的力。我们的模拟结果表明，这种显着的机械稳定性是通过蛋白质结构实现的，该蛋白质结构引导分子变形沿着垂直于拉伸轴的路径。X-模块被发现在屏蔽邻近的蛋白质复合物免受机械破裂方面起着至关重要的作用。这些蛋白质机械稳定的机制在生物技术中具有潜在的应用，用于开发表现出剪切增强粘附或可调力学的系统。
Can molecular dynamics simulations predict the mechanical behavior of protein complexes? Can simulations decipher the role of protein domains of unknown function in large macromolecular complexes? Here, we employ a wide-sampling computational approach to demonstrate that molecular dynamics simulations, when carefully performed and combined with single-molecule atomic force spectroscopy experiments, can predict and explain the behavior of highly mechanostable protein complexes. As a test case, we studied a previously unreported homologue from Ruminococcus flavefaciens called X-module-Dockerin (XDoc) bound to its partner Cohesin (Coh). By performing dozens of short simulation replicas near the rupture event, and analyzing dynamic network fluctuations, we were able to generate large simulation statistics and directly compare them with experiments to uncover the mechanisms involved in mechanical stabilization. Our single-molecule force spectroscopy experiments show that the XDoc-Coh homologue complex withstands forces up to 1 nN at loading rates of 10(5) pN/s. Our simulation results reveal that this remarkable mechanical stability is achieved by a protein architecture that directs molecular deformation along paths that run perpendicular to the pulling axis. The X-module was found to play a crucial role in shielding the adjacent protein complex from mechanical rupture. These mechanisms of protein mechanical stabilization have potential applications in biotechnology for the development of systems exhibiting shear enhanced adhesion or tunable mechanics.