Institute for Computational Sciences and Technology, Ho Chi Minh City 71506, Vietnam.
Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, Ho Chi Minh City 72700, Vietnam.
Biomolecules. 2024 Oct 18;14(10):1327. doi: 10.3390/biom14101327.
Single-molecule force spectroscopy (SMFS) experiments can monitor protein refolding by applying a small force of a few piconewtons (pN) and slowing down the folding process. Bell theory predicts that in the narrow force regime where refolding can occur, the folding time should increase exponentially with increased external force. In this work, using coarse-grained molecular dynamics simulations, we compared the refolding pathways of SARS-CoV-1 RBD and SARS-CoV-2 RBD (RBD refers to the receptor binding domain) starting from unfolded conformations with and without a force applied to the protein termini. For SARS-CoV-2 RBD, the number of trajectories that fold is significantly reduced with the application of a 5 pN force, indicating that, qualitatively consistent with Bell theory, refolding is slowed down when a pulling force is applied to the termini. In contrast, the refolding times of SARS-CoV-1 RBD do not change meaningfully when a force of 5 pN is applied. How this lack of a Bell response could arise at the molecular level is unknown. Analysis of the entanglement changes of the folded conformations revealed that in the case of SARS-CoV-1 RBD, an external force minimizes misfolding into kinetically trapped states, thereby promoting efficient folding and offsetting any potential slowdown due to the external force. These misfolded states contain non-native entanglements that do not exist in the native state of either SARS-CoV-1-RBD or SARS-CoV-2-RBD. These results indicate that non-Bell behavior can arise from this class of misfolding and, hence, may be a means of experimentally detecting these elusive, theoretically predicted states.
单分子力谱 (SMFS) 实验可以通过施加几皮牛顿 (pN) 的小力并减缓折叠过程来监测蛋白质的重折叠。贝尔理论预测，在可以发生重折叠的狭窄力范围内，折叠时间应该随外部力的增加呈指数增加。在这项工作中，我们使用粗粒分子动力学模拟，比较了来自无折叠构象和施加蛋白质末端力的 SARS-CoV-1 RBD 和 SARS-CoV-2 RBD（RBD 是指受体结合域）的重折叠途径。对于 SARS-CoV-2 RBD，施加 5 pN 力会显著减少折叠轨迹的数量，这表明与贝尔理论定性一致，当向末端施加拉力时，重折叠会减慢。相比之下，当施加 5 pN 的力时，SARS-CoV-1 RBD 的重折叠时间没有明显变化。在分子水平上，这种缺乏贝尔响应的情况是如何产生的尚不清楚。对折叠构象的缠结变化的分析表明，在 SARS-CoV-1 RBD 的情况下，外部力最小化了错误折叠进入动力学捕获状态的可能性，从而促进了有效的折叠，并抵消了由于外部力可能导致的任何潜在减速。这些错误折叠的状态包含非天然的缠结，而这些缠结不存在于 SARS-CoV-1-RBD 或 SARS-CoV-2-RBD 的天然状态中。这些结果表明，非贝尔行为可能源于这种错误折叠，因此可能是实验检测这些难以捉摸的、理论预测状态的一种手段。
