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首页> 外文期刊>The Journal of Chemical Physics >A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain
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A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

机译：基于结构的模型无法探究titin I27结构域的机械展开途径

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摘要

We discuss the use of a structure based Cα-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that a simple Go-model does detect correctly the origin of the mechanical stability of this domain. The unfolding free energy landscape parameters x_u and ?G?, extracted from dependencies of unfolding forces on pulling speeds, are found to agree reasonably well with experiments.We predict that above v = 10~4 nm/s the additional force-induced intermediate state is populated at an end-to-end extension of about 75 ?. The force-induced switch in the unfolding pathway occurs at the critical pulling speed vcrit ≈ 10~6-10~7 nm/s. We argue that this critical pulling speed is an upper limit of the interval where Bell's theory works. However, our results suggest that the Go-model fails to reproduce the experimentally observed mechanical unfolding pathway properly, yielding an incomplete picture of the free energy landscape. Surprisingly, the experimentally observed intermediate state with the A strand detached is not populated in Go-model simulations over a wide range of pulling speeds. The discrepancy between simulation and experiment is clearly seen from the early stage of the unfolding process which shows the limitation of the Go model in reproducing unfolding pathways and deciphering the complete picture of the free energy landscape.
机译：我们讨论了基于结构的Cα-Go模型和Langevin动力学的使用，以详细研究titin I27域的力学性质和展开途径。我们表明，简单的Go模型可以正确检测此域的机械稳定性的起源。从展开力对拉速的依赖关系中提取的展开自由能态参数x_u和？G？被发现与实验相当吻合。我们预测在v = 10〜4 nm / s以上，附加力诱导的中间态以大约75？的端到端扩展填充。展开路径中的力诱导切换以临界拉动速度vcrit≈10〜6-10〜7 nm / s发生。我们认为，这种临界拉动速度是贝尔理论发挥作用的区间的上限。但是，我们的结果表明，Go模型无法正确再现实验观察到的机械展开路径，从而产生了不完整的自由能态图。出人意料的是，在Go-model模拟中，在很宽的拉速范围内，没有观察到A链分离的实验观察到的中间状态。从展开过程的早期阶段就可以清楚地看出仿真与实验之间的差异，这表明Go模型在再现展开路径和破译自由能态图的过程中存在局限性。

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