标题： 分子阻塞 - 全原子模拟中的半胱氨酸滑结机械夹具 显示英文标题

标题： Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations

摘要： 最近对17 134种蛋白质的调查发现了一类新的蛋白质，预计它们在拉伸过程中会产生1 nN范围内的力峰。 这种高力峰应归因于滑环通过胱氨酸环的强制，即通过生成胱氨酸滑结。 该调查是在一个简单的粗粒模型中进行的。 在这里，我们对15种胱氨酸结蛋白质进行了全原子导向分子动力学模拟，并确定了它们抵抗拉伸的能力。 与基于粗粒结构的先前研究一致，发现抵抗水平明显高于通过剪切作用进行机械夹紧的蛋白质。 大的拉伸力是通过形成胱氨酸滑结机械夹紧和由此产生的立体阻塞产生的。 我们详细阐明了这种夹紧的工作原理。 我们还研究了五种以剪切为基础的机械稳定性蛋白质，其中不涉及阻塞。 我们表明，在原子模型中，阻塞状态是通过一次移动一个氨基酸来解除的，并且在选择首先推进的氨基酸方面有选择。 相比之下，粗粒模型也允许两个氨基酸同时通过。 显示英文摘要

摘要： A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e. by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.