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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Dynamics of Disordered Proteins under Confinement: Memory Effects and Internal Friction
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Dynamics of Disordered Proteins under Confinement: Memory Effects and Internal Friction

机译：监禁下无序蛋白质的动态：记忆效应和内部摩擦

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摘要

Many proteins are disordered under physiological conditions. How efficiently they can search for their cellular targets and how fast they can fold upon target binding is determined by their intrinsic dynamics, which have thus attracted much recent attention. Experiments and molecular simulations show that the inherent reconfiguration timescale for unfolded proteins has a solvent friction component and an internal friction component, and the microscopic origin of the latter, along with its proper mathematical description, has been a topic of considerable debate. Internal friction varies across different proteins of comparable length and increases with decreasing denaturant concentration, showing that it depends on how compact the protein is. Here we report on a systematic atomistic simulation study of how confinement, which induces a more compact unfolded state, affects dynamics and friction in disordered peptides. We find that the average reconfiguration timescales increase exponentially as the peptide's spatial dimensions are reduced; at the same time, confinement broadens the spectrum of relaxation timescales exhibited by the peptide. There are two important implications of this broadening: First, it limits applicability of the common Rouse and Zimm models with internal friction, as those models attempt to capture internal friction effects by introducing a single internal friction timescale. Second, the long-tailed distribution of relaxation times leads to anomalous diffusion effects in the dynamics of intramolecular distances. Analysis and interpretation of experimental signals from various measurements that probe intramolecular protein dynamics (such as single-molecule fluorescence correlation spectroscopy and single-molecule force spectroscopy) rely on the assumption of diffusive dynamics along the distances being probed; hence, our results suggest the need for more general models allowing for anomalous diffusion effects.
机译：许多蛋白质在生理条件下紊乱。它们有效地搜索其蜂窝目标以及它们在目标结合时可以折叠的速度是多么的倍数由其内在动态决定，从而引起了最近的关注。实验和分子模拟表明，展开蛋白质的固有重新配置少量尺度具有溶剂摩擦部件和内部摩擦分量，以及后者的微观起源，以及其适当的数学描述，这是一个相当大的辩论的主题。内部摩擦在相当长度的不同蛋白质上变化，并且随着变性浓度的降低而增加，表明它取决于蛋白质的程度。在这里，我们报告了一个系统原子模拟研究，对诱导更紧凑的展开状态，影响无序肽中的动态和摩擦。我们发现随着肽的空间尺寸减小的平均重新配置时间尺度增加;同时，限制拓宽肽表现出的弛豫时间尺寸。这种扩展有两个重要意义：首先，它限制了共同的rouse和zimm模型与内部摩擦的适用性，因为这些模型试图通过引入单个内部摩擦速度来捕获内部摩擦效应。其次，松弛时间的长尾分布导致分子内距离动态的异常扩散效应。从各种测量的实验信号分析和解释探测分子内蛋白质动态（如单分子荧光相关光谱和单分子力谱）依赖于探测距离的漫射动力学的假设;因此，我们的结果表明需要更多的一般模型，允许异常的扩散效果。

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