标题： 折叠和固有无序蛋白质中的重构动力学：溶剂质量和变性剂的影响 显示英文标题

标题： Reconfiguration Dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant

摘要： 我们考虑一种具有内摩擦的聚合物的幻影链模型，在谐波约束下，并采用平均场方法扩展它以考虑溶剂质量的影响，其中引入了一个指数$\nu$。该模型称为“溶剂依赖的紧缩Rouse内摩擦模型”（SDCRIF），然后用于计算与最近关于折叠蛋白和固有无序蛋白（IDPs）的Förster共振能量转移（FRET）研究相关的链重配置时间，并能够解释溶剂质量以及变性剂浓度对重配置动力学的影响。根据一个假设，即谐波约束的强度（$k_c$）与链的内摩擦（$\xi_{int}$）相关，SDCRIF可以令人信服地再现实验数据，并解释变性剂如何改变内摩擦的时间尺度。它还可以预测在IDPs情况下接近零的内摩擦。此外，我们的计算表明，环化时间以及重配置时间与链长$N$成$\sim N^\alpha$的比例，其中$\alpha$对内摩擦的依赖较弱，但对溶剂质量的依赖较强。在没有任何内摩擦的情况下，$\alpha=2\nu+1$，但在存在内摩擦的情况下会下降，但一般来说，环化会变慢。相反，溶剂越差，链重配置和形成环的速度越快，尽管人们预期在坍塌状态下会有高的内摩擦。然而，如果内摩擦过高，则即使在不良溶剂中，环化和重配置动力学也会变得缓慢。 显示英文摘要

摘要： We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $\nu$ is introduced. The model termed as "Solvent Dependent Compacted Rouse with Internal Friction (SDCRIF)" is then used to calculate the reconfiguration time of a chain that relates to recent F\"{o}rster resonance energy transfer (FRET) studies on folded and intrinsically disordered proteins (IDPs) and can account for the effects of solvent quality as well as the denaturant concentration on the reconfiguration dynamics. Following an ansatz that relates the strength of the harmonic confinement ($k_c$) with the internal friction of the chain ($\xi_{int}$), SDCRIF can convincingly reproduce the experimental data and explain how the denaturant can change the time scale for the internal friction. It can also predict near zero internal friction in case of IDPs. In addition, our calculations show that the looping time as well as the reconfiguration time scales with the chain length $N$ as $\sim N^\alpha$, where $\alpha$ depends weakly on the internal friction but has rather stronger dependence on the solvent quality. In absence of any internal friction, $\alpha=2\nu+1$ and it goes down in presence of internal friction, but looping slows down in general. On the contrary, poorer the solvent, faster the chain reconfigures and forms loop, even though one expects high internal friction in the collapsed state. However, if the internal friction is too high then the looping and reconfiguration dynamics become slow even in poor solvent.