The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time
The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time
复制标题
DOI：
10.1038/nphys3553
复制
发表时间：
2016-02-01
期刊：
影响因子：
19.6
通讯作者：
Smith, Jeremy C.
中科院分区：
文献类型：
--
作者：
Hu, Xiaohu;Hong, Liang;Smith, Jeremy C.
蛋白质的内部运动对其功能至关重要。蛋白质结构波动的时间依赖性非常复杂，表现出亚扩散、非指数行为，有效弛豫时间存在于几十年的时间内，从ps到大约10（2）s（参考文献1-4）。在这里，使用分子动力学模拟，我们表明，从10（-12）到10（-5）秒的时间尺度上，在单个蛋白质的运动是自相似的，非平衡的，并表现出老化。距离波动的特征弛豫时间，如域间运动，是观测时间依赖性的，增加一个简单的，幂律的方式，所产生的分形性质的拓扑结构和几何形状的能量景观探索。能量景观上的扩散遵循非遍历连续时间随机游走。与单分子实验的比较表明，非平衡自相似动力学行为持续到接近单个蛋白质分子体内寿命的时间尺度。
Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behaviour with effective relaxation times existing over many decades in time, from ps up to similar to 10(2) s (refs 1-4). Here, using molecular dynamics simulations, we show that, on timescales from 10(-12) to 10(-5) s, motions in single proteins are self-similar, non-equilibrium and exhibit ageing. The characteristic relaxation time for a distance fluctuation, such as inter-domain motion, is observation-time-dependent, increasing in a simple, power-law fashion, arising from the fractal nature of the topology and geometry of the energy landscape explored. Diffusion over the energy landscape follows a non-ergodic continuous time random walk. Comparison with single-molecule experiments suggests that the non-equilibrium self-similar dynamical behaviour persists up to timescales approaching the in vivo lifespan of individual protein molecules.