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上海交通大学自然科学研究院最新成果:蛋白质在正常生理环境下动力学的非平衡态现象

洪亮课题组与合作者在不同时间尺度研究了蛋白质内部与其功能相关的大尺度动力学。发现常温常压下,蛋白质的大尺度运动会随着观测时间变长而减慢。这种现象从皮秒量级持续到~100秒量级,横跨10几个时间级数。这说明蛋白质的内部运动处于非平衡态。更重要的是大多数蛋白的生物功能时间短于100秒这个数量级,也就是说蛋白质的生物功能是在其非平衡状态下发生的。然而当今生物化学领域很多常用的公式都是基于平衡态的假设, 洪亮及合作者的工作给这些基本假设画上了问号。 这个工作被发表在【自然物理】(Nature Physics)。【自然物理】是物理学领域影响最高的期刊, 影响因子20.147。

参考文献:X. Hu, L. Hong, M. Smith, T. Neusius, X. Cheng, and J.C. Smith “The Dynamics of Single Protein Molecules is Nonequilibrium and Self-Similar over Thirteen Decades in Time.” Nature Physics

Internal motions of proteins are essential to their function. The time dependence of protein structural fluctuations is highly complex, manifesting subdiffusive, non-exponential behavior with effective relaxation times existing over many decades in time, from picosecond up to 102 s. 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 behavior persists up to timescales approaching the in vivo lifespan of individual protein molecules.【Nature Physics, http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys3553.html#access.】.

(左)PGK蛋白的大尺度功能运动 (右)功能运动的自相关函数随观测时间加长而减慢。