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生物分子凝聚物中的极端动力学。

Extreme dynamics in a biomolecular condensate.

机构信息

Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Department of Physics, University of Zurich, Zurich, Switzerland.

出版信息

Nature. 2023 Jul;619(7971):876-883. doi: 10.1038/s41586-023-06329-5. Epub 2023 Jul 19.

DOI:10.1038/s41586-023-06329-5
PMID:37468629
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11508043/
Abstract

Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular condensates. The functions of condensates span many length scales: they modulate interactions and chemical reactions at the molecular scale, organize biochemical processes at the mesoscale and compartmentalize cells. Understanding the underlying mechanisms of these processes will require detailed knowledge of the rich dynamics across these scales. The mesoscopic dynamics of biomolecular condensates have been extensively characterized, but their behaviour at the molecular scale has remained more elusive. Here, as an example of biomolecular phase separation, we study complex coacervates of two highly and oppositely charged disordered human proteins. Their dense phase is 1,000 times more concentrated than the dilute phase, and the resulting percolated interaction network leads to a bulk viscosity 300 times greater than that of water. However, single-molecule spectroscopy optimized for measurements within individual droplets reveals that at the molecular scale, the disordered proteins remain exceedingly dynamic, with their chain configurations interconverting on submicrosecond timescales. Massive all-atom molecular dynamics simulations reproduce the experimental observations and explain this apparent discrepancy: the underlying interactions between individual charged side chains are short-lived and exchange on a pico- to nanosecond timescale. Our results indicate that, despite the high macroscopic viscosity of phase-separated systems, local biomolecular rearrangements required for efficient reactions at the molecular scale can remain rapid.

摘要

蛋白质和核酸可以在细胞中相分离形成浓缩的生物分子凝聚物。凝聚物的功能跨越多个长度尺度:它们在分子尺度上调节相互作用和化学反应,在介观尺度上组织生化过程,并在细胞水平上分隔细胞。理解这些过程的潜在机制需要详细了解这些尺度上的丰富动力学。生物分子凝聚物的介观动力学已经得到了广泛的描述,但它们在分子尺度上的行为仍然更加难以捉摸。在这里,我们以两种高度带电和带相反电荷的人类无序蛋白质的复杂共凝聚物为例进行研究。它们的密集相比稀释相浓缩 1000 倍,由此产生的渗透相互作用网络导致其体粘度比水大 300 倍。然而,针对单个液滴内测量进行优化的单分子光谱学揭示,在分子尺度上,无序蛋白质仍然非常动态,其链构象在亚微秒时间尺度上相互转换。大规模的全原子分子动力学模拟再现了实验观察结果,并解释了这种明显的差异:单个带电侧链之间的基础相互作用是短暂的,在皮秒到纳秒的时间尺度上发生交换。我们的结果表明,尽管相分离系统的宏观粘度很高,但分子尺度上进行有效反应所需的局部生物分子重排仍可以保持快速。

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