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可视化液-液相转变。

Visualizing liquid-liquid phase transitions.

作者信息

Sahoo Bikash R, Deng Xiexiong, Wong Ee Lin, Clark Nathan, Yang Harry, Subramanian Vivekanandan, Guzman Bryan B, Harris Sarah E, Dehury Budheswar, Miyashita Emi, Hoff J Damon, Kocaman Vojč, Saito Hirohide, Dominguez Daniel, Plavec Janez, Bardwell James C A

机构信息

Howard Hughes Medical Institute.

Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI-48109, USA.

出版信息

bioRxiv. 2024 Oct 28:2023.10.09.561572. doi: 10.1101/2023.10.09.561572.

DOI:10.1101/2023.10.09.561572
PMID:39554013
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11565804/
Abstract

Liquid-liquid phase condensation governs a wide range of protein-protein and protein-RNA interactions in vivo and drives the formation of membrane-less compartments such as the nucleolus and stress granules. We have a broad overview of the importance of multivalency and protein disorder in driving liquid-liquid phase transitions. However, the large and complex nature of key proteins and RNA components involved in forming condensates such as stress granules has inhibited a detailed understanding of how condensates form and the structural interactions that take place within them. In this work, we focused on the small human SERF2 protein. We show here that SERF2 contributes to the formation of stress granules. We also show that SERF2 specifically interacts with non-canonical tetrahelical RNA structures called G-quadruplexes, structures which have previously been linked to stress granule formation. The excellent biophysical amenability of both SERF2 and RNA G4 quadruplexes has allowed us to obtain a high-resolution visualization of the multivalent protein-RNA interactions involved in liquid-liquid phase transitions. Our visualization has enabled us to characterize the role that protein disorder plays in these transitions, identify the specific contacts involved, and describe how these interactions impact the structural dynamics of the components involved in liquid-liquid phase transitions, thus enabling a detailed understanding of the structural transitions involved in early stages of ribonucleoprotein condensate formation.

摘要

液-液相凝聚在体内调控着广泛的蛋白质-蛋白质和蛋白质-RNA相互作用,并驱动无膜区室的形成,如核仁与应激颗粒。我们对多价性和蛋白质无序在驱动液-液相转变中的重要性有了广泛的认识。然而,参与形成应激颗粒等凝聚物的关键蛋白质和RNA组分的庞大且复杂的性质,阻碍了我们对凝聚物如何形成以及其中发生的结构相互作用的详细理解。在这项工作中,我们聚焦于人类的小分子SERF2蛋白。我们在此表明,SERF2有助于应激颗粒的形成。我们还表明,SERF2特异性地与一种名为G-四链体的非经典四螺旋RNA结构相互作用,这种结构此前已被证明与应激颗粒的形成有关。SERF2和RNA G4四链体出色的生物物理适应性,使我们能够对液-液相转变中涉及的多价蛋白质-RNA相互作用进行高分辨率可视化。我们的可视化使我们能够表征蛋白质无序在这些转变中所起的作用,确定其中涉及的特定接触,并描述这些相互作用如何影响液-液相转变中相关组分的结构动力学,从而使我们能够详细了解核糖核蛋白凝聚物形成早期阶段所涉及的结构转变。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8324c3be33bb/nihpp-2023.10.09.561572v2-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/5da3b14c2635/nihpp-2023.10.09.561572v2-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8ebeb143abbe/nihpp-2023.10.09.561572v2-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/e9b44580ed77/nihpp-2023.10.09.561572v2-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8e78f5f96284/nihpp-2023.10.09.561572v2-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/d9eaa5048e3e/nihpp-2023.10.09.561572v2-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8324c3be33bb/nihpp-2023.10.09.561572v2-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/5da3b14c2635/nihpp-2023.10.09.561572v2-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8ebeb143abbe/nihpp-2023.10.09.561572v2-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/e9b44580ed77/nihpp-2023.10.09.561572v2-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8e78f5f96284/nihpp-2023.10.09.561572v2-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/d9eaa5048e3e/nihpp-2023.10.09.561572v2-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3160/11565804/8324c3be33bb/nihpp-2023.10.09.561572v2-f0006.jpg

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本文引用的文献

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Nat Commun. 2024 Jul 19;15(1):6104. doi: 10.1038/s41467-024-50575-8.
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CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.用于建模和模拟复杂多组分系统的 CHARMM-GUI 多组分组装器。
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Biomolecular condensates form spatially inhomogeneous network fluids.生物分子凝聚体能在空间上形成不均匀的网络流体。
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GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.GENESIS CGDYN:用于异质生物分子系统的具有动态负载平衡的大规模粗粒度 MD 模拟。
Nat Commun. 2024 Apr 20;15(1):3370. doi: 10.1038/s41467-024-47654-1.
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Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation.蛋白 G-四链体相互作用及其对相变和蛋白质聚集的影响。
Nucleic Acids Res. 2024 May 8;52(8):4702-4722. doi: 10.1093/nar/gkae229.
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Expanding the molecular language of protein liquid-liquid phase separation.扩展蛋白质液-液相分离的分子语言。
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