MUT-16支架蛋白相分离和客户端识别的多尺度模拟。

IF 3.1 3区 生物学 Q2 BIOPHYSICS
Kumar Gaurav, Virginia Busetto, Diego Javier Páez-Moscoso, Arya Changiarath, Sonya M Hanson, Sebastian Falk, René F Ketting, Lukas S Stelzl
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引用次数: 0

摘要

蛋白质的相分离在细胞组织中起着至关重要的作用。相分离的蛋白质凝聚物如何支撑生物功能以及凝聚物如何实现特异性仍然是难以捉摸的。我们研究了Mutator focal中的支架蛋白MUT-16的相分离及其在募集客户蛋白MUT-8中的作用,MUT-8是线虫RNA沉默的关键成分。我们采用了一种多尺度方法,结合了粗粒度(残留物级CALVADOS2和近原子的Martini3)和原子模拟。不同分辨率下的模拟为mut16凝析油如何吸收mut8提供了一致的视角,从而在平衡计算成本的同时实现了化学细节的微调。两个粗粒度模型(CALVADOS2和Martini3)都预测了mut16无序区的相对相分离倾向,我们通过体外实验证实了这一点。模拟还发现了关键序列特征和驱动相分离的残基,同时揭示了CALVADOS2和Martini3之间残基相互作用倾向的差异。此外,对MUT-8的n端朊病毒样结构域与MUT-16 M8BR簇的Folding@Home进行了Martini3和350 μs原子模拟,强调了MUT-8的Tyr残基与MUT-16 M8BR的Arg残基之间阳离子-π相互作用的重要性。在Martini3中观察到赖氨酸残基更容易相互作用。原子模拟表明,Arg的胍基也参与了与Tyr骨架的sp2-π相互作用和氢键,这可能是Arg-Tyr的相互作用强度大于Lys-Tyr的原因,在Lys-Tyr中,这些额外的有利接触是不存在的。与我们的模拟结果一致,体外共表达下拉实验表明,在MUT-16 M8BR中Arg突变为Lys或Ala后,MUT-8募集逐渐减少,证实了Arg在这种相互作用中的关键作用。这些发现促进了我们对mutt -16相分离和随后的mutt -8募集的理解,这是在秀丽隐杆线虫中组装驱动RNA沉默的Mutator焦点的关键过程。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition.

Phase separation of proteins plays a critical role in cellular organization. How phase-separated protein condensates underpin biological function and how condensates achieve specificity remain elusive. We investigated the phase separation of MUT-16, a scaffold protein in Mutator foci, and its role in recruiting the client protein MUT-8, a key component in RNA silencing in Caenorhabditis elegans. We employed a multi-scale approach that combined coarse-grained (residue-level CALVADOS2 and near-atomistic Martini3) and atomistic simulations. Simulations across different resolutions provide a consistent perspective on how MUT-16 condensates recruit MUT-8, enabling the fine-tuning of chemical details and balancing the computational cost. Both coarse-grained models (CALVADOS2 and Martini3) predicted the relative phase-separation propensities of MUT-16's disordered regions, which we confirmed through in vitro experiments. Simulations also identified key sequence features and residues driving phase separation and revealed differences in residue interaction propensities between CALVADOS2 and Martini3. Furthermore, Martini3 and 350-μs atomistic simulations on Folding@Home of MUT-8's N-terminal prion-like domain with MUT-16 M8BR cluster highlighted the importance of cation-π interactions between Tyr residues of MUT-8 and Arg residues of MUT-16 M8BR. Lys residues were observed to be more prone to interact in Martini3. Atomistic simulations revealed that the guanidinium group of Arg also engages in sp2-π interactions and hydrogen bonds with the backbone of Tyr, possibly contributing to the greater strength of Arg-Tyr interactions compared to Lys-Tyr, where these additional favorable contacts are absent. In agreement with our simulations, in vitro co-expression pull-down experiments demonstrated a progressive loss of MUT-8 recruitment after the mutation of Arg in MUT-16 M8BR to Lys or Ala, confirming the critical role of Arg in this interaction. These findings advance our understanding of MUT-16 phase separation and subsequent MUT-8 recruitment, key processes in assembling Mutator foci that drive RNA silencing in C. elegans.

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来源期刊
Biophysical journal
Biophysical journal 生物-生物物理
CiteScore
6.10
自引率
5.90%
发文量
3090
审稿时长
2 months
期刊介绍: BJ publishes original articles, letters, and perspectives on important problems in modern biophysics. The papers should be written so as to be of interest to a broad community of biophysicists. BJ welcomes experimental studies that employ quantitative physical approaches for the study of biological systems, including or spanning scales from molecule to whole organism. Experimental studies of a purely descriptive or phenomenological nature, with no theoretical or mechanistic underpinning, are not appropriate for publication in BJ. Theoretical studies should offer new insights into the understanding ofexperimental results or suggest new experimentally testable hypotheses. Articles reporting significant methodological or technological advances, which have potential to open new areas of biophysical investigation, are also suitable for publication in BJ. Papers describing improvements in accuracy or speed of existing methods or extra detail within methods described previously are not suitable for BJ.
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