基于widom603 DNA序列的核小体核心粒子的结构和动力学

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Structure Pub Date : 2025-03-17 DOI:10.1016/j.str.2025.02.007

Grigoriy A. Armeev, Andrey V. Moiseenko, Nikita A. Motorin, Dmitriy A. Afonin, Lei Zhao, Veniamin A. Vasilev, Pavel D. Oleinikov, Grigory S. Glukhov, Georgy S. Peters, Vasily M. Studitsky, Alexey V. Feofanov, Alexey K. Shaytan, Xiangyan Shi, Olga S. Sokolova

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引用次数: 0

摘要

核小体是染色质组织的基本元素，参与压缩基因组DNA，并作为许多调节蛋白结合的靶标。目前，已知的核小体结构超过500种。尽管有大量的核小体结构，但它们都是在大约20种不同的DNA序列上形成的。利用低温电子显微镜，我们以4 Å分辨率确定了在高亲和度的widom603 DNA序列上形成的核小体的结构；建立了一个原子模型。我们提出了一种基于低温电子显微镜（cryo-EM）数据的综合建模方法来研究核小体DNA展开。我们还利用小角度x射线散射和单粒子Förster共振能量转移测量证明了widom603核小体的DNA展开。我们的结果与核小体DNA展开的不对称性是一致的。我们的数据揭示了核小体结构和动力学对核小体DNA序列的依赖性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence

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Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence

Nucleosomes are fundamental elements of chromatin organization that participate in compacting genomic DNA and serve as targets for the binding of numerous regulatory proteins. Currently, over 500 different nucleosome structures are known. Despite the large number of nucleosome structures, all of them were formed on only about twenty different DNA sequences. Using cryo-electron microscopy, we determined the structure of the nucleosome formed on a high-affinity Widom 603 DNA sequence at 4 Å resolution; an atomic model was built. We proposed an integrative modeling approach to study the nucleosomal DNA unwrapping based on the cryoelectron microscopy (cryo-EM) data. We also demonstrated the DNA unwrapping of the Widom 603 nucleosome using small angle X-ray scattering and single particle Förster resonance energy transfer measurements. Our results are consistent with the asymmetry of nucleosomal DNA unwrapping. Our data revealed the dependence of nucleosome structure and dynamics on the sequence of nucleosomal DNA.

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来源期刊

Structure 生物-生化与分子生物学

CiteScore

8.90

自引率

1.80%

发文量

155

审稿时长

3-8 weeks

期刊介绍： Structure aims to publish papers of exceptional interest in the field of structural biology. The journal strives to be essential reading for structural biologists, as well as biologists and biochemists that are interested in macromolecular structure and function. Structure strongly encourages the submission of manuscripts that present structural and molecular insights into biological function and mechanism. Other reports that address fundamental questions in structural biology, such as structure-based examinations of protein evolution, folding, and/or design, will also be considered. We will consider the application of any method, experimental or computational, at high or low resolution, to conduct structural investigations, as long as the method is appropriate for the biological, functional, and mechanistic question(s) being addressed. Likewise, reports describing single-molecule analysis of biological mechanisms are welcome. In general, the editors encourage submission of experimental structural studies that are enriched by an analysis of structure-activity relationships and will not consider studies that solely report structural information unless the structure or analysis is of exceptional and broad interest. Studies reporting only homology models, de novo models, or molecular dynamics simulations are also discouraged unless the models are informed by or validated by novel experimental data; rationalization of a large body of existing experimental evidence and making testable predictions based on a model or simulation is often not considered sufficient.