Dps的结构和结合性质 - 一种核状相关蛋白质
Matty Gaines1,2, Daniel Parrell1,2, Kaylee Jo Rajek1
1Department of Biochemistry, University of Wisconsin, Madison, WI USA.
bioRxiv : the preprint server for biology
|November 26, 2025
概括
大肠杆菌中饥饿细胞 (Dps) 的DNA结合蛋白在pH值变化中保持其结构,但改变了DNA结合亲和力. 这种响应pH的行为影响了细菌基因组在压力下如何紧缩.
科学领域:
- 微生物学 微生物学
- 结构生物学 结构生物学
- 生物物理学的生物物理.
背景情况:
- Prokaryotic DNA 的紧缩依赖于与核相关的蛋白质 (NAP).
- 来自饥饿细胞的DNA结合蛋白 (Dps) 是具有铁氧化酶活性的关键NAP,形成十二体组件以保护压力下的基因组.
- 了解DPS的功能需要分析其在不同环境条件下的结构和结合动态.
研究的目的:
- 在广泛的pH范围 (3-11) 中研究大肠杆菌Dps的结构和生物物理特性.
- 阐明pH如何影响dps组装,DNA结合亲和力和基因组紧缩机制.
- 探索Dps作为细菌核组织中的pH响应因子的作用.
主要方法:
- 单粒子冷电子显微镜 (cryo-EM) 用于高分辨率的结构分析 (~1.75 Å).
- 适应式Poisson-Boltzmann静电建模用于预测表面电荷分布.
- 电泳运动转移试验 (EMSAs) 用于量化DNA结合亲和力.
- 低温电子断层扫描 (cryo-ET) 用于可视化Dps-DNA复合体的形成.
主要成果:
- 在测试的pH范围 (3-11) 中,Dps的正规费里类折叠保持稳定.
- 表面静电学随着pH值的增加而从正变为负,显著调节DNA结合亲和力 (EC50值在pH5的73.4nM到pH11的815.5nM之间).
- Dps形成无形的~50纳米球状或管状复合体,具有短的DNA片段,与具有较长DNA支架的格子共晶形成鲜明对比.
结论:
- Dps作为细菌核体紧缩的pH敏感调节器起作用.
- 提出了一种两阶段的组装模型:在N-终端溶酶上以质子驱动的核化,然后在扩展的DNA上进行晶格排序.
- 这些发现凸显了DPs在适应基因组组织以适应环境pH波动方面的动态性质.
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