在全原子模拟中观察到的非本地纠蛋白错折,并得到实验结构组合的支持
Quyen V Vu1,2, Ian Sitarik2, Yang Jiang2
1Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
Science advances
|August 8, 2025
概括
蛋白质错误折叠可以通过拉索纠发生,作为动力陷. 这些状态在模拟和实验中持续存在,特别是在像IspE这样的大型蛋白质中.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 蛋白质折叠的动态 蛋白质折叠的动态
背景情况:
- 蛋白质错误折叠是各种疾病的已知原因之一.
- 粗粒度模拟表明了一种新的错折路径,涉及非共价拉索纠.
- 这些拉索纠是长期存在的动力陷,类似于本地蛋白质结构.
研究的目的:
- 在全原子蛋白质折叠模拟中调查拉索纠错折状态的发生和稳定性.
- 为了验证,将模拟结果与实验数据进行比较.
主要方法:
- 乌比奎和兰巴达抑制剂的长时间全原子分子动力学模拟.
- 较大的蛋白质IspE.E的粗粒模拟.
- 阿雷尼乌斯推断来估计错误折叠状态的寿命.
- 对有限的蛋白质解和交联质谱数据的分析.
主要成果:
- 在高分辨率模型中观察到纠错折状态,但在小蛋白质 (ubiquitin,lambda-repressor) 中寿命短暂.
- 粗粒度模拟预测了较大的蛋白质IspE.长期存在的错误折叠状态.
- 估计的IspE错误折叠状态具有与原生相似的寿命和可溶性.
- 错误折叠的状态与质谱学实验数据一致.
结论:
- 非原生拉索纠代表了蛋白质中持续的错误折叠状态.
- 这些错误折叠状态可以长期存在,特别是在较大的蛋白质中.
- 这些发现得到了计算模拟和实验证据的支持.
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