转录因子PhoB在DNA结合时的侧链形状变化:一个人口转移机制
Tsutomu Yamane1, Hideyasu Okamura, Yoshifumi Nishimura
1Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan.
分子动力学模拟显示了转录因子PhoBB的明显灵活性.
科学领域:
- 结构生物学是结构生物学.
- 计算生物物理学的计算生物物理.
背景情况:
- 转录因子PhoB的DNA结合/交换活化域在DNA结合时具有小的脊柱形状变化.
- 了解疏水核中的侧链动态对于蛋白质功能至关重要.
研究的目的:
- 在DNA结合过程中调查PhoB的疏水核中的侧链形状变化.
- 将分子动力学 (MD) 模拟与NMR放松顺序参数相关联.
主要方法:
- 分子动力学 (MD) 模拟.分子动力学 (MD) 模拟.
- 分析NMR放松顺序参数 (包括正常化顺序参数).
- 甲基组配置的主要成分分析 (PCA).
主要成果:
- MD模拟准确地重现了实验顺序参数.
- 规范化的顺序参数显示了PhoB的"软"和"硬"疏水芯之间的明显灵活性.
- "软"核表现出更高的灵活性,在DNA结合时减少.
- PCA显示了"软"核心的动态配置变化,在DNA相互作用时转向结合配置.
结论:
- 侧链动态,特别是在"软"核心,对于PhoB的DNA结合机制至关重要.
- DNA 结合诱导"软"核心的种群转移,限制侧链动态.
- 规范化顺序参数有效地捕捉侧链动态,克服拓效应.
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