洞察由U-U和T-T不匹配在RNA和DNA复合体中的U-U和T-T不匹配形成的符合性合奏,来自基于结构的调查,NMR和分子动力学模拟
Ainan Geng1, Rohit Roy2, Stephanie Gu1
1Department of Biochemistry, Duke University School of Medicine, Durham, NC 27701, USA.
Journal of molecular biology
|May 9, 2025
概括
核酸中的 uracil-uracil 和 thymine-thymine 不匹配在纳米秒时间尺度上的摇摆形状之间动态互转. 这些无处不在的次微秒运动影响了核酸的可塑性和功能.
科学领域:
- 结构生物学 结构生物学
- 生物物理学的生物物理.
- 核酸化学的核酸化学
背景情况:
- 核酸基对表现出结构之间的动态相互转换,这对于分子识别,折叠和催化是至关重要的.
- 乌拉-乌拉 (U-U) 和氨酸-氨酸 (T-T) 不匹配可以存在两个几乎相同的能量摇摆形状,在剪切位移方面有所不同.
- 以前的研究表明,RNA U-U不匹配中存在动态互转,但U-U和T-T不匹配的普遍性仍然不清楚.
研究的目的:
- 为了研究RNA和DNA复杂体中U-U和T-T不匹配的摇摆动态.
- 为了确定这些不匹配是否无处不在地经历着形态转换.
- 阐明这些动态过程的时间尺度和能量格局.
主要方法:
- 核磁共振 (NMR) 光谱,包括非共振R1ρ放松分散.
- 蛋白质数据库 (PDB) 的基于结构的调查.
- 分子动力学 (MD) 模拟和分析X射线晶体学数据.
主要成果:
- 一项PDB的调查表明,U-U不匹配倾向于采用其他摇摆形状.
- 核磁共振放松分散实验没有检测到U-U或T-T不匹配的微到毫秒动态.
- 替代适应器精制,NOE,化学转移,RDC数据和MD模拟揭示了纳米秒时间尺度上两个摇摆形态之间的动态平衡,次要状态超过30%.
结论:
- U-U 和 T-T 不匹配无处不在地经历微秒以下的摇摆运动.
- 这些动态有助于核酸的能量格局和可塑性.
- 这些发现对涉及核酸不匹配的生物过程有重大影响.
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