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2.8K Views
•
09:17 min
March 1st, 2022
DOI :
10.3791/63406-v
Chapters
0:04
Introduction
0:45
Construction of the Markov State Model from Atomic Molecular Dynamics Simulations
6:26
Conducting Coarse-Grained Simulation to Sample Long-Time Dynamics
6:57
Results: Structure-Based Simulation and Sampling of Transcription Factor Protein Movements
8:45
Conclusion
Transcript
该协议的目标是揭示蛋白质沿DNA的一维扩散的结构动力学,使用植物转录因子WRKY结构域蛋白作为示例系统。马尔可夫状态模型构建下的原子模拟揭示了蛋白质在原子细节下沿DNA的1-bp步进运动。而粗粒度模拟侧重于沿DNA的蛋白质过程扩散超过10个bps的采样。
首先,使用10微秒的全原子MD轨迹来平均向前提取10, 000帧,一个基本对步进路径。通过单击文件和保存坐标,在 VMD 中准备具有 10, 000 帧的过渡路径。然后,在“选定的原子”框中键入蛋白质或细胞核。
在
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Summary
该协议的目标是揭示蛋白质沿DNA的一维扩散的结构动力学,使用植物转录因子WRKY结构域蛋白作为示例系统。为此,已经实施了原子和粗粒度分子动力学模拟以及广泛的计算采样。
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