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基于结构的转录因子蛋白沿DNA从原子级步进到粗晶扩散运动的模拟和采样
JoVE Journal
Biology
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JoVE Journal Biology
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
DOI:

09:17 min

March 01, 2022

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Chapters

  • 00:04Introduction
  • 00:45Construction of the Markov State Model from Atomic Molecular Dynamics Simulations
  • 06:26Conducting Coarse-Grained Simulation to Sample Long-Time Dynamics
  • 06:57Results: Structure-Based Simulation and Sampling of Transcription Factor Protein Movements
  • 08:45Conclusion

Summary

Automatic Translation

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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