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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
Published on: March 9, 2022
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Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome
Mehmet Ali Öztürk1, Georgi V Pachov2, Rebecca C Wade3
1Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg 69118, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg 69120, Germany.
Nucleic Acids Research
|June 9, 2016
Summary
Linker histones (gH5) exhibit dynamic conformational changes, influencing chromatosome structure and DNA binding. These dynamics reveal alternative binding modes and configurations essential for DNA compaction.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- Linker histones are crucial for DNA compaction within chromatin.
- They bind nucleosomes to form chromatosomes, with proposed alternative configurations for histone H5 (gH5).
- The dynamic assembly pathways of chromatosomes remain poorly understood.
Purpose of the Study:
- To investigate the conformational plasticity of unbound and nucleosome-bound globular histone H5 (gH5).
- To elucidate the dynamic pathways and alternative configurations of chromatosome assembly.
Main Methods:
- Classical and accelerated molecular dynamics simulations of gH5.
- Brownian dynamics simulations of chromatosome assembly.
- Analysis of nucleosome opening amplitudes and DNA sequences.
Main Results:
- Unbound gH5 transitions between open and closed conformations, favoring the closed form.
- Open gH5 increases chromatosome rigidity and restricts linker DNA motion via thymidine interactions.
- Closed gH5 can open and reorient within the chromatosome.
- Simulations support both on- and off-dyad gH5 binding modes, revealing sequence and conformation-dependent configurations.
Conclusions:
- Conformational dynamics of linker histones and nucleosomes enable alternative chromatosome structures.
- Chromatosome assembly involves an interplay of induced fit and conformational selection.
- These findings provide insights into the mechanisms of DNA compaction and gene regulation.
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