Relaxation dynamics of nucleosomal DNA

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Proteins and water exhibit complex relaxation dynamics, including stretched exponential and power law behaviors.
• Nucleosomes, fundamental units of DNA packaging, involve intricate interactions between DNA and histone proteins.

Purpose of the Study:

• To investigate the dynamics of DNA-histone interactions within a yeast nucleosome using all-atom molecular dynamics.
• To characterize the relaxation dynamics of DNA in both bound and unbound states to histones.

Main Methods:

• Performed a 50 nanosecond (ns) all-atom molecular dynamics simulation of a yeast nucleosome.
• Explicitly modeled interactions between DNA, histone proteins, water, and ions.
• Conducted control simulations of protein-free DNA in B-form and superhelical conformations.

Main Results:

• Identified 14 DNA-histone interaction sites exhibiting anomalously slow power law relaxation up to 10 ns.
• Observed fast picosecond-scale exponential relaxation in DNA regions outside interaction sites.
• Demonstrated ubiquitous 1/f(alpha) noise (pink noise) in DNA dynamics, with alpha approaching 1 at histone-bound sites.

Conclusions:

• Protein-DNA interactions significantly alter DNA dynamics, inducing complex power law relaxation.
• The parameter alpha serves as a potential quantitative measure for protein-DNA interaction complexity.
• These findings offer new insights into the dynamic nature of chromatin and its regulation.