Analysis of nucleosome structures based on molecular dynamics

In this paper, we present a method to analyze the molecular structure and dynamics of nucleosomes, which are the basic unit in eukaryotic cells. In nucleosomal DNA chains, periodic dinucleotides are key patterns in protein-DNA interactions. This paper aims at revealing the significances of these periodic dinucleotides in the nucleosomal DNA motions. Normal mode analysis (NMA) is used to detect significant structural deformations of nucleosomal DNA. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently.