Dynamics of the Nucleosome Core Particle Revealed from a New Database of High-Resolution X-Ray Crystallographic and Simulated Structures

The nucleosome core particle is a highly conserved structure which can play diverse roles depending on the organism, cell, or part of chromatin in which it resides. The Protein Data Bank currently contains approximately 70 nucleosome core particle structures, over half of which were determined in the last three years. The recent emergence of the field of epigenetics, and the increase in data available from experiments, warrants a need to develop new approaches to quantitatively compare various features of interest across multiple structures. As a first step, we have developed a database and new computational tools to allow researchers to quantitatively analyze and compare the nucleosome core particle structures deposited in the Protein Data Bank. The features of the DNA-protein assembly can be examined in novel coordinate frames placed on the structure, allowing researchers to obtain a better understanding of the organization and subtleties of the macomolecular complexes. This comparison allows one to exa...