55 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 examine the ‘motion’ of any specific residue of interest, including sites of post-translational histone modification. The database also includes DNA-histone contact points, DNA conformational parameters, and information about protein features, such as the secondary structure in the globular histone core and the ‘motion’ of the histone tails. Along with these features, we also characterize the dynamics of the global structure of the nucleosome core particle, including the changes in superhelical path of the DNA and the rearrangements of the histone tetramers. In addition to data obtained from crystallographically solved structures, we are working to incorporate data from in silico experiments. The data and the results of the analysis are available to the public as an automatically updated, online-accessible web server. Cartoon diagrams of crystal structures are shown with their reference frames aligned. The frames were computed by PCA of the globular core of the histone octamer. The anionic atoms of aspartic acid and glutamic acid are marked in light red. The cationic atoms of the arginines and lysines are marked in dark blue. Note the channels that the charges may occupy.     

Insights into gene expression and packaging from computer simulations

Within the nucleus of each cell lies DNA—an unfathomably long, twisted, and intricately coiled molecule—segments of which make up the genes that provide the instructions that a cell needs to operate. As we near the 60th anniversary of the discovery of the DNA double helix, crucial questions remain about how the physical arrangement of the DNA in cells affects how genes work. For example, how a cell stores the genetic information inside the nucleus is complicated by the necessity of maintaining accessibility to DNA for genetic processing. In order to gain insight into the roles played by various proteins in reading and compacting the genome, we have developed new methodologies to simulate the dynamic, three-dimensional structures of long, fluctuating, protein-decorated strands of DNA. Our a priori approach to the problem allows us to determine the effects of individual proteins and their chemical modifications on overall DNA structure and function. Here, we present our recent treatment of the communication between regulatory proteins attached to precisely constructed stretches of chromatin. Our simulations account for the enhancement in communication detected experimentally on chromatin compared to protein-free DNA of the same chain length, as well as the critical roles played by the cationic ‘tails’ of the histone proteins in this signaling. The states of chromatin captured in the simulations offer new insights into the ways that the DNA, histones, and regulatory proteins contribute to long-range communication along the genome.