Determining Rotational Conformations of Substituted DNA Sequences On the Nucleosome Core Particle

摘要

Nucleosomes form preferentially over some chromosomal regions due in part to DNA-sequence dependence on the free-energy of nucleosome formation. This phenomenon is observed in competitive nucleosome reconstitution experiments. In addition, preferences for rotational orientation of the DNA have been observed. One or more rotational states may be preferred over a non-specific rotational orientation at a given position. The ability to select preferred rotational states among the others is of interest in computational modeling. Considerable insight has been obtained from structural and dynamical studies of high-resolution X-ray structures of nucleosomes. These atomic-level X-ray structures may be also used for studies of nucleosomes with custom DNA sequences. As a step toward enabling this modeling with arbitrary DNA sequences substituted onto the DNA sequence, we report our methodology for rotating a DNA helix on the nucleosome. We rotated the phosphate sugar backbone around the helical axis in three degree increments. Between rotations, the DNA backbone was allowed to reorient in the new position through a molecular dynamics simulations with constraints applied to other parts of the system. Periodically, the entire system was allowed to undergo unconstrained molecular dynamics to allow the DNA and protein to relax out of high-energy conformations. Each rotated structure was allowed to relax further after the rotations with a 200 picosecond run of molecular dynamics. In these relaxations, hydrogen bonded interactions between the DNA and histones increase considerable. Evaluation of the fitness of the rotational orientation can then be performed with a variety of methods.