Molecular Basis of DNA Packaging in Bacteria Revealed by All-Atoms Molecular Dynamic Simulations: The case of histone like proteins in Borrelia burgdoferi.

DNA compaction is essential to ensure the packaging of the genetic material in living cells, and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, DNA packaging is achieved by specific well-conserved proteins. Here by means of all-atom molecular dynamics simulations, including the determination of relevant free energy profiles, we rationalize the molecular bases for this remarkable process in bacteria, illustrating the crucial role played by positively charged amino acids of a small histone-like protein. We also present compelling evidence that this histone-like protein alone can induce strong bending of a DNA duplex around its core domain, a process that requires overcoming a major free energy barrier.