Abstract
The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same duplex. Based on scanning force microscopy imaging and optical trap-driven unzipping assays, it has recently been suggested that DNA compaction may result from the antagonistic effects of H-NS binding to DNA in trans and cis configurations. To get more insight into the compaction mechanism, we constructed a coarse-grained model description of the compaction of bacterial DNA by H-NS. These simulations highlight the fact that DNA compaction indeed results from the subtle equilibrium between several competing factors, which include the deformation dynamics of the plasmid and the several binding modes of protein dimers to DNA, i.e., dangling configurations, cis- and trans-binding. In particular, the degree of compaction is extremely sensitive to the difference in binding energies of the cis and trans configurations. Our simulations also point out that the conformations of the DNA-protein complexes are significantly different in bulk and in planar conditions, suggesting that conformations observed on mica surfaces may differ significantly from those that prevail in living cells.