  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. In
order 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.
