  The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated
protein, which is involved in both gene regulation and DNA compaction. Although
it is a key player in genome organization by forming bridges between DNA
duplexes, the precise structure of complexes of DNA and H-NS proteins is still
not well understood. In particular, it is not clear whether the structure of
DNA/H-NS complexes in the living cell is similar to that of complexes deposited
on mica surfaces, which may be observed by AFM microscopy. A coarse-grained
model, which helps getting more insight into this question, is described and
analyzed in the present paper. This model is able of describing both the
bridging of bacterial DNA by H-NS in the bulk and the deposition and
equilibration of the complex on a charged surface. Simulations performed with
the model reveal that a slight attraction between DNA and the charged surface
is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar
plasmids bridged by H-NS proteins similar to those observed by AFM microscopy.
They furthermore highlight the antagonistic effects of the interactions between
DNA and the surface. Indeed, increasing these interactions slows down the
equilibration of naked plasmids on the surface but, on the other hand, enables
a faster equilibration of DNA/H-NS complexes. Based on the distribution of the
lifetimes of H-NS bridges and the time evolution of the number of trans-binding
protein dimers during equilibration of the complexes on the surface, it is
argued that the decrease of the equilibration time of the complex upon increase
of the interaction strength between DNA and the surface is ascribable to the
associated decrease of the probability to form new bridges between DNA and the
proteins.
