  The chromosomal DNA of bacteria is folded into a compact body called the
nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number
of different proteins (10%). These nucleoid proteins act as regulators of gene
expression and influence the organization of the nucleoid by bridging, bending,
or wrapping the DNA. These so-called architectural properties of nucleoid
proteins are still poorly understood. For example, the reason why certain
proteins compact the DNA coil in certain environments but make instead the DNA
more rigid in other environments is the matter of ongoing debates. Here, we
address the question of the impact of the self-association of nucleoid proteins
on their architectural properties and try to determine whether differences in
self-association are sufficient to induce large changes in the organization of
the DNA coil. More specifically, we developed two coarse-grained models of
proteins, which interact identically with the DNA but self-associate
differently by forming either clusters or filaments in the absence of the DNA.
We showed through Brownian dynamics simulations that self-association of the
proteins increases dramatically their ability to shape the DNA coil. Moreover,
we observed that cluster-forming proteins compact significantly the DNA coil
(similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming
proteins increase instead significantly the stiffness of the DNA chain (similar
to the DNA-stiffening mode of H-NS proteins). This work consequently suggests
that the knowledge of the DNA-binding properties of the proteins is in itself
not sufficient to understand their architectural properties. Rather, their
self-association properties must also be investigated in detail, because they
might actually drive the formation of different DNA/protein complexes.
