Laboratoire de Physique Théorique
Toulouse - UMR 5152

In this talk, I will present recent results dealing with facilitated diffusion and H-NS mediated compaction of bacterial DNA, which were obtained by investigating the properties of coarse-grained models. These models, where 15 DNA base pairs are represented by a single site and proteins by a few ones, lack most of the details of atomistic models and are not appropriate for investigating specific interactions between precise DNA sequences and proteins. In contrast, they are sufficient to model certain non-specific (mostly electrostatic) DNA/protein interactions and allow for the numerical integration of quite long trajectories for rather large systems.

Facilitated diffusion describes the alternation of 3D diffusion in the medium and 1D sliding along the DNA, by which some proteins, like transcription factors, search for their target in a DNA sequence. The question, which I will address in the first part of the talk, is whether coarse-grained models agree with or cast doubts on the popular belief according to which facilitated diffusion can accelerate the search speed by order(s) of magnitude.

H-NS is a small nucleoid-associated protein, which is involved in both gene regulation and bacterial DNA compaction. Despite the enormous effort of many research groups, there are several aspects of H-NS and H-NS/DNA interactions, which remain controversial or unknown. In the second part of the talk, I will discuss the light shed by coarse-grained models on the antagonistic effects on DNA compaction of H-NS binding to DNA in trans and cis configurations and on the possible consequences of the deposition of H-NS/DNA complexes on a surface.