How nucleoid associated proteins stabilize supercoiled DNA

Nucleoid associated proteins (NAPs) play an important physical role in prokaryotic cells by manipulating the shape and structure of the DNA within the nucleoid. These NAPs bend or twist DNA, and there are indications that NAPs bind preferentially to DNA that is already locally deformed. We hypothesize that these binding behaviors and local deformations strongly impact the stability and structure of DNA.
We use coarse-grained simulation of NAPs and DNA that allow us to achieve the time and length scales where DNA supercoiling occurs. Supercoils are twist-induced structures that are the result of relaxing highly-twisted DNA by inducing higher degrees of bending and writhe. This model can capture experimentally observed supercoiling behavior, and also shows that NAPs that locally bend DNA enhance DNA supercoiling. We are able to show that NAPs tend to localize along the contour of the supercoil, and this binding preference is capable of stabilizing supercoils that form within the nucleoid. By tracking different energies within the system, such as the energy due to bending, extension, or excluded volume, we gain insights into what is driving this protein-mediated supercoiling.