Atomistic simulation of interactions between DNA and integration host factor

The prokaryotic genome is structured by many proteins known collectively as nucleoid-associated proteins (NAPs), which have many functions relevant to gene regulation; among them is integration host factor (IHF), a DNA-binding protein which induces some of the sharpest DNA bends found in nature. This thesis presents the results of advanced all-atom molecular dynamics simulations of the IHF–DNA complex. These simulations confirm previous observations that IHF bends DNA in multiple states with distinct bend angles, finding three states with varying sequence specificity, and provide for the first time their structures in atomistic detail. These include an “associated” state corresponding to a DNA bend of 66° and a “half-wrapped” state with a 115° bend angle, in addition to the previously known “fully wrapped” (157°) state, and agree with data from complementary atomic force microscopy (AFM) experiments. These states differ primarily in the position of the DNA “arms” on each side of the protein’s binding site; by performing advanced simulations using a modified potential to improve sampling of the conformation space and applying the weighted histogram analysis method, the free-energy landscape for binding of each arm is obtained and a remarkable asymmetry and interdependence are observed, explaining the three binding modes. This technique also reveals that the bridging of two pieces of DNA by IHF is highly energetically favourable, explaining the formation of large DNA–IHF clusters and the role of IHF in stabilising biofilms associated with bacterial infections. Simulations of DNA minicircles illustrate the complex interplay between DNA topology and DNA bending, finding that supercoiling—a change in the number of turns in the double helix—changes the distribution of IHF binding states and bend angles, while IHF binding consistently controls the minicircle conformation, always being positioned at the apex of plectonemes.