Nucleoid-associated proteins are crucial in compacting prokaryotic DNA, but how they generate higher-order structures is unclear. Integration host factor, IHF, is a key nucleoid-associated protein in bacteria, creating sharp bends in DNA. We show that the IHF–DNA complex structural multimodality is far more elaborate than previously proposed and provide insights into how this enables mechanical molecular switching. Using single-molecule atomic force microscopy and all-atom molecular dynamics simulations we find three topological modes in roughly equal proportions: “associated” (73° of DNA bend), “half-wrapped” (107°) and “fully-wrapped” (147°), with only the latter occurring with sequence specificity. DNA bridging is seen in the presence of multiple binding sites, with simulations showing this occurs through another recognition mode that does not depend on sequence and gives IHF a stoichiometry greater than one. We present a model of these states and propose a crucial biological role for these observed behaviors.
S Yoshua, G Watson, J Howard, V Velasco-Berrelleza, MC Leake, A Noy* (2020). “A nucleoid-associated protein bends and bridges DNA in a multiplicity of topological states with varying specificity” bioRxiv. https://doi.org/10.1101/2020.04.17.047076