Role of salt valency in the switch of H-NS proteins between DNA-bridging and DNA-stiffening modes

TL;DR

This study uses computer simulations to understand how multivalent cations influence H-NS proteins to switch from DNA-stiffening to DNA-bridging modes, revealing a threshold mechanism based on cation valency.

Contribution

It introduces a coarse-grained model that explains the salt-dependent switch in H-NS protein modes, highlighting the role of cation valency in DNA binding behavior.

Findings

Multivalent cations decrease H-NS/DNA interaction strength.

Above a certain cation valency threshold, H-NS forms 3D clusters for DNA bridging.

Below the threshold, H-NS forms filaments that stiffen DNA.

Abstract

This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer, but is still not understood. Unravelling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties. The simulations reported here support a mechanism, according to which the primary role of multivalent cations consists in decreasing the strength of H-NS/DNA interactions compared to H-NS/H-NS interactions, with the latter ones becoming energetically favored with respect to the former ones above a certain threshold of the effective valency of the cations of the buffer. Below the threshold, H-NS dimers form filaments, which stretch along the DNA molecule but are quite inefficient in bridging genomically distant DNA sites (DNA-stiffening mode). In contrast, just above the threshold, H-NS dimers form 3-dimensional clusters, which are able to connect DNA sites that are distant from the genomic point of view (DNA-bridging mode). The model provides clear rationales for the experimental observations that the switch between the two modes is a threshold effect and that the ability of H-NS dimers to form higher order oligomers is crucial for their bridging capabilities.