Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view

TL;DR

This study uses a coarse-grained model to investigate how DNA and H-NS protein complexes equilibrate on charged surfaces, revealing the effects of surface interactions on their structure and dynamics, with implications for understanding genome organization.

Contribution

The paper introduces a coarse-grained simulation model that captures the formation and surface deposition of DNA/H-NS complexes, providing new insights into their structural reorganization.

Findings

Slight attraction to charged surfaces reorganizes DNA/H-NS complexes into planar structures.

Increased DNA-surface interactions slow naked plasmid equilibration but speed up DNA/H-NS complex equilibration.

Higher surface interaction strength reduces bridge formation probability, decreasing complex equilibration time.

Abstract

The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins.