A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

J Johnson and CA Brackley and PR Cook and D Marenduzzo, JOURNAL OF PHYSICS-CONDENSED MATTER, 27, 064119 (2015).

DOI: 10.1088/0953-8984/27/6/064119

We present computer simulations of the phase behaviour of an ensemble of proteins interacting with a polymer, mimicking non-specific binding to a piece of bacterial DNA or eukaryotic chromatin. The proteins can simultaneously bind to the polymer in two or more places to create protein bridges. Despite the lack of any explicit interaction between the proteins or between DNA segments, our simulations confirm previous results showing that when the protein-polymer interaction is sufficiently strong, the proteins come together to form clusters. Furthermore, a sufficiently large concentration of bridging proteins leads to the compaction of the swollen polymer into a globular phase. Here we characterise both the formation of protein clusters and the polymer collapse as a function of protein concentration, protein-polymer affinity and fibre flexibility.

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