A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction. (7th January 2015)

• Record Type: Journal Article
• Authors: Johnson, J; Brackley, C A; Cook, P R; Marenduzzo, D
• Is Part Of: Journal of physics. Volume 27:Number 6(2015)
• Publication Date: 2015-01-07
• Subjects: bridging induced attraction -- polymer physics -- chromatin looping -- Brownian dynamics; Condensed matter -- Periodicals; Matière condensée -- Périodiques; Vaste stoffen; Vloeistoffen; Natuurkunde; Electronic journals; Computer network resources; 530.4105
• DOI: 10.1088/0953-8984/27/6/064119
• Languages: English
• ISSNs: 0953-8984

Abstract

Abstract: 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.