title: A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction.
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.
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, UK.
authors.forename: J
authors.initials: J
authors.lastname: Johnson
authors.forename: C A
authors.initials: CA
authors.lastname: Brackley
authors.forename: P R
authors.initials: PR
authors.lastname: Cook
authors.forename: D
authors.initials: D
authors.lastname: Marenduzzo
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D015894:Genome, Human; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins