Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

Journal article

Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites...

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Authors: Brackley, C; Taylor, S; Papantonis, A; Cook, P; Marenduzzo, D

• Publication status: Published
• Journal: Proceedings of the National Academy of Sciences of the United States of America
• Volume: 110
• Issue: 38
• Pages: E3605-E3611
• Publication date: 2013-09-01
• DOI: 10.1073/pnas.1302950110
• EISSN: 1091-6490
• ISSN: 0027-8424
• Language: English
• Keywords: Binding Sites; Humans; DNA; Models, Molecular; DNA-Binding Proteins; Chromatin; Protein Binding; Nucleic Acid Conformation; NF-kappa B; Chromosomes, Human; Molecular Dynamics Simulation; Multiprotein Complexes; RNA Polymerase II