Brackley, Chris A., Taylor, Stephen, Papantonis, Argyris ORCID: 0000-0001-7551-1073, Cook, Peter R. and Marenduzzo, Davide ORCID: 0000-0003-3974-4915 (2013). Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc. Natl. Acad. Sci. U. S. A., 110 (38). S. E3605 - 7. WASHINGTON: NATL ACAD SCIENCES. ISSN 0027-8424

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Abstract

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 (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NF kappa B) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Brackley, Chris A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Taylor, StephenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Papantonis, ArgyrisUNSPECIFIEDorcid.org/0000-0001-7551-1073UNSPECIFIED
Cook, Peter R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Marenduzzo, DavideUNSPECIFIEDorcid.org/0000-0003-3974-4915UNSPECIFIED
URN: urn:nbn:de:hbz:38-475851
DOI: 10.1073/pnas.1302950110
Journal or Publication Title: Proc. Natl. Acad. Sci. U. S. A.
Volume: 110
Number: 38
Page Range: S. E3605 - 7
Date: 2013
Publisher: NATL ACAD SCIENCES
Place of Publication: WASHINGTON
ISSN: 0027-8424
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
MOLECULAR-DYNAMICS; ESCHERICHIA-COLI; CHROMATIN; TRANSCRIPTION; POLYELECTROLYTE; NANOPARTICLES; COMPACTION; IMINE); GENES; MODELMultiple languages
Multidisciplinary SciencesMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/47585

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