Universität zu Köln

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:	Creators Email ORCID ORCID Put Code Brackley, Chris A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Taylor, Stephen UNSPECIFIED UNSPECIFIED UNSPECIFIED Papantonis, Argyris UNSPECIFIED orcid.org/0000-0001-7551-1073 UNSPECIFIED Cook, Peter R. UNSPECIFIED UNSPECIFIED UNSPECIFIED Marenduzzo, Davide UNSPECIFIED orcid.org/0000-0003-3974-4915 UNSPECIFIED
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:	Keywords Language MOLECULAR-DYNAMICS; ESCHERICHIA-COLI; CHROMATIN; TRANSCRIPTION; POLYELECTROLYTE; NANOPARTICLES; COMPACTION; IMINE); GENES; MODEL Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/47585