Dr. Davide Marenduzzo: Modelling DNA organisation by DNA-binding proteins
Povzetek:
Modelling DNA organisation by DNA-binding proteins: the bridging-induced attraction and in silico chromatin reconstitution
Dr. Davide Marenduzzo*, School of Physics & Astronomy, University of Edinburgh, UK
DNA in living cells of both bacteria and eukaryotes associates with proteins that continuously bind and dissociate. Some proteins affect local structure (such as histones and histone-like proteins), whereas others act globally to compact whole chromosomal segments (such as CCCTC-binding factors). Brownian dynamics simulations are used here to model both DNA and DNA-binding proteins. In the absence of any explicit interaction between proteins, or between templates, we find that binding of protein which are able to bridge the DNA, spontaneously induces local DNA compaction and protein aggregation. Small proteins interacting with naked DNA form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], and large proteins into quasi-spherical aggregates (as on nanoparticle binding). We also explore how these ideas apply to the self-assembly, or reconstitution,of chromatin, which can be made \textit{in vitro} from DNA and histone octamers, provided that appropriate experimental protocols are followed accurately.
* Collaborators: C. A. Brackley, J. Allan, D. Keszenman-Pereyra (Edinburgh); A. Papantonis (Cologne); S. Taylor, P. R. Cook (Oxford)
