DNA and chromosomes in living cells of both bacteria and eukaryotes associate wit 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).
I will first show and discuss some results from Brownian dynamics simulations which include both DNA and its associating proteins. We will show that non-specific proteins have a generic tendency to cluster, and discuss the relevance of this finding to DNA in vivo. We will then present simulations of chromatin and chromosome folding in mammalian nuclei, in the presence of proteins with a sequence-dependent affinity for the chromatin fibre. While our simulations are based simply on 1D bioinformatic data on the DNA-protein binding landscape, they can accurately predict contact maps and 3D chromosome conformations, as assessed experimentally via chromosome conformation capture techniques (such as Hi-C and Capture-C).