Polymer compaction and bridging-induced clustering of protein-inspired patchy particles
C A Brackley
Abstract
Abstract There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro , and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo . In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the ‘bridging-induced attraction’. The latter is a mechanism observed in previous simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA 110 E3605], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein–protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple ‘patchy particles’ interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.