  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., Proc. Natl. Acad. Sci. USA 110 (2013)], 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.
