Using a hybrid model to simulate protein-DNA interactions

Our goal is to devise a model to represent the interactions between proteins and DNA during computational simulations. We propose a hybrid model where the protein is represented through an atomistic model and DNA is represented through a coarse-grained model, in particular the Oxford oxDNA model. We have used the system composed by a single nucleotide and a glycine molecule to parameterize the coarse-grained model by comparing it to an atomistic reference. Once parameterization was complete, we tested our model by using Brownian Dynamics simulations on a 11 base pair long strand of rigid DNA and the protein colicin E7 (NColE7) from Escherichia coli. Our model seems to closely resemble its atomistic reference, which may make it useful for looking at other protein-DNA systems that are more computationally challenging to investigate.