Description of nonspecific DNA-protein interaction and facilitated diffusion with a dynamical model

We propose a dynamical model for nonspecific DNA-protein interaction, which is based on the "bead-spring" model previously developed by other groups, and investigate its properties using Brownian dynamics simulations. We show that the model successfully reproduces some of the observed properties of real systems and predictions of kinetic models. For example, sampling of the DNA sequence by the protein proceeds via a succession of three-dimensional motion in the solvent, one-dimensional sliding along the sequence, short hops between neighboring sites, and intersegmental transfers. Moreover, facilitated diffusion takes place in a certain range of values of the protein effective charge, that is, the combination of one-dimensional sliding and three-dimensional motion leads to faster DNA sampling than pure three-dimensional motion. At last, the number of base pairs visited during a sliding event is comparable to the values deduced from single-molecule experiments. We also point out and discuss some discrepancies between the predictions of this model and some recent experimental results as well as some hypotheses and predictions of kinetic models.