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

摘要

We propose a dynamical model for non-specific DNA-protein interaction, whichis based on the 'bead-spring' model previously developed by other groups, andinvestigate its properties using Brownian Dynamics simulations. We show thatthe model successfully reproduces some of the observed properties of realsystems and predictions of kinetic models. For example, sampling of the DNAsequence by the protein proceeds via a succession of 3d motion in the solvent,1d sliding along the sequence, short hops between neighboring sites, andintersegmental transfers. Moreover, facilitated diffusion takes place in acertain range of values of the protein effective charge, that is, thecombination of 1d sliding and 3d motion leads to faster DNA sampling than pure3d motion. At last, the number of base pairs visited during a sliding event iscomparable to the values deduced from single-molecule experiments. We alsopoint out and discuss some discrepancies between the predictions of this modeland some recent experimental results as well as some hypotheses and predictionsof kinetic models.