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

TL;DR

This paper introduces a dynamical model for non-specific DNA-protein interactions, demonstrating how facilitated diffusion enhances DNA sampling efficiency and aligns with experimental observations through Brownian Dynamics simulations.

Contribution

It presents a new dynamical model based on the bead-spring approach that reproduces key properties of DNA-protein interactions and explores facilitated diffusion mechanisms.

Findings

Facilitated diffusion accelerates DNA sampling compared to pure 3D motion.

The model's predictions align with single-molecule experimental data.

Discrepancies between model predictions and some experimental results are discussed.

Abstract

We propose a dynamical model for non-specific 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 3d motion in the solvent, 1d 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 1d sliding and 3d motion leads to faster DNA sampling than pure 3d 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.