Dynamical model of DNA-protein interaction: effect of protein charge distribution and mechanical properties

TL;DR

This study enhances a mechanical DNA-protein interaction model by representing proteins as interconnected beads, allowing detailed analysis of how protein charge distribution, shape, and deformability influence DNA sampling efficiency and facilitated diffusion.

Contribution

The paper introduces an improved model of DNA-protein interactions with proteins as interconnected beads, enabling analysis of effects of charge distribution and shape on DNA sampling dynamics.

Findings

Protein charge distribution affects DNA sampling speed.

Protein shape and deformability influence facilitated diffusion efficiency.

The updated model aligns better with experimental observations.

Abstract

The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of single beads. In this paper, we first compare the results obtained with the updated model with those of the original one and then use it to investigate several aspects of the dynamics of DNA sampling, which could not be accounted for by the original model. These aspects include the effect on the speed of DNA sampling of the regularity and/or randomness of the protein charge distribution, the charge and location of the search site, and the shape and deformability of the protein. We also discuss the efficiency of facilitated diffusion, that is, the extent to which the combination of 1D sliding along the DNA and 3D diffusion in the cell can lead to faster sampling than pure 3D diffusion of the protein.