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

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.

accepted in JCP

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• Preferential localization of the bacterial nucleoid
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Role of salt valency in the switch of H-NS proteins between DNA-bridging and DNA-stiffening modes
• Coarse-Grained model of the demixing of DNA and non-binding globular macromolecules
• Impact of self-association on the architectural properties of bacterial nucleoid proteins
• Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
• Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view