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

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