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.Comment: accepted in JC