  The binding of proteins onto DNA contributes to the shaping and packaging of
genome as well as to the expression of specific genetic messages. With a view
to understanding the interplay between the presence of proteins and the
deformation of DNA involved in such processes, we developed a new method to
minimize the elastic energy of DNA fragments at the mesoscale level. Our method
makes it possible to obtain the optimal pathways of protein-decorated DNA
molecules for which the terminal base pairs are spatially constrained. We focus
in this work on the deformations induced by selected architectural proteins on
circular DNA. We report the energy landscapes of DNA minicircles subjected to
different levels of torsional stress and containing one or two proteins as
functions of the chain length and spacing between the proteins. Our results
reveal cooperation between the elasticity of the double helix and the
structural distortions of DNA induced by bound proteins. We find that the
imposed mechanical stress influences the placement of proteins on DNA and that,
the proteins, in turn, modulate the mechanical stress and thereby broadcast
their presence along DNA.
