Mechanical response of the RecA nucleoprotein filament to increasing D-loop length

Protein filaments play fundamental functions in the cell, ranging from scaffolding like in the cytoskeleton to sensing and transmitting forces and torques. Here we address the case of the nucleoprotein filaments (NPFs) of homologous recombination (HR) formed by the polymerization of the RecA protein on DNA. In contrast to the cytoskeleton filaments, the HR filaments are not known to exert or sense forces. However the stress in the stretched and unwound DNA bound to those filaments was shown to play a role in promoting DNA strand exchange during the early stage of the HR mechanism. Here we use molecular dynamics simulations to examine whether the strain in the nucleoprotein filament upon strand exchange progression and D-loop formation may influence subsequent steps of the HR process. Our results indicate that the filament mechanical properties are sensitive to the length of DNA incorporated in the D-loop. The response we observe upon increasing the D-loop length is first elastic, up to a threshold that we estimate to be 27 incorporated base pairs, after which the NPF enters a plastic stage where the protein-DNA connectivities are reorganized. Notably, the DNA displaced strand locally switches from site II to site III, a newly characterized binding site. We discuss the possible consequence of this mechanical response of the NPFs for the course of the HR process.