Unraveling the molecular mechanisms of vimentin interaction with G-quadruplex repeats

Vimentin is a cytoskeletal protein that exists as soluble tetramers or polymerized filaments. Its tetrameric form selectively interacts with DNA non-canonical secondary structures called G-quadruplex repeats. Here, we applied optimized experimental conditions to preferentially trap the protein at selected oligomerization states. All of them were analyzed by hydrogen–deuterium exchange mass spectrometry to map the vimentin domains that undergo structural changes upon DNA binding and compare them to those associated with its polymerization. G-quadruplex repeats induced unique perturbations of vimentin structure. Among them, the exposure of coil-1B was the most relevant and it had been associated with a reduction in the protein α-helical content. In addition, few protein structural changes were observed both upon G-quadruplex repeats binding and vimentin polymerization, such as the stabilization of coil-1A and coil-2A. This suggests that DNA complex formation impairs the contribution of these regions to vimentin oligomerization. Finally, a peptide from the protein N-terminal domain (residues 11–30) has been identified as a specific G-quadruplex binder, underscoring its direct role in stabilizing the vimentin–DNA complex. Overall, these findings provide detailed insights into the molecular mechanisms that allow DNA to finely modulate the composite structural equilibrium of vimentin and, accordingly, its functions at nuclear level.