DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43

Understanding
the molecular mechanisms governing protein–nucleic
acid interactions is fundamental to many nuclear processes. However,
how nucleic acid binding affects the conformation and dynamics of
the substrate protein remains poorly understood. Here we use a combination
of single molecule force spectroscopy AFM and biochemical assays to
show that the binding of TG-rich ssDNA triggers a mechanical switch
in the RRM1 domain of TDP-43, toggling between an entropic spring
devoid of mechanical stability and a shock absorber bound-form that
resists unfolding forces of ∼40 pN. The fraction of mechanically
resistant proteins correlates with an increasing length of the TGn oligonucleotide, demonstrating that protein
mechanical stability is a direct reporter of nucleic acid binding.
Steered molecular dynamics simulations on related RNA oligonucleotides
reveal that the increased mechanical stability fingerprinting the
holo-form is likely to stem from a unique scenario whereby the nucleic
acid acts as a “mechanical staple” that protects RRM1
from mechanical unfolding. Our approach highlights nucleic acid binding
as an effective strategy to control protein nanomechanics.