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

J Phys Chem Lett. 2018 Jul 19;9(14):3800-3807. doi: 10.1021/acs.jpclett.8b01494. Epub 2018 Jun 28.


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 TG n 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.

MeSH terms

  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Genes, Switch*
  • Humans
  • Mechanical Phenomena
  • Protein Domains
  • Ribonucleoside Diphosphate Reductase
  • Tumor Suppressor Proteins / chemistry*


  • DNA-Binding Proteins
  • TARDBP protein, human
  • Tumor Suppressor Proteins
  • RRM1 protein, human
  • Ribonucleoside Diphosphate Reductase