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

TitleDNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43
Publication TypeJournal Article
Year of Publication2018
AuthorsWang YJian, Rico-Lastres P, Lezamiz A, Mora M, Solsona C, Stirnemann G, Garcia-Manyes S
JournalJ Phys Chem Lett
Volume9
Pagination3800-3807
Date PublishedJul
Abstract

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.

DOI10.1021/acs.jpclett.8b01494
Citation Key2018|2134
PubMed ID29924934