Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43

TDP-43 is an RNA-binding protein that presents four domains comprising an N-terminal region, two RNA recognition motifs and a C-terminal region. The N-terminal domain (NTD) has a relevant role in the oligomerization and splicing activity of TDP-43. In this work, we have expressed, purified and biophysically characterized the region that includes residues 1 to 102 that contains the nuclear localization signal (residues 80–102, NLS). Furthermore, we have evaluated the oligomerization equilibrium for this protein fragment. Also, we have determined changes in the tertiary structure and its stability in a broad range of pH values by means of different spectroscopic methods. Additionally, we compared this fragment with the one that lacks the NLS employing experimental and computational methods. Finally, we evaluated the motion of dimeric forms to get insights into the conformational flexibility of this TDP-43 module in an oligomeric state. Our results suggest that this domain has a conformational plasticity in the vicinity of the single tryptophan of this domain (Trp68), which is enhanced by the presence of the nuclear localization signal. All these results help to understand the molecular features of the NTD of TDP-43. [Display omitted] •This work presents a conformational and oligomeric state analysis of the N-terminal domain (NTD) of TDP-43 containing the nuclear localization signal (NLS) by different spectroscopic methods.•In addition, we explored the influence of the NLS by fluorescence spectroscopy and computational methods.•Finally, we evaluated the dimeric form of this region by molecular dynamic simulation and bioinformatic tools. All these results suggest that NTD has some conformational plasticity that can be modulated by intra- and inter-protein interactions.