Insight into the Folding and Dimerization Mechanisms of the N-Terminal Domain from Human TDP-43

Abstract

TAR DNA-binding protein 43 (TDP-43) is a 414-residue long nuclear protein whose deposition into intraneuronal insoluble inclusions has been associated with the onset of amyotrophic lateral sclerosis (ALS) and other diseases. This protein is physiologically a homodimer, and dimerization occurs through the N-terminal domain (NTD), with a mechanism on which a full consensus has not yet been reached. Furthermore, it has been proposed that this domain is able to affect the formation of higher molecular weight assemblies. Here, we purified this domain and carried out an unprecedented characterization of its folding/dimerization processes in solution. Exploiting a battery of biophysical approaches, ranging from FRET to folding kinetics, we identified a head-to-tail arrangement of the monomers within the dimer. We found that folding of NTD proceeds through the formation of a number of conformational states and two parallel pathways, while a subset of molecules refold slower, due to proline isomerism. The folded state appears to be inherently prone to form high molecular weight assemblies. Taken together, our results indicate that NTD is inherently plastic and prone to populate different conformations and dimeric/multimeric states, a structural feature that may enable this domain to control the assembly state of TDP-43.

S-nitrosylated TDP-43 triggers aggregation, cell-to-cell spread, and neurotoxicity in hiPSCs and in vivo models of ALS/FTD

“…Accordingly, following S-nitrosylation of TDP-43, an intramolecular disulfide bond between Cys173 and Cys175 results in a conformational change facilitating aggregation (29,31). Interestingly, an intermolecular disulfide linkage was recently reported to occur at Cys244 between two TDP-43 protein molecules (30), producing TDP-43 dimers and oligomers (69,70). In the present study, our molecular dynamics simulations suggested that the intramolecular disulfide bridge that we observed between Cys173 and Cys175 would trigger conformational alterations leading to increased solvent exposure at Cys244, potentially facilitating intermolecular disulfide linkage at that residue.…”

Computational Insights of Unfolding of N-Terminal Domain of TDP-43 Reveal the Conformational Heterogeneity in the Unfolding Pathway

“…The non-native unfolded intermediate states might facilitate protein oligomerization and aggregation. Very recently, Vivoli-Vega et al ( 2020 ) biophysically characterized the folding/dimerization of NTD and identified a head-to-tail arrangement during the dimerization of NTD. The authors also found that the folding of NTD proceeds through the formation of a collapsed state and an intermediate state.…”

“…Through all-atom MD simulation, we have studied the stability and dynamics of the NTD mutations, L27A, L28A, and V31R, and provide insights into the mechanisms of the destabilization of NTD variants (Kumar et al, 2019 ). A recent study also demonstrated the presence of different partially folded states during the folding pathways of NTD (Vivoli-Vega et al, 2020 ). Therefore, the folding dynamics and confirmational stability studies of NTD are essential to underpinning the role of folding intermediates behind the dichotomy of TDP-43.…”

hnRNP A1B, a Splice Variant of HNRNPA1, Is Spatially and Temporally Regulated

“…For example, another member of the hnRNP family, hnRNP C, can multimerize which improves its binding to RNA by a cooperative RRM dimer binding model (Cieniková et al, 2015). TDP-43 can also dimerize via its N-terminal region (RBD) (Vivoli-Vega et al, 2020). Interestingly, TDP-43 dimers are enriched in the cytoplasm and found in physiological conditions as well as in ALS patient brains (Shiina et al, 2010).…”