Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43

Abstract

The N-terminal domain of the RNA binding protein TDP-43 (NTD) is essential to both physiology and proteinopathy; however, elucidation of its folding/unfolding still remains a major quest. In this study, we have investigated the biophysical behavior of intermediate ensembles employing all-atom molecular dynamics simulations in 8 M urea accelerated with high temperatures to achieve unfolded states in a confined computation time. The cumulative results of the 2.75 ms simulations show that unfolding of the NTD at 350 K evolves through different stable and meta-stable intermediate states. The free-energy landscape reveals two meta-stable intermediates (I N and I U ) stabilized by non-native interactions, which are largely hydrophilic and highly energetically frustrated. A single buried tryptophan residue, W80, undergoes solvent exposure to different extents during unfolding; this suggests a structurally heterogeneous population of intermediate ensembles. Furthermore, the structure properties of the I N state show a resemblance to the molten globule (MG) state with most of the secondary structures intact. The unfolding of the NTD is initiated by the loss of b-strands, and the unfolded (U) states exhibit a population of non-native a-helices. These non-native unfolded intermediate ensembles may mediate protein oligomerization, leading to the formation of pathological, irreversible aggregates, characteristics of disease pathogenesis.

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach

“…Similarly, a hydrophobic interaction was defined by the condition that the distance between two residues ( i and j , with | i − j | > 3) is less than 4.5 Å. Principal component analysis performed using the projection of principal components (PCs), PC1 and PC2, along the native structure [ 61 , 62 ] and gmx-sham utilized for the FEL [ 63 , 64 ].…”

Purification and Structural Characterization of Aggregation-Prone Human TDP-43 Involved in Neurodegenerative Diseases

“…Wang et al (2018) added a maltose-binding protein fusion to TDP-43 directly C terminal to the lowcomplexity domain where it effectively increased solubility. To obtain detergent-free TDP-43 without recourse to fusions proteins, and with the knowledge that several TDP-43 tryptophan residues are involved in folding (Prakash et al, 2018) and phase transitioning (Li et al, 2018a(Li et al, , 2018b, together with the role of aromatic residues in low-complexity aromatic-rich kinked segment formation (Hughes et al, 2018), we created a construct where all tryptophan residues in the TDP-43 primary sequence are replaced with alanine (TDP-43 WtoA ). Cell lysis and protein purification with standard immobilized metal ion chromatography buffers without any detergent facilitated production of full-length TDP-43 WtoA that was stable for 3 days at 4 C (Figure 3), sufficient to undertake non-crystallographic structural studies.…”

Discovery of Natural Phenol Catechin as a Multitargeted Agent Against SARS-CoV-2 For the Plausible Therapy of COVID-19

“…Similarly, a hydrophobic interaction was defined by the condition that the distance between two residues (i and j, with |i − j| > 3) is less than 4.5 Å. Principal component analysis performed using the projection of principal component (PCs), PC1, and PC2 along the native structure (Laberge and Yonetani, 2008;Prakash et al, 2018a) and gmx-sham utilized for the free energy landscape Prakash et al, 2018b).…”