Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, China.
ACS Chem Neurosci. 2022 Sep 21;13(18):2743-2754. doi: 10.1021/acschemneuro.2c00416. Epub 2022 Sep 2.
The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is implicated in amyotrophic lateral sclerosis (ALS), and some hereditary mutations localized in the low complexity domain (LCD) facilitate the formation of pathogenic TDP-43 fibrils. A recent cryo-EM study reported the atomic-level structures of the A315E TDP-43 LCD (residues 288-319, TDP-43) core fibril in which the protofilaments have R-shaped structures and hypothesized that A315E U-shaped protofilaments can readily convert to R-shaped protofilaments compared to the wild-type (WT) ones. There are no atomic structures of WT protofilaments available yet. Herein, we performed extensive all-atom explicit-solvent molecular dynamics simulations on A315E and WT protofilaments starting from both the cryo-EM-determined R-shaped and our constructed U-shaped structures. Our simulations show that WT protofilaments also adopt the R-shaped structures but are less stable than their A315E counterparts. Except for R293-E315 salt bridges, N312-F316 hydrophobic interactions and F316-F316 π-π stacking interactions are also crucial for the stabilization of the neck region of the R-shaped A315E protofilaments. The loss of R293-E315 salt bridges and the weakened interactions of N312-F316 and F316-F316 result in the reduced stability of the R-shaped WT protofilaments. Simulations starting from U-shaped folds reveal that A315E protofilaments can spontaneously convert to the cryo-EM-derived R-shaped protofilaments, whereas WT protofilaments convert to R-shape-like structures with remodeled neck regions. The R-shape-like WT protofilaments could act as intermediate states slowing down the U-to-R transition. This study reveals that A315E mutation can not only enhance the structural stability of the R-shaped TDP-43 protofilaments but also promote the U-to-R transition, which provides atomistic insights into the A315E mutation-enhanced TDP-43 pathogenicity in ALS.
TDP-43 蛋白的聚集与肌萎缩性侧索硬化症（ALS）有关，一些位于低复杂度结构域（LCD）的遗传性突变可促进致病性 TDP-43 纤维的形成。最近的一项低温电子显微镜研究报告了 A315E TDP-43 LCD（残基 288-319，TDP-43）核心纤维的原子水平结构，其中原纤维具有 R 形结构，并假设与野生型（WT）相比，A315E 纤维的 U 形原纤维可以很容易地转化为 R 形原纤维。目前还没有 WT 原纤维的原子结构。在此，我们从低温电镜确定的 R 形结构和我们构建的 U 形结构出发，对 A315E 和 WT 原纤维进行了广泛的全原子显式溶剂分子动力学模拟。我们的模拟表明，WT 原纤维也采用 R 形结构，但不如 A315E 原纤维稳定。除了 R293-E315 盐桥外，N312-F316 疏水相互作用和 F316-F316 π-π 堆积相互作用对于 R 形 A315E 原纤维颈部区域的稳定也至关重要。R293-E315 盐桥的缺失和 N312-F316 和 F316-F316 相互作用的减弱导致 R 形 WT 原纤维稳定性降低。从 U 形折叠开始的模拟表明，A315E 原纤维可以自发地转化为低温电镜衍生的 R 形原纤维，而 WT 原纤维则转化为具有重塑颈部区域的 R 形样结构。R 形样 WT 原纤维可能作为中间状态，减缓 U 到 R 的转变。该研究表明，A315E 突变不仅可以增强 R 形 TDP-43 原纤维的结构稳定性，还可以促进 U 到 R 的转变，这为 ALS 中 A315E 突变增强 TDP-43 致病性提供了原子水平的见解。
