School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States.
J Chem Inf Model. 2021 Feb 22;61(2):966-975. doi: 10.1021/acs.jcim.0c01319. Epub 2021 Jan 14.
Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature of these aggregation intermediates. To uncover the structural characteristics of toxic oligomeric intermediates, we compared the self-assembly dynamics and structures of SOD1, a cytotoxic fragment of the superoxide dismutase 1 (SOD1) associated with the amyotrophic lateral sclerosis, with its two nontoxic mutants G33V and G33W using molecular dynamics simulations. Single-point glycine substitutions in SOD1 have been reported to abolish the amyloid toxicity. Our simulation results showed that the toxic SOD1 and its nontoxic mutants followed different aggregation pathways featuring distinct aggregation intermediates. Specifically, wild-type SOD1 initially self-assembled into random-coil-rich oligomers, among which fibrillar aggregates composed of well-defined curved single-layer β-sheets were nucleated via coil-to-sheet conversions and the formation of β-barrels as intermediates. In contrast, the nontoxic G33V/G33W mutants readily assembled into small β-sheet-rich oligomers and then coagulated with each other into cross-β fibrils formed by two-layer β-sheets without forming β-barrels as the intermediates. The direct observation of β-barrel oligomers during the assembly of toxic SOD1 fragments but not the nontoxic glycine-substitution mutants strongly supports β-barrels as the toxic oligomers in amyloidosis, probably via interactions with the cell membrane and forming amyloid pores. With well-defined structures, the β-barrel might serve as a novel therapeutic target against amyloid-related diseases.
在淀粉样蛋白聚集的早期阶段形成的可溶性低分子量低聚物被认为是淀粉样变性中的主要毒性物质。由于这些聚集中间体的异质性和瞬态性质，寡聚体组装体与细胞毒性之间的结构-功能关系仍然难以捉摸。为了揭示有毒寡聚中间体的结构特征，我们使用分子动力学模拟比较了超氧化物歧化酶 1（SOD1）的毒性片段（与肌萎缩性侧索硬化症相关的 SOD1）与其两个非毒性突变体 G33V 和 G33W 的自组装动力学和结构。据报道，SOD1 中的单点甘氨酸取代可消除淀粉样毒性。我们的模拟结果表明，有毒 SOD1 及其非毒性突变体遵循不同的聚集途径，具有不同的聚集中间体。具体而言，野生型 SOD1 最初自组装成富含无规卷曲的寡聚体，其中由明确的弯曲单层β-片层组成的纤维状聚集体通过从无规卷曲到β-折叠的转变以及β-桶的形成作为中间体进行成核。相比之下，非毒性 G33V/G33W 突变体很容易组装成小的β-片层丰富的寡聚体，然后相互凝聚成由双层β-片层组成的交叉β纤维，而没有形成β-桶作为中间体。在有毒 SOD1 片段的组装过程中直接观察到β-桶寡聚体，而不是非毒性甘氨酸取代突变体，这强烈支持β-桶作为淀粉样变性中的毒性寡聚体，可能通过与细胞膜相互作用并形成淀粉样孔。具有明确结构的β-桶可能成为针对与淀粉样蛋白相关疾病的新型治疗靶标。
