Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha‐synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids that hydrogen bond with these confined waters modulate primary and seeded aggregation. Here, we extend our aSyn molecular dynamics (MD) simulations with three new polymorphs and correlate MD trajectory information with known post‐translational modifications (PTMs) and experimental data. We show that cavity residues are more evolutionarily conserved than non‐cavity residues and are enriched with PTM sites. As expected, the confinement within hydrophilic cavities results in more stably hydrated amino acids. Interestingly, cavity PTM sites display the longest protein‐water hydrogen bond lifetimes, three‐fold greater than non‐PTM cavity sites. Utilizing the deep mutational screen dataset by Newberry et al. and the Thioflavin T aggregation review by Pancoe et al. parsed using a fibril cavity/non‐cavity definition, we show that hydrophobic changes to amino acids in cavities have a larger effect on fitness and aggregation rate than residues outside cavities, supporting our hypothesis that these sites are involved in the inhibition of aSyn toxic fibrillization. Finally, we expand our study to include analysis of fibril structures of tau, FUS, TDP‐43, prion, and hnRNPA1; all of which contained hydrated cavities, with tau, FUS, and TDP‐43 recapitulating our PTM results in aSyn fibril cavities.

中文翻译：

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翻译后修饰位点存在于 α-突触核蛋白、tau、FUS 和 TDP-43 原纤维的亲水腔中：分子动力学研究

水合作用在本质上无序的蛋白质重新折叠成淀粉样原纤维的过程中起着至关重要的作用。然而，水和蛋白质之间可能促成这一过程的具体相互作用仍然未知。在我们之前对α-突触核蛋白（aSyn）的研究中，我们已经证明，限制在原纤维腔中的水可以稳定这种病理折叠的特征；与这些受限水域形成氢键的氨基酸调节初级和种子聚集。在这里，我们用三种新的多晶型物扩展了 aSyn 分子动力学 (MD) 模拟，并将 MD 轨迹信息与已知的翻译后修饰 (PTM) 和实验数据相关联。我们发现空腔残基比非空腔残基在进化上更加保守，并且富含 PTM 位点。正如预期的那样，亲水性空腔内的限制导致更稳定的水合氨基酸。有趣的是，空腔 PTM 位点显示出最长的蛋白质-水氢键寿命，比非 PTM 空腔位点长三倍。利用 Newberry 等人的深度突变筛选数据集。以及 Pancoe 等人对硫磺素 T 聚集的回顾。使用原纤维空腔/非空腔定义进行解析，我们发现空腔中氨基酸的疏水性变化比空腔外残基对适应性和聚集率的影响更大，支持我们的假设，即这些位点参与抑制 aSyn 毒性纤维化。最后，我们扩展了我们的研究范围，包括对 tau、FUS、TDP-43、朊病毒和 hnRNPA1 的原纤维结构的分析；所有这些都含有水合空腔，其中 tau、FUS 和 TDP-43 概括了我们在 aSyn 原纤维空腔中的 PTM 结果。