PDF(Pubmed)
Abstract：
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.
摘要：
水合在将内在无序的蛋白质重折叠成淀粉样纤维中起着至关重要的作用；然而，水和蛋白质之间的特定相互作用可能有助于这一过程仍然是未知的。在我们先前对α-突触核蛋白(aSyn)的研究中，我们已经表明，局限在原纤维腔中的水正在稳定这种病理褶皱的特征；与这些密闭水氢键结合的氨基酸调节初级和种子聚集。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。我们表明，空腔残基比非空腔残基在进化上更保守，并且富含PTM位点。不出所料,在亲水腔内的限制导致更稳定的水合氨基酸。有趣的是,腔PTM位点显示出最长的蛋白质-水氢键寿命，比非PTM腔部位大三倍。利用Newberry等人的深度突变筛选数据集。以及Pancoe等人对硫黄素T聚集的综述。使用原纤维腔/非腔定义进行解析，我们表明，与空腔外的残基相比，空腔中氨基酸的疏水变化对适应性和聚集率的影响更大。支持我们的假设，即这些位点参与了aSyn毒性纤维化的抑制。最后,我们扩大了研究范围，包括对tau纤维结构的分析，FUS,TDP-43,朊病毒,和hnRNPA1；所有这些都含有水合的空腔，有了tau,FUS,和TDP-43概括了我们的PTM结果在一个Syn原纤维腔中。
