Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080.
Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2309995120. doi: 10.1073/pnas.2309995120. Epub 2023 Nov 20.
The PHF6 (Val-Gln-Ile-Val-Tyr-Lys) motif, found in all isoforms of the microtubule-associated protein tau, forms an integral part of ordered cores of amyloid fibrils formed in tauopathies and is thought to play a fundamental role in tau aggregation. Because PHF6 as an isolated hexapeptide assembles into ordered fibrils on its own, it is investigated as a minimal model for insight into the initial stages of aggregation of larger tau fragments. Even for this small peptide, however, the large length and time scales associated with fibrillization pose challenges for simulation studies of its dynamic assembly, equilibrium configurational landscape, and phase behavior. Here, we develop an accurate, bottom-up coarse-grained model of PHF6 for large-scale simulations of its aggregation, which we use to uncover molecular interactions and thermodynamic driving forces governing its assembly. The model, not trained on any explicit information about fibrillar structure, predicts coexistence of formed fibrils with monomers in solution, and we calculate a putative equilibrium phase diagram in concentration-temperature space. We also characterize the configurational and free energetic landscape of PHF6 oligomers. Importantly, we demonstrate with a model of heparin that this widely studied cofactor enhances the aggregation propensity of PHF6 by ordering monomers during nucleation and remaining associated with growing fibrils, consistent with experimentally characterized heparin-tau interactions. Overall, this effort provides detailed molecular insight into PHF6 aggregation thermodynamics and pathways and, furthermore, demonstrates the potential of modern multiscale modeling techniques to produce predictive models of amyloidogenic peptides simultaneously capturing sequence-specific effects and emergent aggregate structures.
PHF6（缬氨酰-谷氨酰-异亮氨酰-缬氨酰-色氨酰-赖氨酸）基序存在于微管相关蛋白 tau 的所有异构体中，是在 tau 病中形成的有序淀粉样纤维核心的组成部分，被认为在 tau 聚集中发挥着基本作用。由于 PHF6 作为一个分离的六肽可以自行组装成有序的纤维，因此它被作为一个最小的模型来研究较大 tau 片段聚集的初始阶段。然而，即使对于这个小肽，与其纤维形成相关的大长度和时间尺度也对其动态组装、平衡构象景观和相行为的模拟研究构成了挑战。在这里，我们为 PHF6 的大规模模拟开发了一个准确的、自下而上的粗粒化模型，用于研究其聚集。我们利用该模型揭示了控制其组装的分子相互作用和热力学驱动力。该模型没有针对纤维结构的任何显式信息进行训练，但预测了形成的纤维与溶液中的单体共存，我们计算了浓度-温度空间中的一个假设平衡相图。我们还描述了 PHF6 低聚物的构象和自由能景观。重要的是，我们用肝素的模型证明，这种广泛研究的辅助因子通过在成核过程中对单体进行有序排列并与生长中的纤维保持关联，从而增强了 PHF6 的聚集倾向，这与实验表征的肝素-tau 相互作用一致。总的来说，这项工作提供了 PHF6 聚集热力学和途径的详细分子见解，并且还展示了现代多尺度建模技术的潜力，这些技术可以同时捕获序列特异性效应和新兴的聚集结构，从而产生淀粉样肽的预测模型。
