Kulshrestha Avijeet, Phan Tien Minh, Rizuan Azamat, Mohanty Priyesh, Mittal Jeetain
Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843.
Department of Chemistry, Texas A&M University, College Station, TX, 77843.
bioRxiv. 2025 May 23:2025.05.19.654960. doi: 10.1101/2025.05.19.654960.
Protein aggregation, which is implicated in aging and neurodegenerative diseases, typically involves a transition from soluble monomers and oligomers to insoluble fibrils. Polyglutamine (polyQ) tracts in proteins can form amyloid fibrils, which are linked to polyQ diseases, including Huntington's disease (HD), where the length of the polyQ tract inversely correlates with the age of onset. Despite significant research on the mechanisms of Httex1 aggregation, atomistic information regarding the intermediate stages of its fibrillation and the morphological characteristics of the end-state amyloid fibrils remains limited. Recently, molecular dynamics (MD) simulations based on a hybrid multistate structure-based model, Multi-eGO, have shown promise in capturing the kinetics and mechanism of amyloid fibrillation with high computational efficiency while achieving qualitative agreement with experiments. Here, we utilize the multi-eGO simulation methodology to study the mechanism and kinetics of polyQ fibrillation and the effect of the N17 flanking domain of Huntingtin protein. Aggregation simulations of polyQ produced highly heterogeneous amyloid fibrils with variable-width branched morphologies by incorporating combinations of β-turn, β-arc, and β-strand structures, while the presence of the N17 flanking domain reduces amyloid fibril heterogeneity by favoring β-strand conformations. Our simulations reveal that the presence of N17 domain enhanced aggregation kinetics by promoting the formation of large, structurally stable oligomers. Furthermore, the early-stage aggregation process involves two distinct mechanisms: backbone interactions driving β-sheet formation and side-chain interdigitation. Overall, our study provides detailed insights into fibrillation kinetics, mechanisms, and end-state polymorphism associated with Httex1 amyloid aggregation.
Polyglutamine (polyQ) aggregation is central to Huntington's disease and related neurodegenerative disorders. Despite extensive experimental efforts, a complete molecular understanding of this process-from early aggregation events to the origins of fibril polymorphism-has remained elusive, with varied interpretations of complex fibril architectures. Through multiscale simulations, we reveal how polyQ fibrils adopt diverse tertiary and quaternary structures and demonstrate how the N-terminal flanking domain (N17) modulates fibril architecture and accelerates aggregation. Our hybrid multi-eGO simulations capture early-stage fibrillation kinetics and identify distinct structural polymorphs that align with experimental observations. This work provides a molecular framework for understanding amyloid polymorphism and illuminates the role of flanking domains in shaping aggregation pathways-offering valuable insights for therapeutic strategies targeting early toxic intermediates.
蛋白质聚集与衰老和神经退行性疾病有关，通常涉及从可溶性单体和寡聚体向不溶性纤维的转变。蛋白质中的多聚谷氨酰胺（polyQ）序列可形成淀粉样纤维，这与多聚谷氨酰胺疾病有关，包括亨廷顿舞蹈病（HD），其中多聚谷氨酰胺序列的长度与发病年龄呈负相关。尽管对Httex1聚集机制进行了大量研究，但关于其纤维化中间阶段的原子信息以及终态淀粉样纤维的形态特征仍然有限。最近，基于混合多状态结构模型Multi-eGO的分子动力学（MD）模拟在以高计算效率捕捉淀粉样纤维化的动力学和机制方面显示出前景，同时与实验达成定性一致。在此，我们利用多eGO模拟方法研究多聚谷氨酰胺纤维化的机制和动力学以及亨廷顿蛋白N17侧翼结构域的作用。通过结合β-转角、β-弧和β-链结构的组合，多聚谷氨酰胺的聚集模拟产生了具有可变宽度分支形态的高度异质淀粉样纤维，而N17侧翼结构域的存在通过促进β-链构象减少了淀粉样纤维的异质性。我们的模拟表明，N17结构域的存在通过促进大的、结构稳定的寡聚体的形成增强了聚集动力学。此外，早期聚集过程涉及两种不同的机制：驱动β-折叠形成的主链相互作用和侧链交叉。总体而言，我们的研究提供了与Httex1淀粉样聚集相关的纤维化动力学、机制和终态多态性的详细见解。
多聚谷氨酰胺（polyQ）聚集是亨廷顿舞蹈病和相关神经退行性疾病的核心。尽管进行了广泛的实验，但对这一过程——从早期聚集事件到纤维多态性的起源——的完整分子理解仍然难以捉摸，对复杂纤维结构有不同的解释。通过多尺度模拟，我们揭示了多聚谷氨酰胺纤维如何采用不同的三级和四级结构，并展示了N端侧翼结构域（N17）如何调节纤维结构并加速聚集。我们的混合多eGO模拟捕捉了早期纤维化动力学，并确定了与实验观察结果一致的不同结构多态性。这项工作为理解淀粉样多态性提供了一个分子框架，并阐明了侧翼结构域在塑造聚集途径中的作用——为针对早期毒性中间体的治疗策略提供了有价值的见解。
