Unravelling the Molecular Mechanism of Progression in Alzheimer's Disease: Implications for therapy

阿尔茨海默病（AD）是一种神经退行性疾病，影响着全世界3600万人。由于预期寿命延长和人口老龄化，预计到2050年将有1.15亿人患有阿尔茨海默病。阿尔茨海默病的病理是由大脑中蛋白质聚集体（称为淀粉样斑块和神经原纤维缠结）的渐进式积累引起的，目前还没有改善疾病的治疗方法。缠结是由Tau蛋白单体组成的，它们错误折叠、自组装并在疾病中积累。在这个项目中，我们将开发新的光谱和硅工具来了解Tau蛋白的结构-致病性关系，以确定其与疾病相关的错误折叠，随后的聚集和疾病传播。通过这种方式，我们将为治疗疾病铺平道路。在之前的工作中，我们已经证明了我们可以获得tau低聚物的振动拉曼光谱，并证明了时间演变为原纤维形式。另外，我们已经证明我们可以计算电场，从而计算蛋白质分子探针的振动频率。在这里，我们将结合新的光谱和分子模拟研究，研究肽的聚集，特别是tau寡聚物的结构和进化成更大的原纤维。为了证实模拟和光谱可以结合并确定Tau种子的构象，将开发和测试两个相关六肽VQIVYK （PHF6）和VQIINK （PHF6*）的方法。两者都是Tau蛋白中纤维形成和自发聚集所必需的。光谱将使用我们之前发表的拉曼方法推导。先进的模拟技术将用于表征多肽聚集体形成的动力学和热力学参数。先进的极化力场将用于计算振动谱。使用校准数据对计算模型进行改进后，将获得六肽作为单体、低聚物和原纤维的拉曼光谱。模拟的预测将首先针对单体光谱进行测试。随后将进行优化，这将允许理解低聚物和原纤维的拉曼光谱，它们更复杂，并且可以由多态组成。因此，根据分子基序、分子内键和分子间键来阐明构象结构将成为可能。通过模拟获得的洞察力将有助于理解相互作用，并允许开发化合物（药物）与tau聚集体相互作用的计算机模型。为了建立和验证结构的基本真相，并进一步将拉曼光谱与模拟相关联，该学生将访问萨塞克斯大学的serbell实验室，准备由PHF6和PHF6*形成的纤维的x射线纤维衍射样品。这将有助于进一步了解成熟原纤维的分子结构。serbell实验室在研究tau肽和其他淀粉样蛋白片段以及使用x射线纤维衍射研究原纤维的结构组织方面拥有丰富的经验。负染色透射电子显微镜将在苏塞克斯进行，以验证细丝的形态。该项目将结合实验和模拟结构集成，允许低聚物形成的机制与分子细节进行跟踪，为潜在的治疗干预提供重要见解。

Alzheimer's disease (AD) is a neurodegenerative disorder that affects 36 million people worldwide. Owing to an increased life expectancy and aging populations, by 2050 more 115 million are predicted to have AD. The pathology of AD results from the progressive accumulation of protein aggregates (called amyloid plaques and neurofibrillary tangles) in the brain and no disease modifying therapies exist. Tangles are made up of Tau protein monomers that misfold, self-assemble and accumulate in disease. In this project, we will develop novel spectroscopic and in silico tools to understand the structure-pathogenicity relationships in Tau protein that determine its disease-related misfolding, subsequent aggregation and spread of disease. In this way we will pave the way for disease-modifying therapies. In previous work, we have demonstrated that we can acquire the vibrational Raman spectra of tau oligomers, and demonstrated time evolution as fibrils form. Separately, we have demonstrated that we can calculate the electric fields, and hence the vibrational frequencies, of molecular probes in proteins. Here we will combine novel spectroscopic and molecular simulation studies, to study peptide aggregation in general, and tau oligomer structure and evolution into larger fibrils, in particular. To confirm that simulation and spectroscopy can be combined and to determine the conformation of Tau seeds, the methodology will be developed and tested on two relevant hexapeptides VQIVYK (PHF6) and VQIINK (PHF6*). Both are essential for fibril formation in Tau and spontaneously aggregate. Spectra will be derived using our previously published Raman approach. Advanced simulation techniques will be used to characterise the kinetic and thermodynamic parameters of peptide aggregate formation. Advanced polarisable force fields will be used to calculate vibrational spectra. Following refinement of computational models using calibration data, Raman spectra of hexapeptides as monomers, oligomers and fibrils will be acquired. Predictions from simulations will be tested against monomer spectra first. This will be followed by optimisation which will allow understanding the Raman spectra of oligomers and fibrils, which are more complex, and can consist of polymorphs. Thus, elucidation of conformational structures in terms of molecular motifs, intra- and inter-molecular bonding will be possible. The insight gained by simulations will help understand interactions and allow the development of in silico models of compound (drug) interactions with tau aggregates. To establish and verify ground truth of the structures, and to further correlate the Raman spectra with simulations, the student will visit the University of Sussex, to the Serpell lab, to prepare X-ray fibre diffraction samples of the fibrils formed by PHF6 and PHF6*. This will help gain further insight into the molecular architecture of the mature fibrils. The Serpell lab have extensively experience of working with tau peptides and other amyloidogenic fragments and investigating the structural organisation of fibrils using X-ray fibre diffraction. Negative stain transmission electron microscopy will be performed at Sussex to verify the morphology of filaments. This project will link experimental and simulation structural ensembles, allowing the mechanism of oligomer formation to be followed with molecular detail, giving vital insights into potential therapeutic interventions.