Milchberg Moses H, Warmuth Owen A, Borcik Collin G, Dhavale Dhruva D, Wright Elizabeth R, Kotzbauer Paul T, Rienstra Chad M
Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, WI, USA, 53706.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA, 53706.
bioRxiv. 2025 May 2:2025.04.30.651534. doi: 10.1101/2025.04.30.651534.
The accumulation of Alpha-synuclein (Asyn) fibrils is the defining pathologic feature in Parkinson Disease (PD), Lewy Body Dementia (LBD), and Multiple System Atrophy (MSA). As such, the process of Asyn fibril formation has been an important research area and fibrils themselves have become attractive targets for disease diagnosis and therapeutic intervention. Due to the presence of mixed populations of fibrillar proteins associated with neurodegenerative diseases in brain tissue, high-resolution structures of Asyn fibrils are essential for the design of high-specificity imaging and therapeutic agents. Approximately one hundred high-resolution solid-state NMR (SSNMR) spectroscopy and cryo-electron microscopy (cryo-EM) structures of Asyn fibrils have been deposited to the Protein Databank (PDB); intriguingly there is significant polymorphism among them. Understanding the molecular makeup and characteristic features of each structural polymorph can determine conserved structural motifs which can be used as templates to design ligands with high specificity for clinical use. Utilizing standard alignment tools and density-based clustering approaches, we objectively classify fibril structures by tertiary structure type. We find that 81% of the structures cluster into two polymorph classes. Within each class, additional subtle variations are observed which position sidechains in specific, conserved orientations, well poised as druggable targets. Furthermore, we find that the conserved structural motifs associated with each class are found in all but one published Asyn fibril structure. We consider these classifications and conserved motifs in the context of disease-relevant fibril structures and offer a perspective on the utility of fibrils as substrates for drug development and models for disease pathogenesis.
α-突触核蛋白（α-synuclein，Asyn）原纤维的积累是帕金森病（PD）、路易体痴呆（LBD）和多系统萎缩（MSA）的标志性病理特征。因此，Asyn原纤维的形成过程一直是一个重要的研究领域，原纤维本身也已成为疾病诊断和治疗干预的有吸引力的靶点。由于脑组织中存在与神经退行性疾病相关的混合原纤维蛋白群体，Asyn原纤维的高分辨率结构对于设计高特异性成像和治疗药物至关重要。大约有100个Asyn原纤维的高分辨率固态核磁共振（SSNMR）光谱和冷冻电子显微镜（cryo-EM）结构已存入蛋白质数据库（PDB）；有趣的是，它们之间存在显著的多态性。了解每个结构多态体的分子组成和特征可以确定保守的结构基序，这些基序可作为模板来设计具有高特异性的临床用配体。利用标准比对工具和基于密度的聚类方法，我们根据三级结构类型对原纤维结构进行客观分类。我们发现81%的结构聚为两类多态体。在每一类中，观察到了额外的细微变化，这些变化使侧链处于特定的、保守的方向，成为良好的可成药靶点。此外，我们发现除了一个已发表的Asyn原纤维结构外，与每一类相关的保守结构基序在所有结构中都存在。我们在与疾病相关的原纤维结构背景下考虑这些分类和保守基序，并就原纤维作为药物开发底物和疾病发病机制模型的实用性提供了一个观点。
