Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland.
Department of Applied Informatics Silesian University of Technology, Gliwice, Poland.
Acta Biochim Pol. 2023 Jun 18;70(2):435-445. doi: 10.18388/abp.2020_6788.
Numerous Alpha-synuclein amyloid structures available in PDB enable their comparative analysis. They are all characterized by a flat structure of each individual chain with an extensive network of inter-chain hydrogen bonds. The identification of such amyloid fibril structures requires determining the special conditions imposed on the torsion angles. Such conditions have already been formulated by the Authors resulting in the model of idealised amyloid. Here, we investigate the fit of this model in the group of A-Syn amyloid fibrils. We identify and describe the characteristic supersecondary structures in amyloids. Generally, the amyloid transformation is suggested to be the 3D to 2D transformation engaging mostly the loops linking Beta-structural fragments. The loop structure introducing the 3D organisation of Beta-sheet change to flat form (2D) introduces the mutual reorientation of Beta-strands enabling the large-scale H-bonds generation with the water molecules. Based on the model of idealised amyloid we postulate the hypothesis for amyloid fibril formation based on the shaking, an experimental procedure producing the amyloids.
PDB 中提供了许多α-突触核蛋白淀粉样结构，可对其进行比较分析。它们的特点是每个单体链都呈扁平结构，并具有广泛的链间氢键网络。鉴定此类淀粉样纤维结构需要确定对扭转角施加的特殊条件。作者已经制定了这样的条件，从而形成了理想化淀粉样模型。在这里，我们研究了该模型在 A-突触核蛋白淀粉样纤维组中的拟合情况。我们确定并描述了淀粉样物中的特征超二级结构。一般来说，淀粉样转化被认为是 3D 到 2D 的转化，主要涉及连接β结构片段的环。引入 3Dβ-折叠结构变化为平面形式（2D）的环结构引入β-链的相互重排，从而能够与水分子生成大规模氢键。基于理想化淀粉样模型，我们提出了基于摇动的淀粉样纤维形成假说，摇动是产生淀粉样物的实验过程。
