Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-533 Kraków, Poland.
Int J Mol Sci. 2020 Jun 30;21(13):4683. doi: 10.3390/ijms21134683.
The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins.
将球状蛋白质的结构改变为淀粉样形式的问题是研究人员关注的焦点。进行了大量的实验研究，并寻求定义淀粉样转化本质的数学模型。本工作集中于淀粉样物中疏水性核心结构的问题。通过类似于球形胶束中疏水性分布的 3D 高斯分布模拟，描述了球状蛋白质中疏水性核心的有序形式。淀粉样原纤维是由许多单独的链组成的带状胶束，每个链代表一个平面结构。包含在原纤维中的单个链内的疏水性分布描述了 2D 高斯分布。这种描述表达了在具有高疏水性的中心的圆上的极性残基的位置。在 Preotin Data Bank (PDB) 中提供的淀粉样形式（原纤维和超原纤维）中存在这种类型的有序性，在本工作中得到了证明。在该系统中，可以假定淀粉样转化是从 3D 高斯有序到 2D 高斯有序的链转变。这意味着将球状结构改变为带状结构。这一观察结果可以为模拟蛋白质的淀粉样转化提供一个简单的数学模型。
