Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-533 Krakow, Poland.
Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
Int J Mol Sci. 2020 Oct 15;21(20):7632. doi: 10.3390/ijms21207632.
Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.
研究蛋白质折叠问题时，会根据该过程的持续时间对其进行区分。当前序列教条中编码的结构似乎是有充分根据的，尤其是对于那些被称为快速折叠、超快速折叠或下坡折叠的蛋白质。在本工作中，尝试使用模糊油滴模型来确定这组蛋白质的特征。根据模糊油滴模型，蛋白质是由氨基酸等双极分子组成的特定胶束。蛋白质折叠被视为球形胶束形成过程。氨基酸之间的共价肽键的存在消除了相邻分子自由相互排列的可能性。例如，构建由多种双极分子组成的共胶束。在快速折叠蛋白质的情况下，氨基酸序列代表生成球形胶束的最佳双极性系统。为了达到天然形式，只需要水环境提供的外部力场，该力场引导折叠过程生成中心疏水性核。外部场的影响可以使用 3D 高斯函数来表示，该函数是折叠过程朝向中心疏水性残基浓度和表面暴露极性残基的数学模型。所研究的蛋白质集揭示了与 3D 高斯分布兼容的疏水性分布，该分布被视为代表理想化的胶束样分布。还讨论了目前疏水性核心的结构与部分展开形式下疏水性残基的分布之间的关系。
