Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

Biomolecules

Leszek Konieczny¹  and Irena Roterman²  Mateusz Banach²  Katarzyna Stapor³  Piotr Fabian³ 

[1] Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland;Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-533 Krakow, Poland;Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;

关键词: hydrophobicity;    hydrophobic core;    secondary structure;    super-secondary structure;    synergy;   

DOI  :  10.3390/biom10050767

来源: DOAJ

【 摘 要 】

Four de novo proteins differing in single mutation positions, with a chain length of 56 amino acids, represent diverse 3D structures: monomeric 3α and 4β + α folds. The reason for this diversity is seen in the different structure of the hydrophobic core as a result of synergy leading to the generation of a system in which the polypeptide chain as a whole participates. On the basis of the fuzzy oil drop model, where the structure of the hydrophobic core is expressed by means of the hydrophobic distribution function in the form of a 3D Gaussian distribution, it has been shown that the composition of the hydrophobic core in these two structural forms is different. In addition, the use of a model to determine the structure of the early intermediate in the folding process allows to indicate differences in the polypeptide chain geometry, which, combined with the construction of a common hydrophobic nucleus as an effect of specific synergy, may indicate the reason for the diversity of the folding process of the polypeptide chain. The results indicate the need to take into account the presence of an external force field originating from the water environment and that its active impact on the formation of a hydrophobic core whose participation in the stabilization of the tertiary structure is fundamental.

【 授权许可】

Unknown