Proteins are biological linear heteropolymers composed of 20 different types of monomers known as amino acids. Proteins are the most abundant biological macromolecules in nature with a very wide range of functions and operating environments. For functionality, a protein needs an appropriate structure. This depends on the amino acid sequence of the protein and the environment in which the protein is found. Under certain conditions, protein aggregation can be observed, which is a multi-step process in which proteins adhere to each other. Aggregation is often seen as a harmful process, as proteins lose their functionality in this process, so researchers are trying to understand the mechanisms and causes of protein aggregation. Using experimental techniques, they came to the interesting conclusion that in the first stages of aggregation, interactions occur between sequences that usually have non-random proportions of representation of individual amino acids. However, since the research of aggregation and hot regions can be very expensive and time-consuming, more and more people want to tackle the study of aggregation with the help of molecular modeling and computational chemistry methods. Various soluble proteins, which are found in high concentrations in the eye lenses of vertebrates, have been classified as crystallins. Due to the specificity of their tasks and their long lifespan, they are very soluble and stable, and they also have an unusually high refractive index. Special groups among crystallins are β-crystallins and γ-crystallins. Both groups have very similar structures, main difference being that β-crystallins are in the form of oligomers, while γ-crystallins are found strictly in monomeric form. In 2021, a study was carried out using molecular dynamics to observe the first stages of aggregation of three proteins, one of which was human γD-crystallin. The aim of the research was to detect hot regions for aggregations without an experiment. The composure of the identified potential hot regions was found to be consistent with the typical proportions of hot regions determined by experimental methods. In the first part of this assignment, with the help of Hartree-Fock method (HF method) in the Spartan'14 program, I determine the energy, ionization and electrostatic potential, of those hot regions in human γD-crystallin, and by analyzing the obtained results, I tried to contribute something to the understanding of the aggregation of this protein. In the second part of the assignment, I tried to do some research on the oligomeric composition of bovine βL-crystallin depending on the concentration of NaCl, using the experimental techniques of zeta potential and dynamic light scattering (DLS) measurements.
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