diplomsko delo
Vid Dobrovoljc (Avtor), Barbara Hribar (Mentor)

Povzetek

Proteini so biološki linearni heteropolimeri, sestavljeni iz 20 različnih tipov monomerov, ki jih imenujemo aminokisline. So v naravi najbolj zastopane biološke makromolekule z zelo širokim naborom funkcij in obratovalnih okolij. Za funkcionalnost proteinov je ključna njihova tridimenzionalna struktura. Ta je odvisna od aminokislinskega zaporedja proteina in okolja, v katerem se protein nahaja. Pod določenimi pogoji lahko opazimo agregacijo proteinov, ki je večstopenjski proces pri katerem se proteini med seboj sprimejo. Na agregacijo pogosto gledamo kot na škodljiv proces, saj pri tem proteini izgubijo funkcionalnost, zato se raziskovalci trudijo razumeti mehanizme in vzroke proteinske agregacije. Z eksperimentalnimi tehnikami so prišli do dognanja, da v prvih stopnjah agregacije pride do interakcij med zaporedji, ki imajo navadno nenaključne deleže zastopanosti posameznih aminokislin. Ker pa so raziskave agregacije in vročih regij lahko zelo drage in zamudne, se vedno več ljudi želi študija agregacije lotiti s pomočjo metod molekulskega modeliranja in računske kemije. Kristalini so različni proteini, ki se v visokih koncentracijah nahajajo v očesnih lečah vretenčarjev. Zaradi specifike svojih nalog in dolge življenjske dobe so zelo dobro topni in stabilni, imajo pa tudi nenavadno visok lomni količnik. Posebni skupini med kristalini sta skupina β-kristalinov in skupina γ-kristalinov. Obe skupini imata zelo podobne strukture, glavna razlika pa je v tem, da so β-kristalini v obliki oligomerov, γ-kristaline pa najdemo strogo le v monomerni obliki. Leta 2021 je bila opravljena raziskava, kjer so z uporabo molekulske dinamike opazovali prve stopnje agregacije treh proteinov. Eden izmed njih je bil tudi človeški γD-kristalin. Cilj raziskave je bila detekcija vročih regij za agregacijo brez eksperimenta. Določene potencialne vroče regije so po sestavi zaporedij konzistentne z deleži, ki so bili določeni kot tipični za te regije z eksperimentalnimi metodami. V prvem delu naloge sem se s pomočjo Hartree-Fockove metode (HF metode) v programu Spartan'14 lotil računanja energije, ionizacijskega in elektrostatskega potenciala vročih regij v človeškem γD-kristalinu, z analizo dobljenih rezultatov pa sem poskusil prispevati nekaj k razumevanju agregacije tega proteina. V drugem delu naloge sem z eksperimentalnima tehnikama merjenja zeta potenciala in dinamičnega sipanja laserske svetlobe (DLS) poskusil opraviti nekaj raziskav oligomerne sestave govejega βL-kristalina v odvisnosti od koncentracije NaCl.

Ključne besede

proteinska tridimenzionalna struktura;agregacija proteinov;kristalini;računska kemija;Hartree-Fockova metoda;zeta potencial;

Podatki

Jezik: Slovenski jezik
Leto izida:
Tipologija: 2.11 - Diplomsko delo
Organizacija: UL FKKT - Fakulteta za kemijo in kemijsko tehnologijo
Založnik: [V. Dobrovoljc]
UDK: 577.322(043.2)
COBISS: 128075267 Povezava se bo odprla v novem oknu
Št. ogledov: 46
Št. prenosov: 14
Ocena: 0 (0 glasov)
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Ostali podatki

Sekundarni jezik: Angleški jezik
Sekundarni naslov: Aggregation of βγ-crystallins
Sekundarni povzetek: 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.
Sekundarne ključne besede: protein three dimensional structure;crystallins;computational chemistry;Hartree-Fock method;zeta potential;Beljakovine;Univerzitetna in visokošolska dela;
Vrsta dela (COBISS): Diplomsko delo/naloga
Študijski program: 1000371
Konec prepovedi (OpenAIRE): 1970-01-01
Komentar na gradivo: Univ. v Ljubljani, Fak. za kemijo in kemijsko tehnologijo, UNI Biokemija
Strani: 35 str.
ID: 16391574