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Title:Interakcije biotehnološko relevantnih encimov : magistrsko delo
Authors:ID Grabrovec, Barbara (Author)
ID Bren, Urban (Mentor) More about this mentor... New window
ID Leitgeb, Maja (Co-mentor)
ID Konc, Janez (Co-mentor)
Files:.pdf MAG_Grabrovec_Barbara_2019.pdf (2,83 MB)
MD5: B4B499CFCDE376D225054A290342C8F9
PID: 20.500.12556/dkum/bab5fb3b-b08a-4f6b-901e-11d6a1e49437
 
Language:Slovenian
Work type:Master's thesis/paper (mb22)
Typology:2.09 - Master's Thesis
Organization:FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:Encimi so protein, ki pospešujejo biokemijske in kemijske reakcije. Njihove interakcije z ligandi so ključnega pomena za številne biokemične interakcije, ki uravnavajo življenje. Uporabljajo se v biotehnologiji, pri analitskih procesih, v človeški in živalski terapiji (za zdravila) ter v različnih industrijskih procesih, kamor spadajo tekstilna industrija, usnjarska industrija, farmacija, živilska industrija in druge. Kljub vsem dobrim lastnostim encimov, njihovo široko industrijsko uporabo pogosto ovirajo kratkotrajna stabilnost, rok uporabe ter njihova nepopolna regeneracija in ponovna uporaba. Te pomanjkljivosti lahko na splošno odpravimo z imobilizacijo encimov. V zadnjih letih so se pojavile podatkovne baze, ki vsebujejo podatke o interakcijah protein-ligand, kar je pripomoglo k razumevanju funkcij novo odkritih proteinov. Razvile so se številne nove računalniške metode, ki lahko uporabijo informacije shranjenih interakcij, da napovedo nove neznane interakcije. Najpogosteje uporabljena metoda za modeliranje interakcij je metoda molekulskega sidranja, ki se uporablja za simuliranje interakcije med majhno molekulo in proteinom na atomski ravni in nam opiše obnašanje majhne molekule v vezavnem mestu encima. V magistrskem delu smo s pomočjo programa molekulskega sidranja na encime vezali nizkomolekularne ligande. Strukture encimov smo pridobili v spletni bazi PDB, datoteke ligandov pa v spletni podatkovni bazi ZINC15. Kot rezultat smo dobili strukture ligandov, ki so se najmočneje vezali in njihovo energijo vezave. Rezultate smo pregledali s programoma Excel in Pymol, kjer smo videli 3D slike ligandov, ki so se na naše encime vezali z najnižjo energijo.
Keywords:encim, ligand, imobilizacija, biotehnologija, molekularno modeliranje, molekulsko sidranje
Year of publishing:2019
Place of performance:Maribor
Publisher:[B. Grabrovec]
Number of pages:VIII, 42 str.
Source:Maribor
PID:20.500.12556/DKUM-75155 New window
UDC:577.15:544.139(043.2)
COBISS.SI-ID:22689046 New window
NUK URN:URN:SI:UM:DK:XRSGSIG1
Publication date in DKUM:18.10.2019
Views:984
Downloads:68
Metadata:XML RDF-CHPDL DC-XML DC-RDF
Categories:KTFMB - FKKT
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Licences

License:CC BY-ND 4.0, Creative Commons Attribution-NoDerivatives 4.0 International
Link:http://creativecommons.org/licenses/by-nd/4.0/
Description:Under the NoDerivatives Creative Commons license one can take a work released under this license and re-distribute it, but it cannot be shared with others in adapted form, and credit must be provided to the author.
Licensing start date:25.09.2019

Secondary language

Language:English
Title:Interactions of biotechnologically relevant enzymes
Abstract:Enzymes are proteins, that accelerate biochemical and chemical reactions. Their interactions with ligands are crucial for many life-regulating biochemical interactions. They are used in biotehnology, in analytical processes, in human and animal therapy (as medicines) and in various industrial processes such as textile, leather, pharmacy, food and others. Despite of all the good properties of enzymes, their widespread industrial use is often hampered by long-term stability, shelf life and their cumbersome renewal and reuse. These disadvantages can generally be eliminated using enzyme immobilization. In recent years, databases containing protein-ligand interactions data have emerged, which has helped us to understand the functions of newly discovered proteins. Many new computional methods have been developed that can use the stored interaction information to predict new uknown interactions. The most commonly used interaction modeling method is molecular docking, which is used to model interactions between a small molecule and a protein on an atomistic scale, as well as to describe the behaviour of small molecules in enzyme binding sites. In this master's thesis low molecular ligands were attached to enzymes using computional method called molecular docking. Enzyme structures were obtained from PDB online database and ligand files were obtained from the ZINC15 online database. As a result we obtained the structures of ligands that bonded best as well as their binding energy. We reviewed the results using Excel and Pymol, where we got 3D structures of ligands that attached to our enzymes with the lowest energy.
Keywords:enzyme, ligand, biotehnology, molecular modeling, molecular docking


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