prikaz prve stranice dokumenta Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori
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master's thesis
Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori
Zagreb: University of Zagreb, Faculty of Science, 2018. urn:nbn:hr:217:904676
Vuković, Vedran
University of Zagreb
Faculty of Science
Department of Biology

Institutional repository: Repository of the Faculty of Science

Cite this document

Vuković, V. (2018). Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:904676

Vuković, Vedran. "Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori." Master's thesis, University of Zagreb, Faculty of Science, 2018. https://urn.nsk.hr/urn:nbn:hr:217:904676

Vuković, Vedran. "Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori." Master's thesis, University of Zagreb, Faculty of Science, 2018. https://urn.nsk.hr/urn:nbn:hr:217:904676

Vuković, V. (2018). 'Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori', Master's thesis, University of Zagreb, Faculty of Science, accessed 17 May 2024, https://urn.nsk.hr/urn:nbn:hr:217:904676

Vuković V. Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2018 [cited 2024 May 17] Available at: https://urn.nsk.hr/urn:nbn:hr:217:904676

V. Vuković, "Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2018. Available at: https://urn.nsk.hr/urn:nbn:hr:217:904676

Metadata
TitleRačunalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori
Title (english)Computational investigation of Helicobacter pylori purine Nucleoside Phosphorylase
AuthorVedran Vuković
MentorBranimir Bertoša (mentor)
Committee memberBranimir Bertoša (član povjerenstva)
Committee memberDamjan Franjević (član povjerenstva)
Committee memberMartina Šeruga Musić (član povjerenstva)
Committee memberIvana Ivančić Baće (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Biology)
Zagreb
Defense date and country2018-02-23, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Biology
Abstract
Purinska nukleozidna fosforilaza (PNP) enzim je koji sudjeluje u metabolizmu razgradnje nukleotida. Ljudski i bakterijski enzimi razlikuju se po primarnom nizu aminokiselina, stupnju oligomerizacije u nativnom stanju (trimeri, odnosno heksameri) te specifičnosti prema supstratima. Cilj je ovog rada bio istražiti strukturna i dinamička svojstva PNP-a iz bakterije Helicobacter pylori (HpPNP), čija je struktura nedavno riješena rendgenskom strukturnom analizom, te utjecaj prirodnih supstrata i potencijalnih inhibitora na enzim HpPNP korištenjem računalnih metoda. Vezanje liganada u vezno mjesto enzima HpPNP proučavano je metodom molekulskog uklapanja (eng. docking). Metoda molekulske dinamike korištena je za izučavanje strukturnih i dinamičkih svojstava enzima HpPNP, samog i u kompleksima s različitim ligandima. Ukupno je napravljeno 9 simulacija duljine 20 ns na temelju 9 različitih sustava, od kojih 7 sadrži ligande u veznim mjestima HpPNP, dok u preostala dva sustava nema liganada. Pronađene su i opisane nekovalentne interakcije liganada s aminokiselinskim ostatcima veznog mjesta. Uočene su razlike u konformaciji vezanih liganada i njihov utjecaj na vodikove veze između podjedinica heksamera. Metodom analize glavnih komponenata zamijećene su veće konformacijske promjene enzima HpPNP.
Abstract (english)
Purine nucleoside phosphorylase (PNP) is an enzyme which participates in nucleoside degradation metabolism. Human and bacterial enzymes differ in primary amino acid sequence, oligomerisation in the native state (trimers and hexamers, respectively) and substrate specificity. The goal of this Thesis was to investigate structural and dynamic properties of Helicobacter pylori PNP (HpPNP) enzyme in apo form and in complexes with different ligands, the structure of which was recently solved using X-ray structure dete rmination, using computational methods. Ligand binding to the HpPNP enzyme active site was studied using molecular docking approach. Molecular dynamics simulations were used to investigate the influence of ligands on the HpPNP enzyme. Nine systems were simulated, up to 20 ns each. Seven of these systems contain ligands in HpPNP enzyme binding sites, while the remaining two contain no ligands. Non-covalent interactions between ligands and binding site amino acid residues were identified and analysed. Differences in conformations of the ligands bound and their influence on hydrogen bonds between hexamer subunits were observed. Large conformational changes of the HpPNP enzyme were detected using principal component analysis.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:904676
Study programmeTitle: Molecular Biology
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
Type of resourceText
File originBorn digital
Access conditionsOpen access
Terms of useLicence In copyright icon
Created on2018-05-03 07:58:32