Računalno istraživanje purinske nukleozidne fosforilaze iz bakterije Helicobacter pylori

master's thesis

• Title (english): Computational investigation of Helicobacter pylori purine Nucleoside Phosphorylase
• Author: Vedran Vuković
• Mentor: Branimir Bertoša (mentor)
• Committee member: Branimir Bertoša (član povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Martina Šeruga Musić (član povjerenstva)
• Committee member: Ivana Ivančić Baće (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2018-02-23, 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: Helicobacter pylori; metabolizam nukleozida; PNP; molekulsko uklapanje; molekulska dinamika
• Keywords (english): Helicobacter pylori; nucleoside metabolism; PNP; molecular docking; molecular dynamics
• Language: croatian
• URN:NBN: urn:nbn:hr:217:904676
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2018-05-03 07:58:32