Računalna i eksperimentalna analiza interakcije između DNA i transkripcijskog faktora MntR-a iz Mycobacterium tuberculosis

master's thesis

• Title (english): Computational and experimental analysis of interaction between Mycobacterium tuberculosis transcription factor MntR and DNA
• Author: Lana Semenić
• Mentor: Branimir Bertoša (mentor)
• Committee member: Branimir Bertoša (predsjednik povjerenstva)
• Committee member: Ivana Ivančić Baće (član povjerenstva)
• Committee member: Martina Šeruga Musić (član povjerenstva)
• Committee member: Gordan Horvat (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2024-09-16, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

MntR (regulator prijenosa mangana, engl. manganese transport regulator) je homodimerni transkripcijski faktor koji kontrolira homeostazu manganovih(II) kationa u bakterijama, među kojima je i ljudski patogen Mycobacterium tuberculosis. Vezanjem manganovih(II) kationa MntR iz neaktivnog apo-oblika prelazi u aktivni holo-oblik, koji se može vezati za DNA. Strukture apo- i holo-oblika riješene su kristalografijom X-zraka, ali to nije slučaj za njegov kompleks s DNA. Cilj ovog diplomskog rada bio je istražiti vezanje proteina MntR za DNA koristeći multidisciplinarni pristup, koji kombinira molekulsku dinamiku, bioinformatiku i eksperimentalne metode. U promotoru gena mntH identificiran je novi MntR-vezujući slijed. Iskorišten je za stvaranje in silico kompleksa molekulskim uklapanjem (engl. docking), tako da se MntR svojim DNA-vezujućim zavojnicama vezao za palindromske sljedove. Provedeno je više simulacija molekulske dinamike kako bi se detektirale nekovalentne interakcije između proteina i DNA te analizirale razlike između apo- i holo-oblika. Oba protomera pokazala su mogućnost stvaranja relativno dugotrajnih vodikovih veza između ostatka Ser46 i dušičnih baza istraživane DNA. Međutim, te vodikove veze uglavnom se nisu pojavljivale istovremeno. Ovo istraživanje predstavlja jedan od početnih koraka prema razumijevanju interakcije između DNA i proteina MntR iz M. tuberculosis.

Abstract (english)

MntR (manganese transport regulator) is a homodimeric transcription factor that controls the homeostasis of manganese(II) cations in bacteria, including the human pathogen Mycobacterium tuberculosis. By binding manganese(II) cations, MntR transitions from an inactive apo-form to an active holo-form, which can bind to DNA. While the crystal structures of its apo- and holo-form have been determined via X-ray crystallography, the structure of the MntR-DNA complex has yet to be explored. This thesis aims to investigate DNA-binding properties of MntR using a multidisciplinary approach that combines molecular dynamics, bioinformatics and experimental methods. A novel MntR-binding motif, identified in the mntH promoter region, was used to form an in silico complex with MntR through the use of protein-DNA docking, wherein the DNA-binding helices were bound to palindromic sequences. Multiple molecular dynamics simulations were carried out in order to analyze non-covalent protein-DNA interactions and to determine differences between the apo- and holo-forms. Both protomers demonstrated the ability to form relatively long-lasting hydrogen bonds between their respective Ser46 residues and subject DNA. For the majority of the simulation time, however, these bonds were not present concurrently. This paper represents one of the initial steps towards understanding the interaction between MntR from M. tuberculosis and DNA.

• Keywords: manganovi metalosenzori; molekulska dinamika; molekulsko uklapanje
• Keywords (english): manganese metallosensors; molecular dynamics; molecular docking
• Language: croatian
• URN:NBN: urn:nbn:hr:217:784793
• Project: Number: IP-2020-02-3446; Title: Manganovi metalosenzori; Title: Manganese Metallosensors; Acronym: MaMes; Leader: Branimir Bertoša; Jurisdiction: Croatia; Funder: Hrvatska zaklada za znanost; Funding stream: Research Projects
• Study programme: Title: Molecular Biology-University graduate programme; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni/a magistar/magistra molekularne biologije (sveučilišni/a magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-09-22 10:57:40