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master's thesis
Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis
Zagreb: University of Zagreb, Faculty of Science, 2023. urn:nbn:hr:217:725506
Batković, Michaela
University of Zagreb
Faculty of Science
Department of Chemistry

Institutional repository: Repository of the Faculty of Science

Cite this document

Batković, M. (2023). Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:725506

Batković, Michaela. "Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis." Master's thesis, University of Zagreb, Faculty of Science, 2023. https://urn.nsk.hr/urn:nbn:hr:217:725506

Batković, Michaela. "Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis." Master's thesis, University of Zagreb, Faculty of Science, 2023. https://urn.nsk.hr/urn:nbn:hr:217:725506

Batković, M. (2023). 'Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis', Master's thesis, University of Zagreb, Faculty of Science, accessed 14 May 2024, https://urn.nsk.hr/urn:nbn:hr:217:725506

Batković M. Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2023 [cited 2024 May 14] Available at: https://urn.nsk.hr/urn:nbn:hr:217:725506

M. Batković, "Računalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2023. Available at: https://urn.nsk.hr/urn:nbn:hr:217:725506

Metadata
TitleRačunalno istraživanje kompleksa DNA i MntR proteina iz bakterije Bacillus subtilis
Title (english)Computational study DNA in complex with the MntR protein from the bacterium Bacillus subtilis
AuthorMichaela Batković
MentorBranimir Bertoša (mentor)
Committee memberBranimir Bertoša (predsjednik povjerenstva)
Committee memberIvan Kodrin (član povjerenstva)
Committee memberMarko Močibob (član povjerenstva)
Committee memberDavor Kovačević (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Chemistry)
Zagreb
Defense date and country2023-09-27, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Chemistry
Abstract
Transkripcijski faktor MntR (engl. Manganese Transport Regulator) homodimerni je protein odgovoran za regulaciju homeostaze manganovih iona u bakteriji Bacillus subtilis. Kada je u svojoj holo-formi, to jest kada su unutarstanične koncentracije manganovih iona previsoke, transkripcijski faktor MntR se veže na ciljnu DNA i ponaša kao represor. Postoji nekoliko mehanizama kojima se proteini vežu na DNA, međutim, mehanizam vezanja proteina MntR na svoju ciljnu DNA nije razjašnjen. U ovom diplomskom radu provedeno je računalno istraživanje koje za cilj ima doprinjeti razumijevanju interakcija između transkripcijskog faktora MntR i njegove ciljne DNA sekvence. Rezultati simulacija molekulske dinamike (MD) kompleksa DNA-MntR ukazuju da će doći do odvajanja sastavnica kompleksa ukoliko zavojnica α3 proteina, odgovorna za prepoznavanje palindromskog slijeda ciljne DNA, nije položena u blizini središta palindromskog slijeda TTT/AAA pri čemu će posljedično doći do značajnih fluktuacija molekule DNA. U suprotnom slučaju, dolazi do stvaranja specifičnih vodikovih veza između proteina i DNA, te su te vodikove veze zastupljene većinu trajanja simulacije, pri čemu dodatno dolazi i do otvaranja velikog utora.
Abstract (english)
The transcription factor MntR ( Manganese Transport Regulator) is a homodimeric protein in Bacillus subtilis responsible for the regulation of manganese homeostasis. When in its holoform, that is when the intracellular concentrations of managanese ions are too high, the transcription factor MntR binds on its target DNA and acts as a repressor. There are few binding mechanisms by which proteins bind to DNA. However, the one by which our protein of interest binds to its target DNA is still unknown. In this Diploma Thesis a computational study was carried out with the aim to contribute to the understanding of the interactions between the transcription factor MntR and its target DNA sequence. Molecular dynamics (MD) simualtions revealed that the components of the DNA-MntR complex will seperate if the recognition helix α3 of the protein is not placed near the center of the palindrome TTT/AAA which will result in significant fluctuations of the DNA molecule. In the opposite case, during the whole simualtion specific hydogen bonds are formed accompanied with major groove opening.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:725506
ProjectNumber: IP-2020-02-3446
Title: Manganovi metalosenzori
Title: Manganese Metallosensors
Acronym: MaMes
Leader: Branimir Bertoša
Jurisdiction: Croatia
Funder: HRZZ
Funding stream: IP
Study programmeTitle: Graduate university studies in chemistry; specializations in: Research programme
Course: Research programme
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra kemije (magistar/magistra kemije)
Type of resourceText
File originBorn digital
Access conditionsOpen access
Terms of useLicence In copyright icon
Created on2023-10-13 09:56:09