Vezanje iona prijelaznih metala u ljudskoj dipeptidil-peptidazi III

doctoral thesis

• Title (english): Binding of transition metal ions into human dipeptidyl peptidase III
• Author: Antonia Matić
• Mentor: Sanja Tomić (mentor)
• Committee member: Aleksandra Maršavelski (predsjednik povjerenstva)
• Committee member: Ivana Leščić Ašler (član povjerenstva)
• Committee member: Ivo Crnolatac (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2024-02-16, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry
• Universal decimal classification (UDC): 54 - Chemistry. Crystallography. Mineralogy

Abstract

Cilj istraživanja bio je odrediti učinak vezanja različitih dvovalentnih iona metala: Zn2+, Mn2+, Co2+, Cu2+, u različitim koncentracijama, na aktivnost ljudske dipeptidil-peptidaze III (hDPP III), istražiti pretpostavku postojanja inhibitornog veznog mjesta metala i ukoliko je točna, identificirati ga. Istraživanja su provedena kombiniranjem različitih eksperimentalnih i računalnih metoda. Za potrebe eksperimentalnog istraživanja pripremljeni su holoenzimi s ionima Zn2+, Mn2+, Co2+ i Cu2+. U tim uzorcima stehiometrija metal-protein određena je spektrometrijom masa s induktivno spregnutom plazmom (ICP-MS) i izotermalnom titracijskom kalorimetrijom (ITC). Koristeći metodu spektroskopije zaustavljenog protoka, pratilo se smanjenje enzimske aktivnosti hDPP III uzrokovano viškom iona metala. Računalnim metodama, kvantno mehaničkim izračunima i molekulsko dinamičkim simulacijama, određeni su afiniteti različitih kationa metala prema aktivnom mjestu hDPP III, identificirana su inhibitorna vezna mjesta za ione bakra i cinka i određen je mehanizam izmjene metalnih iona vezanih u inhibitorno i katalitičko vezno mjesto.

Abstract (english)

The aim of the study was to determine the binding effect of various divalent ionic metals: Zn2+, Mn2+, Co2+, Cu2+, in different concentrations, on the activity of human dipeptidyl peptidase III (hDPP III), to verify our assumption of the existence of an inhibitory metal binding site and, if correct, to identify this site. The investigations were carried out by combining different experimental and computational methods. For the experimental studies, holoenzymes with Zn2+, Mn2+, Co2+, and Cu2+ ions were prepared. In these samples, the metal-protein stoichiometry was determined by inductively coupled plasma mass spectrometry (ICP-MS) and isothermal titration calorimetry (ITC). Stopped flow spectroscopy was used to monitor the decrease in hDPP-III enzyme activity due to an excess of metal ions. Computational methods, quantum mechanical calculations and molecular dynamics simulations were used to determine the affinities of different metal dications to the active site of hDPP III, to identify the inhibitory binding site for copper and zinc ions and to determine the mechanism of exchange of metal ions bound to the inhibitory and catalytic binding sites.

• Keywords: judska dipeptidil–peptidaza III; kvantna mehanika; ioni metala; molekulska dinamika
• Keywords (english): human dipeptidyl peptidase III; metal ions; molecular dynamics; quantum mechanics
• Language: croatian
• URN:NBN: urn:nbn:hr:217:874265
• Promotion: 2024
• Project: Number: IP-2018-01-2936; Title: Biološka važnost dipeptidil peptidaze III i njezin utjecaj na zdravlje čovjeka; Acronym: DPP3BioRe; Leader: Sanja Tomić; Jurisdiction: Croatia; Funder: HRZZ; Funding stream: IP
• Study programme: Title: Doctoral study; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor/doktorica u području prirodnih znanosti (doktor/doktorica u području prirodnih znanosti)
• Type of resource: Text
• Extent: 115 str. ; 30 cm
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-02-29 10:48:58