Molekulsko modeliranje bakterijskih dipeptidil-peptidaza III

doctoral thesis

• Title (english): Molecular modellling of bacterial dipeptidyl-peptidases III
• Author: Marko Tomin
• Mentor: Sanja Tomić (mentor)
• Committee member: Branimir Bertoša (predsjednik povjerenstva)
• Committee member: Zlatko Mihalić (član povjerenstva)
• Committee member: Marija Abramić (član povjerenstva)
• Committee member: David Matthew Smith (član povjerenstva); MBZ: 260506
• Granter: University of Zagreb; Faculty of Science; (Department of Chemistry); Zagreb
• Defense date and country: 2018-05-24, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Chemistry
• Universal decimal classification (UDC): 54 - Chemistry. Crystallography. Mineralogy

Abstract

Dipeptidil-peptidaza III (DPP III) dvodomenski je protein, metalopeptidaza iz porodice M49, koja u aktivnom mjestu sadrži ion cinka te otcjepljuje dipeptide s N-kraja svojih supstrata. Fokus ove doktorske disertacije bilo je proučavanje strukture i dinamike dviju bakterijskih DPP III: iz mezofila Bacteroides thetaiotaomicron i iz termofila Caldithrix abyssi, te njihovih kompleksa sa sintetičkim supstratima i odabranim inhibitorima. Metodama molekulske dinamike izučavane su konformacijske promjene dugog dosega unutar enzima i pritom je ispitana uspješnost nekoliko polja sila u reproduciranju eksperimentalnih struktura i očekivanih gibanja. Usporedbom strukture i dinamike proteina iz termofilnog i mezofilnog mikroorganizma pružen je uvid u strukturnu osnovu za termalnu stabilnost DPP III iz Caldithrix abyssi. Određeni su biološki relevantni načini vezanja supstrata, odnosno inhibitora, što je omogućilo povezivanje supstratne specifičnosti i aktivnosti pojedinih ortologa sa strukturnim karakteristikama kompleksa i fleksibilnosti enzima. Dobiveni rezultati korišteni su za izradu modelnog sustava DPP III iz Bacteroides thetaiotaomicron koji je podvrgnut kvantno-mehaničkim računima te je predložen mehanizam hidrolize peptidne veze kataliziran od strane navedene peptidaze.

Abstract (english)

Dipeptidyl peptidase III (DPP III) is a two-domain protein, a metallopeptidase from the M49 family which contains a zinc ion within its active site and cleaves dipeptides from the N-terminus of its substrates. The aim of this thesis was was to study the structure and flexibility of DPP III from the mesophilic bacterium Bacteroides thetaiotaomicron and the thermophile Caldithrix abyssi as well as their complexes with synthetic substrates and selected inhibitors. Several force fields have been tested in order to determine the most suitable one for studying the long-range conformational motions of the enzyme. Comparison of results obtained for a termophile with those of a mesophile revealed the structural reasons for thermal stability of DPP III from Caldithrix abyssi. The biologically relevant binding modes of substrates and inhibitors were identified and correlated with structural characteristics of the respective complexes, as well as with the enzyme flexibility. These results were used to build a model system of the Bacteroides thetaiomicron DPP III which was used in a quantum mechanics study in order to propose the reaction mechanism of the peptide bond hydrolysis.

• Keywords: dipeptidil-peptidaza III; DPP III; molekulska dinamika; supstratna specifičnost; termofil; mehanizam reakcije; peptidaza
• Keywords (english): dipeptidyl peptidase III; DPP III; molecular dynamics; substrate specificity; thermophile; reaction mechanism; peptidase
• Language: croatian
• URN:NBN: urn:nbn:hr:217:561583
• Study programme: Title: Doctoral study in chemistry; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija (doktor/doktorica znanosti, područje prirodnih znanosti, polje kemija)
• Type of resource: Text
• Extent: 124 str. ; 30 cm
• File origin: Born digital
• Access conditions: Open access
• Created on: 2018-06-05 11:12:12