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master's thesis
Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike
Zagreb: University of Zagreb, Faculty of Science, 2013. urn:nbn:hr:217:468247
Petrović, Saša
University of Zagreb
Faculty of Science
Department of Biology

Institutional repository: Repository of the Faculty of Science

Cite this document

Petrović, S. (2013). Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:468247

Petrović, Saša. "Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike." Master's thesis, University of Zagreb, Faculty of Science, 2013. https://urn.nsk.hr/urn:nbn:hr:217:468247

Petrović, Saša. "Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike." Master's thesis, University of Zagreb, Faculty of Science, 2013. https://urn.nsk.hr/urn:nbn:hr:217:468247

Petrović, S. (2013). 'Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike', Master's thesis, University of Zagreb, Faculty of Science, accessed 25 November 2024, https://urn.nsk.hr/urn:nbn:hr:217:468247

Petrović S. Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2013 [cited 2024 November 25] Available at: https://urn.nsk.hr/urn:nbn:hr:217:468247

S. Petrović, "Istraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2013. Available at: https://urn.nsk.hr/urn:nbn:hr:217:468247

Metadata
TitleIstraživanje supstratne specifičnosti acil-CoA tioesteraze I iz bakterije Pseudomonas aeruginosa korištenjem simulacije molekularne dinamike
Title (english)Investigation of substrate specificity of acyl-CoA thioesterase I from the bacteria Pseudomonas aeruginosa using molecular dynamics
AuthorSaša Petrović
MentorBranimir Bertoša (mentor)
Committee memberBranimir Bertoša (predsjednik povjerenstva)
Committee memberIta Gruić Sovulj (član povjerenstva)
Committee memberKristian Vlahoviček (član povjerenstva)
Committee memberDijana Škorić (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Biology)
Zagreb
Defense date and country2013-09-19, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Biology
Abstract
Acil-­CoA-­tioesteraza I (TesA) iz bakterije Pseudomonas aeruginosa lipolitički je enzim koji pripada obitelji GDSL hidrolaza. Obitelj GDSL hidrolaza relativno je nova i neistražena skupina enzima s velikim potencijalom za primjenu u farmaceutskoj i prehrambenoj industriji, kao i za daljnja biokemijska istraživanja. Posebnost ove enzimske obitelji su izuzetna supstratna nespecifičnost te tipični GDSL motiv oko serina iz katalitičke trijade, koji se razlikuje od GXSXG motiva iz većine dosad istraženih lipaza. TesA sudjeluje u putu sinteze masnih kiselina te katalizira hidrolizu čitavog niza supstrata (estera i tioestera različite duljine lanca masnih kiselina). U ovom radu pokušali smo razjasniti molekularnu osnovu supstratne specifičnosti i supstratnog promiskuiteta enzima TesA korištenjem računalnih metoda temeljenih na polju sila, prvenstveno molekularne dinamike (MD). Rezultati simulacija poduprti su eksperimentalnim mjerenjem aktivnosti enzima prema različitim supstratima. Simulacijama smo objasnili smještanje supstrata različitih veličina i oblika u aktivno mjesto TesA te promjene u strukturi i dinamici aktivnog mjesta izazvanih prisutnošću različitih supstrata te uvođenjem mutacija. Utjecaj izabranih mutacija istražen je in silico i eksperimentalnim metodama.
Abstract (english)
Acyl-­CoA thioesterase I (TesA) from the bacterium Pseudomonas aeruginosa is a lipolytic enzyme that belongs to the family of GDSL hydrolases. The GDSL hydrolase family is a relatively new and not so well investigated group of enzymes with a great potential for application in pharmaceutical and food industry. Members of this enzyme family have typical GDSL motif surrounding the serine form the catalytic triad, which is different from the GXSXG motif found in other lipases. Some members of the GDSL family show large substrate promiscuity. Enzyme TesA is engaged in the fatty acid synthesis, and it hydrolyses a large number of different substrates (esters and thioesters with different fatty acid chain length). In this thesis we have tried to determine the molecular basis of substrate specificity and promiscuity of enzyme TesA using force field based computational methods, primarily molecular dynamics (MD) simulations. Simulation results are supported by experimentally determined enzyme activity towards different substrates. We have investigated the positioning of differently sized and shaped substrates in the binding site of the enzyme TesA, as well as the changes in structure and dynamics of the binding site caused by the presence of different substrates. According to the simulation results, mutations that should affect TesA activity were proposed. The proposed mutants were investigated by in silico and experimental methods.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:468247
Study programmeTitle: Molecular Biology
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
Type of resourceText
File originBorn digital
Access conditionsAccess restricted to students and staff of home institution
Terms of useLicence In copyright icon
Created on2017-04-27 12:29:23