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master's thesis
Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze
Zagreb: University of Zagreb, Faculty of Science, 2016. urn:nbn:hr:217:773199
Živković, Igor
University of Zagreb
Faculty of Science
Department of Chemistry

Institutional repository: Repository of the Faculty of Science

Cite this document

Živković, I. (2016). Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:773199

Živković, Igor. "Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze." Master's thesis, University of Zagreb, Faculty of Science, 2016. https://urn.nsk.hr/urn:nbn:hr:217:773199

Živković, Igor. "Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze." Master's thesis, University of Zagreb, Faculty of Science, 2016. https://urn.nsk.hr/urn:nbn:hr:217:773199

Živković, I. (2016). 'Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze', Master's thesis, University of Zagreb, Faculty of Science, accessed 25 November 2024, https://urn.nsk.hr/urn:nbn:hr:217:773199

Živković I. Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2016 [cited 2024 November 25] Available at: https://urn.nsk.hr/urn:nbn:hr:217:773199

I. Živković, "Mehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2016. Available at: https://urn.nsk.hr/urn:nbn:hr:217:773199

Metadata
TitleMehanizam diskriminacije leucina u mjestu za popravak pogreške leucil-tRNA-sintetaze
Title (english)The mechanism of leucine discrimination in the editing site of leucyl-tRNA synthetase
AuthorIgor Živković
MentorIta Gruić Sovulj (mentor)
MentorBranimir Bertoša (mentor)
Committee memberIta Gruić Sovulj (predsjednik povjerenstva)
Committee memberBranimir Bertoša (član povjerenstva)
Committee memberBiserka Prugovečki (član povjerenstva)
Committee memberPredrag Novak (član povjerenstva)
Committee memberJasmina Rokov Plavec (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Chemistry)
Zagreb
Defense date and country2016-07-12, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Chemistry
Abstract
Enzimi leucil-tRNA-sintetaze (LeuRS) kovalentno vežu leucin na tRNALeu. Osim leucina, LeuRS na tRNALeu mogu prenositi i nepripadne aminokiseline, pri čemu je najveća prijetnja točnosti te reakcije neproteinogeni norvalin. Iz tog razloga LeuRS posjeduje mehanizme za popravak pogreške. Većina popravka odvija se nakon prijenosa aminokiseline na tRNA u zasebnoj domeni za popravak pogreške. Kako bismo odgovorili na pitanje diskriminira li domena za popravak Leu-tRNALeu na temelju vezanja, kao što je dosad smatrano, ili kinetike, provedene su simulacije molekularne dinamike (MD) divljeg tipa i mutanta T252A, za koji je poznato da hidrolizira Leu-tRNALeu, s analozima supstrata leucil- i norvalil-2'-adenozinom u domeni za popravak pogreške. Naši rezultati sugeriraju da vezanje leucina u konformaciji opisanoj torzijskim kutem N-Cα-Cβ-Cγ od oko ±180° uzrokuje kaskadu događaja koja dovodi do udaljavanja katalitičke vode od veze koja se hidrolizira i do smanjenog vremenskog udjela koji ona provodi u aktivnom mjestu tijekom simulacije. Ovo se ne odvija kod simulacija T252A mutanta, kao ni kod simulacija T252S i T252V mutanata. Kinetički rezultati sugeriraju da mutanti T252S i T252V akumuliraju Leu-tRNALeu kao i divlji tip enzima, što je donekle u neslaganju s rezultatima dobivenim MD simulacijama.
Abstract (english)
Leucyl-tRNA synthetase (LeuRS) covalently couples leucine with tRNALeu. These enzymes can also transfer several non-cognate amino acids on tRNALeu with the biggest threat to fidelity posed by non-proteinogenic norvaline. To prevent misacylation, LeuRS employs editing. The predominant editing pathway occurs at the separate editing domain following aminoacyl transfer to tRNA. To address the question if the editing domain discriminates leucine based on ground state binding, as anticipated, or based on the kinetics, we employed molecular dynamics (MD) simulation for the wild type LeuRS and the mutant T252A, which hydrolyses Leu-tRNALeu, with the substrate analogues leucyl- and norvalyl-2’-adenosine in the editing active site. Our results suggest that binding of leucine in a conformation defined by N-Cα-Cβ-Cγ torsion angle of approximately ±180° triggers a cascade of events that result in distancing of the catalytic water from the susceptible bond and decrease in time the water molecule occupies the active site. This was not observed in T252A, nor in the mutants T252S and T252V. Kinetic results suggest that T252S and T252V accumulate Leu-tRNALeu wild type alike, which is somewhat in disagreement with MD results.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:773199
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
Embargo expiration date: 2017-07-12
Terms of useLicence In copyright icon
Created on2017-03-14 17:10:42