Vpliv polimorfizma posameznega nukleotida rs4880 na genu SOD2 na sekundarno strukturo encima manganove superoksid-dismutaze

magistrsko delo

Matic Broz (Author), Urban Bren (Mentor), Veronika Furlan (Co-mentor)

Abstract

Reaktivne kisikove spojine so reaktivni prosti radikali, ki nastajajo kot stranski produkt presnove kisika pri celičnem dihanju. Čeprav škodujejo celicam in povzročajo t.i. oksidativni stres, igrajo pomembno vlogo pri celični signalizaciji in v imunskem odzivu, zato je konstanta koncentracija teh molekul ključna za pravilno delovanje celic. V mitohondriju, največjem viru kisikovih prostih radikalov, deluje encim MnSOD, ki katalizira razgradnjo superoksidnega aniona. V magistrskem delu smo s pomočjo računalniških simulacij molekulske dinamike želeli ugotoviti, kako dimorfizem Ala16Val vpliva na sekundarno strukturo 24 aminokislin dolge mitohondrijske tarčne sekvence MnSOD, ki je ključna za uspešen transporta prekurzorske MnSOD v mitohondrijski matriks in posledično za uspešen transport MnSOD v mitohondrij, kjer le-ta opravlja svojo funkcijo. Za načrtovanje treh modelov obeh variant smo uporabili predpostavljeno strukturo iz literature in spletni orodji za določevanje sekundarne strukture peptidov PEPFOLD3 in Phyre2. S pomočjo programa PyMOL in spletnega orodja H++ smo pripravili vhodne datoteke za poganjanje simulacij molekulske dinamike s programskim paketom GROMOS++. Dobljeni rezultati kažejo, da sta najstabilnejša modela za obe varianti napovedana z orodjem Phyre2: dvakrat prekinjen α-heliks za alanin in neprekinjen α-heliks za valin, kot stabilna, pa sta se izkazala tudi modela, napovedana s PEPFOLD3. Rezultati za varianto z alaninom kažejo na α-heliks, katerega enkrat prekine zavoj. Rezultati za valin so deloma razdvojeni in kažejo, da je najbolj stabilen krajši α-heliks, kot ga je predvideval začetni model. Obe ugotovitvi sta tudi v skladu z literaturo, ki pravi, da imajo prekurzorske sekvence večinoma obliko amfifilnih α-heliksov. V svoji raziskavi smo ovrgli hipotezo, da sta strukturi, predpostavljeni v dosedanji literaturi, stabilni.

Keywords

manganova superoksid-dismutaza;polimorfizem rs4880;mutacija Ala16Val;simulacije molekulske dinamike;magistrske naloge;

Data

Language:	Slovenian
Year of publishing:	2019
Typology:	2.09 - Master's Thesis
Organization:	UM FKKT - Faculty of Chemistry and Chemical Engineering
Publisher:	[M. Broz]
UDC:	575.224(043.2)
COBISS:	22688790
Views:	861
Downloads:	124
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	English
Secondary title:	The effect of single nucleotide polymorphism rs 4880 on sod2 gene on secondary structure of manganese superoxide-dismutase enzyme
Secondary abstract:	Reactive oxygen species (ROS) are reactive free radicals that are formed as a by-product of oxygen metabolism in cellular respiration. Although ROS can damage cells and cause so-called oxidative stress, they play an important role in cell signaling and in the immune response, which makes maintaining a constant concentration of these molecules crucial for the proper functioning of cells. In the mitochondria, the largest source of oxygen free radicals, the enzyme MnSOD acts as a catalyst for the dismutation of the superoxide anion. In master's thesis, we aimed to determine through molecular dynamics simulations how Ala16Val dimorphism affects the secondary structure of the 24 amino acid MnSOD mitochondrial target sequence, which is crucial for successful transport of the precursor MnSOD into the mitochondrial matrix where it scavenges for superoxide anions. For both sequence variants, alanine and valine, three models were designed by using the structure determined in the literature and online tools (PEPFOLD3 and Phyre2) for determining the secondary structure of peptides. Using the program PyMOL and the H++ web tool, we have prepared input files for running molecular dynamics simulations with the GROMOS ++ software package. The obtained results indicate that the most stable models for both variants were predicted by the Phyre2 tool, a twice bend broken α-helix for alanine and unbroken α-helix for valine, however, the models predicted by PEPFOLD3 were comparable to Phyre2. The results indicate that the most stable secondary structure for alanine is a by a bend broken α-helix that extends across the most part of the peptide. The results for valine are divided but overall indicate a shorter α-helix than predicted by initial models. Both findings are in the agreement with the literature, which suggests that mitochondrial targeting sequences adopt an amphiphilic α-helixes. We disproved the hypothesis that the structures predicted in the literature till date are stable.
Secondary keywords:	manganese superoxide-dismutase;polymorphism rs4880;mutation Ala16Val;simulations of molecular dynamics;
Type (COBISS):	Master's thesis/paper
Thesis comment:	Univ. v Mariboru, Fak. za kemijo in kemijsko tehnologijo
Pages:	XIII, 60 str.
ID:	11214607