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Title:
Računalniške simulacije kooperativnosti interkalacije aflatoksina B1 v dvoverižno DNK
Authors:
ID
Kuna, Tibor
(Author)
ID
Bren, Urban
(Mentor)
More about this mentor...
Files:
MAG_Kuna_Tibor_2015.pdf
(2,67 MB)
MD5: 73EC05BAAE931E16D8222980604F1177
Language:
Slovenian
Work type:
Master's thesis/paper
Typology:
2.09 - Master's Thesis
Organization:
FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:
Aflatoksin B1 predstavlja enega najbolj močnih naravnih hepatokarcinogenov poznanih znanih človeku in povzroča rakava oboljenja pri primatih, miših, ptičih ipd. Ima zelo veliko afiniteto do interkalacije v dvoverižno DNK in nadalnje alkilacije z dušikovimi bazami, še posebej z gvaninom. Zato ne preseneča, da je bilo na njem narejeno veliko eksperimentalnega in teoretičnega dela. Namen tega magistrskega dela je ugotoviti kooperativnost vezave reaktivnega metabolita molekule aflatoksina B1 v dvoverižno DNK s pomočjo računalniških simulacij. V ta namen smo uporabili simulacije, ki temeljijo tako na principih kvantne mehanike kot na klasični fiziki. Da smo lahko izključili vplive okolja na vezavo preiskovane molekule, smo uporabili simetričen segment dvoverižne DNK, ki so nam ga posredovali ameriški eksperimentalni sodelavci. Za določevanje atomskih nabojev na molekuli reaktivnega metabolita aflatoksina B1 smo uporabili metodi Merz-Kollmana in RESP. Ustrezne parametre za simulacije molekulske dinamike (MD) smo prevzeli iz modificirane verzije AMBER-jevih topoloških in parametrskih datotek. Simulacije molekulske dinamike (50 ns) smo izvajali s programskim paketom Q. Na podlagi rezultatov MD smo izračunali Gibbsove proste energije solvatacije po metodah LIE in LRA ter kooperativnost vezave molekule reaktivnega metabolita aflatoksina. Kooperativnost alkilacije pa smo določali kot pogostost števila dogodkov, kjer sta vezavna atoma C7 in N8 znotraj določene odrezne razdalje, pri kateri lahko sklepamo, da nastane kovalentna vez. Dobljeni rezultati kažejo na podobnost metod LIE in LRA pri izračunu prostih energij solvatacije ter na znatno pozitivno kooperativnost pri procesu interkalacije molekul reaktivnega metabolita aflatoksina. Pri alkilaciji pa smo opazili, da vezava prve molekule reaktivnega metabolita aflatoksina v dvoverižno DNK zgolj rahlo pozitivno vpliva na alkilacijo naslednje molekule aflatoksina.
Keywords:
DNK
,
aflatoksin
,
prosta energija
,
molekulska dinamika
,
kooperativnost
Place of publishing:
Maribor
Publisher:
[T. Kuna]
Year of publishing:
2015
PID:
20.500.12556/DKUM-54427
UDC:
[66.093.1+66.095.253]:577.21(043.2)
COBISS.SI-ID:
18968854
NUK URN:
URN:SI:UM:DK:O2TK5LWA
Publication date in DKUM:
22.10.2015
Views:
2499
Downloads:
230
Metadata:
Categories:
KTFMB - FKKT
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:
KUNA, Tibor, 2015,
Računalniške simulacije kooperativnosti interkalacije aflatoksina B1 v dvoverižno DNK
[online]. Master’s thesis. Maribor : T. Kuna. [Accessed 17 April 2025]. Retrieved from: https://dk.um.si/IzpisGradiva.php?lang=eng&id=54427
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Secondary language
Language:
English
Title:
Computer simulations of aflatoxin B1 intercalation cooperativity into DNA double helix
Abstract:
Aflatoxin B1 (AFB1) represents one of the most powerful natural hepatocarcinogents known to man, since it causes cancer in primates, mice, birds, etc. It has a high affinity for intercalation into double stranded DNA and for subsequent alkylation with its nitrogen atoms, especially at guanine. So it comes as no surprise, that a lot of experimental and theoretical work has been performed on this topic. The goal of this master thesis is to examine the potential AFB1 binding cooperativity to the double stranded DNA with the help of computer simulations. To this goal, we applied computer simulations that have foundations both in quantum mechanics and in classical physics. To exclude any major differences in environment for the binding of the first and the second AFB1 molecule, we used a symetrical segment of double stranded DNA, which was provided to us by our American experimental colegues. For asigning partial atomic charges to the molecule of AFB1 the methods of Merz-Kollman and RESP were applied. Parameters for molecular dynamics simulations (MD) were obtained from a modified version of AMBER topological and parameter files. The molecular dynamics simulations (50 ns) were performed with the Q programme. From its results we calculated the Gibbs solvation free energies using the LIE and LRA methods, as well as the cooperativity of AFB1 binding. Cooperativity of alkylation was calculated on the basis of the frequency of events, when the biding atoms C7 and N8 were within a certain cut-off distance, which we suspect suitable for a covalent bond formation. The results show that both LIE and LRA methods provide similar solvatation free energies and that AFB1 intercalation proceeds with a high degree of positive homotropic cooperativity. For the alkylation cooperativity we observed, that the binding of the first AFB1 molecule only slighty positively affects the binding of the next AFB1 molecule.
Keywords:
DNA
,
aflatoxin
,
free energy
,
molecular dynamics
,
cooperativity
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