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MD simulations of complexes between nucleic acids and RNase H
Bartek, Tomáš ; Burda, Jaroslav (referee) ; Barvík, Ivan (advisor)
The aim of this diploma thesis was to study interactions between human Rase H enzyme and a natural and modified substrate using molecular dynamics simulations (altogether 9 MD runs ere produced). Conformational preferences of internucleotide linkages (undergoing contacts with the RNase H enzyme) were studied using several versions of the AMBER force field. Either one or two copies of RNase H were included into the simulated system. As the most important DNA-binding residues were recognized Trp93 and Ser101 in the first DNA binding site and Thr49 and Arg47 in the second DNA binding site. Further, the AMBER force field was re-parameterized slightly using ab initio calculations to produce force constants for the modified phosphonate internucleotide linkage. Biologically active version of the modified internucleotide linkage C3-O3-P-C-O5-C5 was able to bind Arg47 using two hydrogen bonds within the 10 ns MD run (even more effciently than in the case of MD runs with natural internucleotide linkages). On the other hand, the biologically inactive C3-O3-C-P-O5-C5 internucleotide linkage lose contacts with Arg47 quickly.
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The Study of hydration models on platinum complexes important in anticancer cure
Bradáč, Ondřej ; Burda, Jaroslav (advisor) ; Záliš, Stanislav (referee)
In this work, there are studied some biologically important platinum complexes, cisplatin analogues, with central platinum atom in state Pt(II), or Pt(IV). I concentrated on the hydration processes of the examined complexes. Thermodynamical and kinetical aspects of reactions were studied and NPA charge analyses were carried out, too. All computations were performed on DFT level with B3LYP functional. All reactions were considered in vacuum. Supermolecular approach was used for energy calculations.
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