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The Interaction of Graphene Oxide with Humic Acids, a Computational Study
FERLIN, Stefan
This study was focused on the interactions of Graphene oxide with humic acids in aqueous solutions. Additionally, to this work, Graphene oxide and water interactions with and without the addition of ions were studied. The behavior of a fulvic acid in the presence of Graphene oxide has been investigated as well. The study was performed using computer simulations that were achieved by Molecular Dynamics simulations. These simulations provided useful data on a nanometer scale.
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Molecular basis of the sperm selection in the mammalian female reproductive tract
Šrámková, Adéla ; Krylov, Vladimír (advisor) ; Postlerová, Pavla (referee)
Internal fertilization is typical for all mammals. The male transfers sperm cells into the female reproductive tract, where usually one of them reach the oocyte and fertilize it. The female reproductive tract must be adapted to provide a suitable environment for the sperm cells to survive until fertilization. On the other hand, it must also be able to select developmentally competent sperm cells and prevent others to get into the close contact with the oocyte. Physical and molecular mutual communication of sperm cells with the female reproductive tract is ensured by sperm surface molecules and the receptors of the female epithelia lining. It appears that these interactions are required for key transformations, both on the sperm surface and in the cells of the female reproductive tract, where gene expression is affected. As a result of these changes, the most suitable sperm cell with all the required characteristics is allowed to fertilize the matured oocyte.
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Bioinformatic analysis of protein/DNA interactions
Božíková, Paulína ; Schneider, Bohdan (advisor) ; Hašek, Jindřich (referee)
In this thesis, we focused on local structural features of the DNA backbone in protein-complexed DNA and non-complexed (naked) DNA, and its dependence on types of a base pairing in DNA, and on the base sequence. To reach this goal we analyzed about 1,400 crystal structures of DNA in complexes with proteins and more than 400 crystal structures of naked DNA. DNA local conformations were structurally classified into 38 dinucleotide conformers ntCs, which were described previously (Svozil et al. Nucleic Acids Res. 2008). The ntC were further clustered into 16 structural alphabet classes ntA to reduce the number of analyzed variables. We assembled base-paired dinucleotides from double helical DNA structures accord- ing to their assigned structural alphabet classes into so called Association matrices. Three basic Association matrices were analyzed; two compare ntA/ntA associations between dinucleotides forming only Watson-Crick base pairs in protein/DNA com- plexes and in naked DNA, respectively; the third one ntA/ntA associations between dinucleotides base-paired also by non-Watson-Crick pairs. We also analyzed As- sociation matrices of dinucleotides as a function of their sequences. The analyzes revealed differences in structural behavior of various ntA and their dependence on dinucleotide sequences.
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Bioinformatic analysis of protein/DNA interactions
Božíková, Paulína ; Schneider, Bohdan (advisor) ; Hašek, Jindřich (referee)
In this thesis, we focused on local structural features of the DNA backbone in protein-complexed DNA and non-complexed (naked) DNA, and its dependence on types of a base pairing in DNA, and on the base sequence. To reach this goal we analyzed about 1,400 crystal structures of DNA in complexes with proteins and more than 400 crystal structures of naked DNA. DNA local conformations were structurally classified into 38 dinucleotide conformers ntCs, which were described previously (Svozil et al. Nucleic Acids Res. 2008). The ntC were further clustered into 16 structural alphabet classes ntA to reduce the number of analyzed variables. We assembled base-paired dinucleotides from double helical DNA structures accord- ing to their assigned structural alphabet classes into so called Association matrices. Three basic Association matrices were analyzed; two compare ntA/ntA associations between dinucleotides forming only Watson-Crick base pairs in protein/DNA com- plexes and in naked DNA, respectively; the third one ntA/ntA associations between dinucleotides base-paired also by non-Watson-Crick pairs. We also analyzed As- sociation matrices of dinucleotides as a function of their sequences. The analyzes revealed differences in structural behavior of various ntA and their dependence on dinucleotide sequences.
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