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Study of the interaction between the C-terminus of DNA-binding domain of FOXO4 and DNA
Zusková, Iva ; Obšil, Tomáš (advisor) ; Teisinger, Jan (referee)
Forkhead transcription factors are structurally similar molecules containing approximately 110-amino-acid-long DNA-binding domain known as a forkhead domain. Protein FOXO4 is a member of subgroup "O" of forkhead transcription factors. Members of this subgroup play a key role in many biologically important processes. For example, FOXO factors participate in metabolism control, cell-cycle control, apoptosis and oxidative stress resistance. The forkhead domain (DNA-binding domain) consists of three α-helices (H1, H2 and H3), three β-strands (S1, S2 and S3) and two flexible loops (called wings W1 and W2). The role of the wing W2 in FOXO binding to the target DNA is still elusive. Wing W2 probably interacts with the DNA in the region upstream of the core motif. It has been speculated that the FOXO DNA-binding affinity depends on A-T content (number of A-T pairs) in the region upstream of the core motif. In order to investigate this hypothesis, DNA- binding domain of the FOXO4 protein was expressed and purified and it was determined its binding affinity for three molecules of double stranded DNA containing different number of A-T pairs in the region upstream of the core motif using steady-state fluorescence anisotropy- based method. Our results show no significant differences between obtained FOXO4...
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Determination of stability constants of charged cyclodextrine complexes by capillary electrophoresis
Beneš, Martin ; Zusková, Iva (advisor) ; Dubský, Pavel (referee)
Martin Beneš Determination of stability constants of charged cyclodextrin comlexes by capillary electrophoresis Abstract Stability constant characterizes binding interaction between an analyte and complexation agent. These interactions play very important role in separation processes of, in other way undistinguishable, compounds, e.g. enantiomers. The most widely used complexation agents are cyclodextrins. Affinity capillary electrophoresis (ACE) belongs to methods suitable for the determination of stability constants. The stability constant is determined from the dependence of the effective mobility of analyte on the increasing concentration of complexation agent in background electrolyte (BGE). If charged CDs are used, the attention must be paid not only to viscosity of the BGE and to the influence of Joule heating on the temperature in the capillary but also to the increasing ionic strength. The thermodynamic stability constants of R,R- and S,S-hydrobenzoin and R- and S-(3-brom- 2-methyl-1-propanol) with cationic modified β-cyclodextrin: 6-monodeoxy-6-mono(3- hydroxy)propylamino-β-cyclodextrin hydrochlorid (PABCD) were determined by affinity capillary electrophoresis. The average temperature (25řC) of the BGE in the capillary was kept constant. This was achieved by decreasing of the cassette temperature...
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Antioxidative effects of the analogues of nucleic acid components.
Procházková, Eliška ; Mertlíková Kaiserová, Helena (advisor) ; Zusková, Iva (referee)
Reactive oxygen species (ROS) naturally occur in the organisms where they play e.g. signaling and antimicrobial roles. The imbalance between ROS production and removal results in the oxidative stress. This condition is largely considered as unfavourable leading to the oxidative damage of the biomolecules (lipids, proteins, nucleic acids). The oxidative stress accompanies a number of civilization diseases and may also arise as a consequence of pharmacotherapy (side effects of some drugs). Modulation of the oxidative stress with the use of antioxidants remains a subject of intense research. The analogs of nucleic acid components represent a structurally diverse class of compounds with important pharmacological potential. While their antiviral and cytostatic activities have been described in detail, information on their potential antioxidant activity is missing. The aim of this study was to identify the antioxidant activity in a series of 126 analogs of nucleotides, nucleosides and nucleobases and to describe structural motives responsible for this activity. Several methodological approaches have been used to reach the goal: 1) determination of the ability of the compounds to scavenge ABTS radical in vitro (TEAC), 2) the influence of the compounds on lipid peroxidation and 3) their ability to...
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Study of the mechanism of DNA recognition by transcription factor FOXO4
Zusková, Iva ; Obšil, Tomáš (advisor) ; Bouřa, Evžen (referee)
Forkhead transcription factor FOXO4 is involved in a wide range of processes including metabolism control, cell cycle regulation, apoptosis, DNA repair or oxidative stress resistance. The crystal structure of FOXO4 DNA-binding domain bound to the target DNA revealed that FOXO4 interacts with DNA in the same manner as other forkhead proteins. The DNA-binding interface consists of helix H3, which binds to the major groove of DNA, the N- terminal segment and flexible loops located at the C-terminus of forkhead domain. However, many questions concerning the regulation of DNA-binding specificity and the role of different parts of forkhead domain in this process remain elusive. In this diploma thesis, the interactions between the DNA-binding domain of FOXO4 and DNA with various sequences were studied. The DNA-binding domain of FOXO4 and its mutants were expressed and purified and their DNA-binding properties were studied using fluorescence spectroscopy techniques and surface plasmon resonance. Results of these experiments revealed that the nucleotide sequence at the 5′ end of the consensus binding motif affects the stability of the complex between the DNA-binding domain of FOXO4 and DNA. In addition, the importance of individual amino acid residues of FOXO4 that are involved in DNA binding for the...
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Ionic effects and online preconcentration techniques in separation systems
Boublík, Milan ; Zusková, Iva (advisor) ; Tůma, Petr (referee) ; Vigh, Gyula (referee)
Online preconcentration techniques in capillary electrophoresis (CE) improving sensitivity of electrophoretic separations and are in the scope of interest of many research groups. Therefore, proposal of new techniques for preconcentration and their theoretical description is desirable for their wider application. In this thesis, new preconcentration techniques are proposed and models of ionic strength effects in separation systems of CE and hydrophilic liquid interaction chromatography (HILIC) are presented and new set of pI markers for isoelectric focusing (IEF) was showed with their utilization for characterization of IEF pH gradient. Part of this thesis is keen on proposal of new preconcentration techniques and their theoretical description. We presented two preconcentration techniques, while first is based on sweeping with neutral complexing agent, the second one utilizes pH boundaries that are induced by disturbing phenomena of system zones. Both techniques are described theoretically by means of numerical simulations and by experiments. Both techniques are even utilized for real drug sample or for mixture of similar analytes. For system peak preconcentration technique, flow chart of how to design such method is presented. Second part of this thesis have rather more fundamental subject and...
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