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Studies to discover new representatives of heme sensor proteins
Pašek, Dominik ; Martínková, Markéta (advisor) ; Dračínská, Helena (referee)
Hemoproteins are diverse and very important group of proteins involved in a wide range of biochemical processes. Their typical roles in living organisms include oxygen storage and distribution, enzymatic catalysis of redox reactions and electron transport in the respiratory chain. In relatively recent times, a fourth group of hemoproteins, the so-called heme sensor proteins, has been discovered. This group includes, among others, proteins that have the ability to reversibly bind heme, which in such cases acts as a signaling molecule. This reversible interaction is essential for cells in certain signalling pathways. As it was found, one of the heme sensor proteins is the p53 protein, which is an important transcription factor The first phase of this diploma thesis was focused to the preparation of p53 family proteins including some of their deletion mutants. Subsequently, the task for selected proteins was to study the influence of heme on their oligomeric state. The essential part of the thesis consists of spectrophotometric studies, which aimed to reveal potential interactions of the studied proteins with heme and to characterize the interactions. Keywords: heme, heme sensor proteins, p53 protein family, transcription factors, signal transduction
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Assessment of runoff conditions on flow in the cadastral area of Dašice
Janovská, Michaela ; Vysloužilová, Lucie (referee) ; Uhmannová, Hana (advisor)
This thesis is aimed at assessment of drainage conditions at the river Loucna in the cadastral area of Dasice. The examined section is 3,88 km long and runs through out of the city and in the city of Dasice. On the left bank of the river there are several historic buildings that are potentially at risk for 100 years of flow. Capacity assessment is performed using the 1D mathematical program HEC - RAS in which the flow model is created and the calculation of the flow rates for individual N - year flows. On the basis of the results of the program is conducted conceptual desing of flood protection measure. At the same time is conducted conceptual desing of fish ladder on the weir and a sluice closure on the intake for the race.
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Assessment of runoff conditions on the river in the Morava River Basin
Serafin, Petr ; Niklová, Věra (referee) ; Uhmannová, Hana (advisor)
The aim of the diploma thesis was to assess the curent state of the Svratka river and propose appropriate measures in accordance with the plans of Povodí Moravy, s.p. Locality of interest is located in the built-up area and non-urban area part of Herálec at river kilometer 163,9809-164,5189 and extends over the cadastral areas of Český Herálec, Herálec na Moravě and Svratka. The assessment of the river was performed on the flow series using the 1D mathematical model HEC – RAS version 5.0.6. On the basis of the results of the flow rate, was the locality od interest divided into four parts. For parts which are located in the urban, was designed a flood protection against of the 20 – year flow. For parts which are located in the non-urban area, was designed revitalization with the possibility of water retention in the landscape. The final design was verified by calculation in the same program HEC – RAS. The diploma thesis contains text part, calculation part and drawing part documenting the proposed measures.
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Production shifting from China to Vietnam: Implications for Global Value Chains
Maderová, Karolína ; Semerák, Vilém (advisor) ; Vacek, Pavel (referee)
This thesis analyzes the importance of China within the global economy and assesses the potential of Vietnam to serve as its replacement, or at least for some industries. Using the network analysis and the hypothetical extraction method (HEM), the most influential sectors of the Chinese economy were identified and an increasing trend of reliance of the Westen countries on China's supply and demand was found. Next, using the trade decomposition method, the participation in GVC for Vietnam and China was calculated. Although Vietnam is increasing its participation and other countries are increasing their demand for inputs from Vietnam, based on the available data, it was not possible to determine whether these changes could mean that Vietnam can replace China in the future. JEL Classification C67, D57, F18, F52 Keywords Input-output model, HEM, network analysis, GVC Title Production shifting from China to Vietnam: Implications for Global Value Chains
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The two-component signal transduction system in bacteria utilizing heme analogues
Bečková, Alexandra ; Martínková, Markéta (advisor) ; Prošková, Veronika (referee)
6 Abstract Hemoproteins are essential components of both prokaryotic and eukaryotic organisms, where they play a role in fulfilling many significant life functions. According to their function, hemoproteins can be divided into several types. One specific type of hemoproteins, which was also the object of interest in this bachelor thesis, is the heme sensor proteins. The function of part of these sensor hemoproteins is the ability to detect diatomic gas molecules and subsequently bind them to the heme molecule in the protein. This process leads to changing the properties of the sensor hemoprotein and the signal then becomes part of the signalling pathways. An example of sensor hemoprotein is the histidine kinase, with a globin structure of the sensor domain, from Anaeromyxobacter sp. Fw 109 (AfGcHK), which was studied during the experimental part of the bachelor thesis. First, a transformation of E. coli BL-21 (DE3) cells with the pET21c(+)/AfGcHK plasmid was performed, followed by cell cultivation and expression of the AfGcHK protein in the cells. The expressed AfGcHK protein was isolated in two forms. One form represented AfGcHK protein containing heme, that is, with iron incorporated in its structure. The second form represented AfGcHK proteins containing a heme analogue, where nickel was incorporated...
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Heme sensor proteins as potential biomarkers of cellular and oxidative stress processes induced by ionizing radiation
Vávra, Jakub ; Martínková, Markéta (advisor) ; Souček, Pavel (referee) ; Tichý, Aleš (referee)
[IN CZECH] Ionizing radiation is a potential inducer of the oxidative stress processes in cells. As a result, reactive radicals are formed in the intracellular space modifying the essential biomolecules. Ionizing radiation has either direct (radiation sickness) or indirect (malignant processes) effect on the organism. Therefore, a fast determination of the dose is required when suspected irradiation of the organism occurs. However, a method routinely applicable, fast enough and at the same time suitable for dose estimation based on biomarkers has not been developed so far. The aim of this thesis is to describe new properties of the selected heme sensor proteins and discuss their potential importance for the cellular adaptation to oxidative stress conditions. Specifically, the thesis is focused on two eukaryotic proteins, heme regulated inhibitor (HRI) and transcription factor p53. The study of functional regulation as well as the conformational changes of these proteins induced by heme is greatly emphasized. Besides, the optimization of the key experimental methods was conducted. Specifically, Phos-tag electrophoresis was applied for the kinetics study of HRI wild type and its Gly202Ser mutant form, which is a characteristics of lung cancer development. Unsurprisingly, for both HRI forms studied,...
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Detail enzymatic characterization of a model heme-containing oxygen sensor
Vojáčková, Lukrécie Sophie ; Martínková, Markéta (advisor) ; Čermáková, Michaela (referee)
This thesis focuses on heme-based gas sensors, particularly phosphodiesterase from the bacterium Escherichia coli, referred to as EcDOS. The enzyme catalyzes the degradation of c-di-GMP, an important signaling molecule in bacteria that affects cellular processes, such as bacterial motility or biofilm formation. The thesis deals with detailed enzyme kinetics of protein forms in different redox and ligand states of the heme iron ion [Fe(III), Fe(II) and Fe(II)-O2], as well as a mutant form of the enzyme (EcDOS H77A) which does not bind heme. Results confirmed that the EcDOS WT Fe(II)-O2 form has higher kcat values than the EcDOS form with the ferrous ion of heme in the reduced state. Other significant result was that the enzyme activity is affected not only by the state of the heme iron ion but also by the presence and concentrations of divalent metal cations. The presence of the metal cation is essential for enzyme function, and suitable metal ions that stimulate enzyme activity are Mg2+ , Mn2+ and Zn2+ or their mixtures, which act synergistically on enzyme activity under chosen conditions. Analysis by ICP-MS also showed that Zn2+ cations are natural components of the enzyme. Thus, for further kinetic studies, it would be appropriate to use Zn2+ or mixtures of metal ions that are physiological for...
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Structure and function relationships of model hemoproteins
Lengálová, Alžběta ; Martínková, Markéta (advisor) ; Hudeček, Jiří (referee) ; Muchová, Lucie (referee)
Heme is one of the most important and most studied cofactors that are essential for proper function of many proteins. Heme-containing proteins comprise of a large group of biologically important molecules that are involved in many physiological processes. The presented dissertation is focused on two groups of heme sensor proteins, namely prokaryotic heme-based gas sensors and eukaryotic heme-responsive sensors. Heme-based gas sensors play an important role in regulation of many bacterial processes and consist usually of two domains, a sensor domain and a functional domain. The dissertation thesis aims at the study of two model bacterial heme-based gas sensors, histidine kinase AfGcHK and diguanylate cyclase YddV, in order to elucidate their mechanism of interdomain signal transduction. Using X-ray crystallography and hydrogen-deuterium exchange coupled to mass spectrometry approaches, significant differences in the structure of the AfGcHK protein between the active and inactive forms were described. The signal detection by the AfGcHK sensor domain affects the structural properties of the protein, and these conformational changes then have indirect impact on the enzyme activity of the functional domain. Further, the dissertation pays more attention to the effect of a sensor domain dimerization...
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Study of the effect of heme analogues on the structural-functional characteristics of a model representative of heme sensor proteins
Ďatko, Peter ; Martínková, Markéta (advisor) ; Vávra, Jakub (referee)
Heme sensor proteins allow bacteria to react to changes of concentration of certain molecules in their environment. This reaction depends on the coordination of the ligand to the heme iron atom. Model representative of this signaling system is a histidine kinase containing a sensor domain with a globin structure, AfGcHK. The aim of this bachelor thesis was to prepare and characterize a modified form of AfGcHK containing manganese within its protoporphyrine complex. To express the protein, E. coli BL-21 (DE3) cells were transformed using a plasmid pET21c(+)/AfGcHK. The protein was isolated and purified using affinity chromatography and gel chromatography. To determine its enyzmatic activity, polyacrylamid gel electrophoresis in the presence of sodium dodecyl sulfate with Phos-Tag was used. It was determined, that this novel form of AfGcHK is enzymatically active. Spectroscopic analysis has shown, that the modified form of AfGcHK containing manganese within its protoporphyrine complex is susceptible to reduction by sodium dithionate. Key words: heme, heme sensor proteins, oxygen sensors, signal transduction [IN CZECH]
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Biochemical characterization of a model heme sensor protein containing a heme analog
Hlubučková, Darina ; Martínková, Markéta (advisor) ; Prošková, Veronika (referee)
An integral part of the life of cells is cell signaling, which is ensured, among other things, by heme proteins, specifically by their members called heme sensor proteins. Heme sensor proteins are divided into two groups, heme sensor proteins detecting heme, which are found more in eukaryotic cells, and heme sensor proteins detecting gaseous molecules, which are more typical of prokaryotic cells. The gas molecules in this case can be CO, NO and O2. A family of oxygen-detecting heme sensor proteins is crucial for bacteria that must adapt to changing oxygen concentrations in the environment. One of these bacteria is the soil bacterium Anaeromyxobacter sp., strain Fw 109-5, which contains a heme sensor protein with the globin structure of the sensor domain and the histidine kinase activity of the functional domain (AfGcHK), enabling the bacteria, among other things, to form a biofilm. As part of the theoretical part of this thesis, the current knowledge about heme sensor proteins was summarized, with a focus on the AfGcHK protein. In the practical part of this bachelor's thesis, bacterial cells E. coli BL-21 (DE3) were transformed with the plasmid pET21(+)/AfGcHK containing the gene encoding AfGcHK, from which two forms of AfGcHK were subsequently isolated, the natural form and the form containing a...
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