National Repository of Grey Literature 174 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Utilization of pulse labelling techniques for studying the dynamics of proteins and protein complexes
Polák, Marek ; Novák, Petr (advisor) ; Obšil, Tomáš (referee) ; Vrbacký, Marek (referee)
(In English) Mass spectrometry (MS) techniques are routinely used to probe the structure and dynamics of proteins and protein complexes. Although MS techniques lack the high resolution of data provided by X-ray crystallography, NMR, or cryo-EM, they excel in providing insights into analyte dynamics, structure, and interactions with other components, such as ligands. This doctoral thesis presents a contribution to the field of structural biology employing and extending covalent labelling approaches, namely Fast Photochemical oxidation of Proteins (FPOP) and oxidation by singlet oxygen (1 O2). These approaches were followed to study the structure, dynamics, and interaction of proteins, nucleic acids, and protein-DNA complexes in solution. Initially, FPOP was used to investigate the interaction interface of FOXO4 and DAF16-DNA response element and to show the possibilities of analyzing such a complex using both 'bottom- up' and 'top-down' approaches. Furthermore, an isotope depletion strategy combined with multiCASI-ECD proved effective in delivering structural information with the highest possible resolution for mapping protein-DNA interfaces. This research showcases how information derived from structural proteomic methods can guide the construction of in-silico models for protein-DNA complexes with...
Design of docking station for mobile robot
Obšil, Tomáš ; Houfek, Martin (referee) ; Krejsa, Jiří (advisor)
The aim of this diploma thesis is design of docking station for an autonomous mobile robot Breach. The task of docking station is to connect this robotic device to power supply without human intervention in order to charge its batteries. The theoretical part of diploma thesis contains research study about autonomous charging of robots. After that it is assessed suitability of using different types of docking stations and it was chosen optimal solution. The practice part of diploma thesis contains design of docking mechanism, which takes account of inaccurate navigation of robot with deviation of several centimeters. One part of this design deals with connector system, which is dimensioned for long-term transmission of electric current with minimal value of 20 A. At the end of diploma thesis there was created 3D model of the complete docking station including connectors for charging in program called SolidWorks.
Design of post climbing machine
Obšil, Tomáš ; Mašek, Petr (referee) ; Krejsa, Jiří (advisor)
This bachelor thesis deals with post climbing machines. The theoretical part of the thesis deals with the basic division of robots and a description of different types of post climbing machines. The practical part of the thesis deals with the conceptual design of the post climbing machine. The machine is designed to carry on external payload in kilograms. The power supply of the post climbing machine will be realized by external power supply. Conceptual design is developed in SolidWorks.
Structural studies of selected protein complexes involved in signal transduction
Honzejková, Karolína ; Obšil, Tomáš (advisor) ; Bouřa, Evžen (referee) ; Pavlíček, Jiří (referee)
Protein-protein interactions are critical for most physiological and pathophysiological processes. Detailed characterization of these interactions is therefore essential not only to understand the nature of these events, but also to design strategies to target these interactions. This work focuses on the study of the structure and interactions of several proteins and their complexes. Apoptosis signal-regulating kinase 1 (ASK1) is a mitogen-activated protein kinase kinase kinase (MAP3K) that activates the p38/JNK protein kinase pathways, thereby directing cells toward an inflammatory response or apoptosis. ASK1 interacts with thioredoxin (TRX), a small dithiol oxidoreductase, which inhibits ASK1, but the mechanism of this inhibition has not been clarified. CaMKK1 and CaMKK2 are Ca2+ /calmodulin (CaM)-dependent protein kinases that regulate cellular energy balance, memory, and inflammation, among others. Both are inhibited by 14-3-3 proteins, but despite their domain and sequence similarities, the extent of 14-3-3 protein- mediated inhibition is different. Estrogen receptor alpha (ERα) is a nuclear receptor involved in breast cancer. Tamoxifen, an ERα antagonist, is used to treat this disease, but resistance often develops. 14-3-3 proteins interact with ERα and inhibit its transcriptional activity,...
Regulatory mechanism of the cyclin-dependent kinase 16 through the cyclin Y/14-3-3 complex
Janáčková, Zuzana ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
CDK16 is a cell-cycle-related cyclin-dependent kinase that functions primarily in neurite growth processes, axonal transport regulation and sperm development. It also plays a role in the progression of X-linked intellectual disability and, together with its activating partner cyclin Y, in the development and progression of various types of cancer. Consequently, CDK16 and cyclin Y could represent potential new therapeutic targets. Both CDK16 and cyclin Y are structurally atypical among similar proteins, and the mechanism of activation of CDK16 by cyclin Y is unclear. However, it is clear from recent studies that the interaction between CDK16 and cyclin Y requires the prior interaction of cyclin Y with 14-3-3 proteins. In addition, for cyclin Y to interact with 14-3-3 proteins, its phosphorylation on the S100 and S326 binding sites of 14-3- 3 is required. To investigate the mechanism of activation of CDK16 by cyclin Y, we decided to characterize the interaction between CDK16, cyclin Y and 14-3-3 proteins in detail. The interaction between CDK16, cyclin Y and 14-3-3 proteins was characterized using biophysical methods including fluorescence anisotropy measurements, native electrophoresis, size exclusion chromatography and protein crystallography. The for- mation of binary pCCNY-14-3-3 and ternary...
Characterization of protein-protein interactions between Forkhead box O (FOXO) and p53 transcription factors
Mandal, Raju ; Obšil, Tomáš (advisor) ; Hrabal, Richard (referee) ; Pavlíček, Jiří (referee)
The transcription factor p53 plays a key role in cell cycle arrest, DNA repair, apoptosis, tumor suppression, and maintaining cellular homeostasis. Under cellular stress, p53 directly interacts with the Forkhead box O (FOXO) 4 transcription factor, thereby upregulating the expression of the p21 gene, resulting in the induction of cellular senescence. However, the detailed molecular mechanism behind FOXO4-p53 interaction remains unclear due to the unavailability of structural data. Therefore, main goal of this doctoral thesis was the characterization of the interaction between FOXO4 and p53 using several biophysical techniques including sedimentation velocity analytical ultracentrifugation (SV AUC), nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled to mass spectrometry. Furthermore, we also investigated the DNA binding properties of both proteins with their respective consensus DNA sequences in the presence or absence of their binding partners by fluorescence anisotropy measurements along with the comparison of p53-binding surfaces of the Forkhead domain of three different FOXO proteins by NMR spectroscopy. In addition, we also optimized small molecule compounds for the inhibition of FOXO3-DNA interaction. Our results revealed that the p53 interacts with FOXO4 through...
Structural characterization of influenza A polymerase PA subunit domains in complex with novel inhibitors
Radilová, Kateřina ; Kožíšek, Milan (advisor) ; Rumlová, Michaela (referee) ; Obšil, Tomáš (referee)
Influenza RNA-dependent RNA polymerase is a heterotrimeric complex and has an essential role in the life cycle of the virus. It is responsible for viral replication and transcription. One of its subunits, the polymerase acidic protein, interacts with the PB1 subunit via a crucial protein- protein interaction at its C-terminal domain. This 310 helix-mediated intersubunit interaction is required for the whole heterotrimer assembly. The N-terminal domain carries the endonuclease active site with two manganese ions. Both domains are considered promising drug targets. Current strategies to fight the influenza virus are limited to seasonal vaccines, and there are only a few anti-influenza drugs targeting mostly other viral proteins. Many used antivirals are susceptible to rapid resistance mutations development or cause severe side effects. This thesis provides structural insights into the two domains of the PA subunit. The first part is devoted to the characterization and optimization of a PB1-derived minimal peptide interacting with the C-terminal domain. Results from this part may be considered as a starting point for the rational design of first-in-class anti-influenza inhibitors of the PA-PB1 protein-protein interaction. In the other half, we have explored the inhibitory potency of flavonoids and...
Is there a direct link between global value chain participation and economic growth? Analysis of EU member countries
Obšil, Tomáš ; Semerák, Vilém (advisor) ; Kábrt, Martin (referee)
This thesis studies the strength of correlation between Global value chain par- ticipation and economic growth in the Czech Republic, Slovakia, Slovenia, Es- tonia, Poland, Austria, Germany, and Hungary from 1995 to 2018. This rela- tionship is demonstrated by using traditional panel data methods, with forward and backward GVC participation as our main explanatory variables and GDP per capita as our response variable. Based on the graphs and initial models, the variables seemed to be correlated; nevertheless, our analysis did not confirm this hypothesis. Furthermore, we use the total value added of the food, textile, and electronic industries as proxy variables for sectoral growth. We found, in most cases, a strong and significant correlation between the growth of these industries and BP and FP. JEL Classification B22, C33, E23, F41, F63, L60, O47, O52 Keywords global value chains, economic growth, central and eastern European countries, forward partic- ipation, backward participation Title Is there a direct link between global value chain participation and economic growth? Analysis of EU member countries.
Characterization of the binding interface between transcription factors FOXO4 and p53
Brzezina, Adam ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
This work deals with the study of human transcription factors FOXO4 and p53. FOXO4 is a member of the "O" subfamily of FOX transcription factors. Genes encoding FOXO proteins are evolutionarily conserved across species. FOXO transcription factors regulate the expression of genes involved in the control of metabolism, cell cycle and cell proliferation, cell survival and stress resistance. They are considered tumour suppressors because of their ability to arrest the cell cycle and induce apoptosis. However, their function in tumorigenesis appears to be more complicated, as recent studies indicate a poorer prognosis for the development of tumours that express higher levels of FOXO4. The p53 protein is a thoroughly studied naturally occurring tumour suppressor. The cellular response after its activation is somewhat similar to that of FOXO4, it can also block cell cycle progression or induce apoptosis depending on the cell type and severity/type of cellular stress. Both FOXO4 and p53 appear to be key molecules affecting aging. Under stress conditions, p53 and FOXO4 interact with each other and together increase the expression of p21 protein, thereby inducing the transition of cells to a senescent state. The accumulation of senescent cells is recognised as one of the main causes of ageing and the...
Cloning, expression and characterization of the viral proteins
Pekárek, Matěj ; Šilhán, Jan (advisor) ; Obšil, Tomáš (referee)
Over the last twenty years three new coronavirus strains have appeared in human population, that cause dangerous infections of respiratory tract. At this moment no approved drug exists, that could mitigate the infection caused by these viruses. One of the possible targets of these drugs are proteins responsible for viral genome replication. Nsp13 is primarily a helicase, that unwinds double stranded nucleic acids in the direction of 5'-3', but it also increases activity of replication and transcription complex, it participates in the synthesis of 5' cap on viral RNA and it probably mediates the backtracking of replication and transcripton complex during the process of RNA repair. On top of that nsp13 is strongly conserved among all coronaviruses and it is possible target not only for COVID-19 treatment, but also infections caused by potential future coronaviruses. Theoretical part of the thesis briefly describes the life cycle of SARS-CoV-2, functions of individual proteins of this virus, that participate in replication and transcription of RNA and it summarizes current knowledge about function of nsp13 and its potential inhibitors. In experimental part we have prepared the expression vector for nsp13, that was used for the production of nsp13. Nsp13 was then isolated and purified. (In Czech) Key...

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