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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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Structural and functional characterization of a flaviviral methyltransferase.
Todd, Matthew Zagorey ; Bouřa, Evžen (advisor) ; Honzejková, Karolína (referee)
Genus flavivirus, member of the Flaviviridae family, is a wide-spread group of viral pathogens that pose a global threat to human health. Infections result in neurological and other diseases such as encephalitis, meningitis, microcephaly or haemorrhagic fever with direct anti-viral treatment restricted to only a few members including Yellow Fever Virus (YFV) and Japanese Encephalitis Virus (JEV). The flaviviral genome consists of a positive sense single-strand RNA, translated into a long viral polyprotein cleaved by host and viral proteases into structural and non-structural proteins. Non-structural protein 5 (NS5) is a highly conserved viral protein consisting of a C-terminal RNA-dependent RNA-polymerase (RdRp) and N-terminal methyltransferase (MTase) domain. Flaviviral MTases catalyse the final step of genomic RNA cap formation, that plays a crucial role in viral translation, replication and host immune system evasion. Due to its conservative nature, the flaviviral MTase is a promising drug target. It's structural analysis is needed for the development of broad-spectrum inhibitors and anti-viral treatment. Key words Flavivirus, St. Louis Encephalitis Virus, Flaviviral methyltransferase (MTase), N-7 methylation, 2'-O methylation.
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Structural and functional characterization of a flaviviral methyltransferase
Kúdelová, Veronika ; Bouřa, Evžen (advisor) ; Faltová, Lenka (referee)
Recently, non-cellular viral agents became the focus of a large number of scientific groups. A prominent and widespread group of these viruses are flaviviruses, which include, for example, Zika virus, Dengue fever virus, tick-borne encephalitis virus and West Nile virus. There is a considerable diversity among these viruses, however, highly conserved proteins can be found throughout this viral genus. The largest and most conserved protein encoded by flaviviruses is the nonstructural NS5 protein. Its N-terminal domain bears the methyltransferase (MTase) activity. Thanks to the methylation of its genome, it allows the virus to initiate translation and at the same time mask it from the host's immune system. By blocking the active site of this enzyme with a small molecule, viral infection could be stopped not only in one flavivirus, but, due to the high conservation of MTases, in all other flaviviruses. This diploma thesis deals with the aforementioned MTase domain of the NS5 protein, specifically of the West Nile virus (WNV). After designing an insert encoding the WNV MTase domain, amplifying it and ligating it into the vector, the MTase domain was prepared by a recombinant expression, followed by purification. Subsequently, complexes of the protein with small molecules (MTase ligands) were formed, in...
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Biophysical characterization of the CAR/RXR protein complex with its binding partners
Duchoslav, Vojtěch ; Bouřa, Evžen (advisor) ; Pavlíček, Jiří (referee)
The constitutive androstane receptor (CAR) plays an important role as a xenosensor in the organism and is therefore widely expressed in the kidney, liver, gallbladder and in the small intestine epithelium, where the biotransformation of xenobiotic occurs. CAR is also an important factor in the elimination of bile acids and bilirubin. CAR has also been shown to have an important role in regulation of glucose and lipid metabolism. Impairment of lipid and glucose metabolism is a common cause of cardiovascular and metabolic diseases such as atherosclerosis, type 2 diabetes, obesity and insulin resistance. These diseases are called metabolic syndrome and result in severe organ damage. CAR respective its complex with RXRα (retinoid X receptor α) has become a promising biological target for drug discovery for metabolic syndrome. The major aim of this study was a structural characterization of the CAR/RXRα protein complex together with the agonist IV676*HCl, which would describe in detail the interaction of this small molecule with the receptor. Obtained structural information would be used to design improved agonists.
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Structure-assisted development of a continuous carboxypeptidase assay
Rakhimbekova, Anastasia ; Bařinka, Cyril (advisor) ; Bouřa, Evžen (referee)
Glutamate carboxypeptidase II (GCPII) is a zinc-dependent carboxypeptidase with high expression levels in prostate carcinoma. As the enzyme represents a validated target for cancer therapy and imaging, the development of new GCPII-specific ligands is still a focus of an active academic and industrial research. However, existing assays to screen inhibitor libraries and determine inhibitor efficacy are suboptimal at best. This thesis is aimed at the development of small internally quenched probes that could be used for continuous measurement of the GCPII enzymatic activity. These probes are derived from natural GCPII substrates and consist of a fluorophore/quencher pair connected by a GCPII-hydrolysable linker. I first characterized biophysical properties of the probes and then determined kinetic parameters of their hydrolysis by GCPII. The optimized activity assay was then used to determine inhibition constants of several GCPII-specific inhibitors. Finally, complexes between the inactive enzyme and several probes were co-crystallized and one of the complexes refined and analyzed. Our data show that the probes are involved in non-covalent interactions with the same amino acid residues of the enzyme's active site as natural substrates. The developed assay could be optimized for high-throughput...
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SARS-CoV-2 methyltransferases as druggable targets
Kocek, Hugo ; Nencka, Radim (advisor) ; Bouřa, Evžen (referee)
Novel coronavirus (earlier referred to as "nCoV2019") became part of our lives in March 2020 and overnight turned everything upside-down. This virus is transmitted via respiratory droplets and causes respiratory diseases COVID-19 which can be severe and even fatal. So far, no effective treatment has been discovered and vaccination is our biggest hope thanks to its high efficacy. It is important to point out, that new mutations may possess problems and escape immunity induced by the vaccination. During the whole pandemic, many approved drugs were tested against SARS-CoV-2 (for example favipiravir, toremifene, and hydroxychloroquine) but none of those drugs showed to be effective against SARS-CoV-2 in clinical trials. The only approved antiviral drug is nucleotide analog remdesivir which showed significant efficacy against SARS-CoV-2 in clinical trials. However, timing and overall patient's health condition play a key role. Development of new antiviral drugs is necessary given the fact that this is the third time we face coronavirus with the potential to cause pandemic since the beginning of the 21st century. Therefore, it is likely that another new coronavirus will emerge. This thesis focuses on S-adenosylmethionine-dependent methyltransferases nsp14 and nsp16 from SARS-CoV-2 because they play a key...
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Expression and purification of recombinant proteins of human Aichi virus and other kobuviruses
Ludvík, Tomáš ; Bouřa, Evžen (advisor) ; Petrvalská, Olívia (referee)
Viral 2Apro plays many important functions in the life cycle of virus. It is protease that is involved in the cleavage of the viral polyprotein in the VP1/2A region. The structure of protein contains active site, thanks to this the protein is able to bind various substrates in the host cell, which is essential for viral infection. With the help of 2Apro , the virus can bypass the host immune response and stop the production of key host proteins. Therefore, 2Apro is suitable target for antiviral intervention. In this work were prepared two recombinant proteins from Aichi virus and Coxsackievirus B3. These are viruses of the family Picornaviridae, which belong among the human pathogens that in some cases cause serious diseases. Aichi virus is the cause of gastroenteritis and Coxsackievirus B3 in the worst cases causes dilated cardiomyopathy. Cardiomyopathy leads to poor heart function due to it is enlargement and can lead to heart failure. (In Czech) Key words: recombinant proteins, 2Apro , Aichi virus, Coxsackievirus B3
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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Structural studies of inhibitory mechanisms of phosphatidylinositol kinases
Gregor, Jiří ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee)
+ssRNA viruses after entering the cell develop platforms for RNA replication called replication organelles. Due to the activity of phosphatidylinositol 4-kinases is in these areas a higher concentration of PI4P, which establishes suitable binding environment for the viral polymerase 3DPOL . One of these kinases is PI4KB, which is recruited to the membrane by the ACBD3 protein, which is itself recruited by giantin. Some kobuviruses and enteroviruses from the Picornaviridae family use their 3A protein to displace ACBD3 protein from the complex with giantin and transfer it from Golgi aparathus to the replication organelles. Here, PI4KB binds to ACBD3 protein and synthesizes PI4P. Recently, two proteins - TBC1D22A and TBC1D22B - were discovered to bind to the same area of ACBD3 protein as PI4KB. The goal of this project was verification of this interaction and its subsequent characterization (e.g. dissociation constant measurements). My goal was to crystallize complexes of these interaction partners and to solve three-dimensional structure. Our results suggest, that interaction of ACBD3 protein with peptides derived from TBC1D22A and TBC1D22B proteins is much lower compared to interaction between ACBD3 protein and PI4KB. I successfully prepared crystals, however, they diffracted poorly, not allowing us to solve...
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Molecular mechanisms of regulation of forkhead transcription factor FOXO4
Bouřa, Evžen ; Obšil, Tomáš (advisor) ; Konvalinka, Jan (referee) ; Schneider, Bohdan (referee)
I 7. Abstract The main goal of this PhD thesis was to investigate the structure of FOXO4-DBD/DNA complex and the molecular mechanism of FOXO4 DNA binding properties. Especially, the role of protein kinase B phosphorylation and the regulatory role of 14-3-3 proteins. This work has been published in four original papers (for full citation see page no. 3). Paper l: The 14-3-3 proteins are a family of regulatory signaling molecules that interact with other proteins in a phosphorylation- dependent manner. 14-3-3 proteins are thought to play a direct role in the regulation of subcellular localization of FoxO forkhead transcription factors. It has been suggested that the interaction with the 14-3-3 protein affects FoxO binding to the target DNA and interferes with the function of nuclear localization sequence (NLS). Masking or obscuring of NLS could inhibit interaction between FoxO factors and nuclear importing machinery and thus shift the equilibrium of Foxo localization toward the cýoplasm. According to our best knowledge, there is no experimental evidence showing a direct interaction between the 14-3-3 protein and NLS of FoxO. Therefore, the main goal of this work was to investigate whether the phosphorylation by protein kinase B, the 14-3-3 protein, and DNA binding affect the structure of FoxO4 NLS. We have...
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