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Structural studies of an abasic site DNA damage repair and DNA interstrand cross-link formation
Landová, Barbora ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Schneider, Bohdan (referee)
DNA damage refers to any alteration or modification in the DNA structure that deviates from its natural state. Abasic site (Ap site) is one of the most common DNA lesions resulting from spontaneous depurination/depyrimidination or enzymatic base excision. When left unrepaired it can lead to a cascade of genetic mutations, potentially causing diseases like cancer. Understanding DNA repair mechanisms is vital for medical research and applications. Bacterial MutM is a DNA repair glycosylase, removing DNA damage generated by oxidative stress and preventing mutations and genomic instability. MutM belongs to the Fpg/Nei family of procaryotic enzymes, sharing structural and functional similarities with their eukaryotic counterparts, such as NEIL1-NEIL3. Here, I present two crystal structures of MutM from pathogenic Neisseria meningitidis: MutM holoenzyme and MutM bound to DNA. The free enzyme exists in an open conformation, while upon binding to DNA, both the enzyme and DNA undergo substantial structural changes and domain rearrangement. One of the DNA lesion repaired by MutM is the Ap site, which, if not repaired, may spontaneously lead to the formation of an abasic site interstrand crosslink (Ap-ICL) with an adjacent adenine in the opposite strand. NEIL3 glycosylase is known to remove Ap-ICL. With a...
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Cancer Immunotherapy exploiting engineered antibody fragments against prostate-specific membrane antigen
Das, Gargi ; Bařinka, Cyril (advisor) ; Vaněk, Ondřej (referee) ; Ormsby, Tereza (referee)
Prostate cancer (PCa) remains a leading cause of male cancer-related mortality, necessitating thus the development of novel therapeutic approaches as conventional treatments have limited efficacy. Prostate-specific membrane antigen (PSMA) is an established biomarker for both imaging and therapy of PCa, as it is highly upregulated in neoplastic PCa tissues and metastatic castration- resistant prostate cancer. Consequently, immunological targeting of PSMA has gained significant attention as a therapeutic platform for the management of the disease. The thesis is focused on engineering of antibody fragments and fusion proteins derived from the high affinity anti-PSMA 5D3 monoclonal antibody that can be used as immune cell engagers to target and eliminate PSMA-positive cells. To this end, we engineered 5D3 single chain variable fragments (scFv) that were subsequently fused to anti-CD3 scFv and CP33 sequences, creating thus immune cell engagers targeting T-cells (BiTE) and monocytes (5D3-CP33), respectively. The engagers were expressed in insect cells, purified to homogeneity and their biophysical and functional characteristics evaluated using size exclusion chromatography, differential scanning fluorimetry, ELISA and flow cytometry. Ensuing cell-based assays revealed that both BiTE and 5D3-CP33 can...
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Capturing chromatin-associated proteins in nucleosomal context
Koutná, Eliška ; Veverka, Václav (advisor) ; Hlouchová, Klára (referee) ; Bařinka, Cyril (referee)
| 9 ABSTRACT Eukaryotic DNA is stored in the nucleus wrapped around histone octamers in the form of nucleosomes. These basic chromatin units can further associate with DNA-binding factors through DNA and the N-terminal histone tails that are subjected to various covalent posttranslational modifications that, in combination with DNA modifications, define the epigenetic code. Eukaryotic transcription is dependent on these specific histone modifications - their recognition by chromatin reader proteins triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated at a molecular level. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. In this thesis, the main focus is put on the transcription coactivator LEDGF/p75, capable of reading the H3K36me2/3 histone mark, and the pioneer transcription factor Sox2. Using structural biological and biophysical techniques, the interaction of LEDGF and Sox2 with nucleosomes is dissected, describing the peculiarities of intrinsically disordered DNA interacting motifs. Two...
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Structural studies of metal-dependent hydrolases: Histone Deacetylase 6 and Glutamate Carboxypeptidase II
Shukla, Shivam ; Bařinka, Cyril (advisor) ; Stříšovský, Kvido (referee) ; Kolenko, Petr (referee)
Zinc-dependent hydrolases are a class of metalloenzymes that require zinc ions to catalyse hydrolytic reactions. Structural studies of these enzymes shall provide detailed information about the processing of their natural substrates, domain organization, and overall structural fold. This thesis describes the structural properties of two different metallohydrolases 1) human histone deacetylase 6 (HDAC6) and 2) glutamate carboxypeptidase II (GCPII) by utilizing a different set of biophysical techniques. HDAC6 is a structurally unique multidomain enzyme comprised of unstructured and globular domains. It regulates the plethora of cellular processes by removing an acetyl group from lysine side chains of target proteins. It has been known to deacetylate non-histone substrates such as tubulin, Hsp90, cortactin, and peroxiredoxins. Given its structural complexity, complete structural information of full-length HDAC6 is missing and available information is limited to its globular domains only. Hence, the integrative approach was employed in combining experimental data from several orthogonal biophysical techniques to build an in-solution structural model of HDAC6. The study reports that HDAC6 adopts multiple conformations due to its unstructured regions and exists as an ensemble of conformers in solution....
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Neuronal cell culture in vitro
Kohoutová, Šárka ; Bařinka, Cyril (advisor) ; Pavlíček, Jiří (referee)
Neuronal cell cultures are in vitro cultures of dissociated neurons that have become an essential part of many neurobiological experiments in the last century. Cultured neurons not only allow to answer questions about their physiology under complex in vivo conditions, but also can serve as a model of neurodegenerative diseases. Neuronal cells can either be isolated directly from the nervous tissue of animals at the prenatal or adult stage of development, or they can be obtained through targeted manipulations of stem cells and secondary cell lines that lead to their neuronal differentiation. Primary neurons are considered the gold standard of neurobiological research not only because of their long tradition of cultivation, but also because primary neurons retain typical neuronal properties under in vivo conditions. There are several disadvantages associated with primary neurons, including the fact that fully differentiated neurons do not proliferate and are relatively demanding in terms of culture conditions For this reason, their role is often replaced by mitotically active secondary cell lines or stem cells. This bachelor thesis summarizes the knowledge about cell cultures used to study the functions of neuronal cells and highlights the advantages and disadvantages of their use. Key words Primary...
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Heat-shock protein 90 (HSP90) in cell physiology.
Karmazin, Alina ; Bařinka, Cyril (advisor) ; Pavlíček, Jiří (referee)
Heat-shock protein 90 (HSP90) is a molecular chaperone that represents one of the most important proteins for cellular homeostasis in all life domains. Chaperones are proteins that assist other proteins in proper folding and refolding. First discovered as a protein of a heat-shock response, HSP90 eventually emerged as a hub connecting multiple cellular functions, such as transcription, translation, DNA repair, immune response, cell signaling, etc. Unsurprisingly, HSP90 also plays a role in the pathogenesis of human diseases: various cancers, and neurodegenerative and respiratory diseases. For that reason, it became a target of medical research. HSP90 is a homodimer consisting of two protomers, each of which is composed of three domains: N-terminal domain, middle domain, and C-terminal domain. To fulfill its functions, HSP90 goes through an ATP-dependent conformational cycle, tightly regulated by a large group of assisting proteins-co-chaperones, and several post-translational modifications, such as phosphorylation and acetylation. Acetylation is known to affect HSP90 binding to nucleotides, clients, and co-chaperones, and thus it is suggested as a control mechanism of HSP90 function. Potentially, HSP90 acetylation can be utilized in the treatment of hormone-dependent cancers. Therefore, regulators of HSP90...
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Molecular basis of interactions between Dishevelled 3 (Dvl3) and Protein Regulator Of Cytokinesis 1 (PRC1)
Kropáčková, Veronika ; Bařinka, Cyril (advisor) ; Macůrková, Marie (referee)
Scaffolding protein Disheveled (Dvl) is a key component of Wnt signaling cascades. Dvl participates in a number of biological processes, such as cell proliferation, differentiation and migration, determination of cell polarity, and also stem cell self-renewal. It is therefore indispensable for the correct embryo development and tissue homeostasis in adulthood. The protein regulator of cytokinesis (PRC1) is a microtubule-associated protein. PRC1 is involved in spindle midzone formation during cell division. Spindle midzone precedes the contractile ring assembly and is essential for normal cell cleavage. In our laboratory, PRC1 was identified as a putative interaction partner of DVL3. This master thesis is focused on delineation of the interaction interface between DVL3 and PRC1 using TIRF microscopy (Total Internal Reflection Fluorescence microscopy). To this end, full-length DVL and PRC1 proteins together with their truncated variants were designed, expressed and purified. It was discovered that PRC1 interacts with all three DVL isoforms and the N-terminal part of PRC1 is required for the interaction between PRC1 and DVL3. Furthermore, the DEP domain of DVL3 is likely involved in PRC1interactions. Key words: Dishevelled 3, DVL3, Protein regulator of cytokinesis 1, PRC1, interaction interface, TIRF...
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Polyglutamylation as a Posttranslational Tubulin Modification
Bašta, Miroslav ; Bařinka, Cyril (advisor) ; Dráber, Pavel (referee)
α-tubulin is an essential protein for every eukaryotic cell. Together with β-tubulin, it polymerises into microtubules and participates thus in creating and maintaining cellular structures and presents a cell-wide interaction platform for a plethora of microtubule associating proteins. Primary sequences of the disordered C-termini of both α- and β-tubulin are the least conserved among tubulin isotypes and their variability is further increased by the presence of various post-translational modifications. The genetically coded, tyrosinated C-terminus of α-tubulin can be either shortened by one, two or three amino acids resulting in detyrosinated, Δ2, or Δ3 variants, respectively or it can be extended by the addition of polyglutamate or polyglycine chains. The tubulin tyrosine ligase-like (TTLL) protein family consists of 14 enzymes that participate in tubulin glutamylation, glycylation, and tyrosination. The glutamylases have two distinct activities, initiation and elongation of the polyglutamate chain. Initiases link the first glutamate residue to the γ-carboxyl group of one of the glutamates of tubulin C-termini to create a fork in the amino acid sequence. Elongases then recognise the branching glutamate and build up the polyglutamate sidechain one residue at the time. TTLL11 is an elongase of...
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In Vitro Selection of Aptamers for Methionine Sulfoxide
Jureček, Matěj ; Míšek, Jiří (advisor) ; Bařinka, Cyril (referee)
Oxidation of methionine to methionine sulfoxide in proteins is considered one of important post-translational modifications of proteins. This modification can activate and also inhibit functions of many proteins and it is a part of regulation mechanisms of various (patho)physiological processes. For further research of the effects of methionine oxidation in proteins it would be very helpful to find its bioindicator. So far however, there has not been found any such antibody, nor any of its alternatives. This thesis was concerned with the search of ssDNA aptamer specific for methionine sulfoxide by the method of in vitro selection (SELEX). Several conditions for in vitro selection of methionine sulfoxide were tested in this diploma thesis. None of them led to the enrichment of the starting oligonucleotide pool and no selective aptamer for methionine sulfoxide has been found. Such results don't necessarily point to the impossibility of finding such aptamer, but the conventional methods used in this thesis weren't suitable for this task. In a control in vitro selection there has been found an enriched ssDNA pool for sulforhodamine B as a ligand. Sequencing of clones of this enriched pool has shown oligonucleotides with G-rich sequences, which is typical for already published aptamers for sulforhodamine B.
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Regulation of the activity of aspartic and serine proteases by selective natural inhibitors
Srp, Jaroslav ; Mareš, Michael (advisor) ; Novák, Petr (referee) ; Bařinka, Cyril (referee)
Proteases are involved in many physiological processes and their dysregulation is associated with various pathologies. Protease activity is effectively controlled by natural inhibitors. This PhD thesis is focused on the inhibitors of aspartic and serine proteases of animal and plant origin and provides the identification, biochemical characterization and structural description of their inhibition mechanisms. Plant Kunitz inhibitors are produced as defensive proteins, and they are able to block activities of a broad spectrum of proteases. In this thesis, the digestive proteolytic system of the Colorado potato beetle, a herbivore pest of potato plants, was described with the help of functional proteomics. It was shown that aspartic and serine proteases from this herbivore are effectively blocked by two potato Kunitz inhibitors (namely PCDI, PSPI). Using structural analysis, novel types of reactive centers were identified on PCDI and PSPI molecules for the inhibition of aspartic protease cathepsin D and the serine proteases trypsin and chymotrypsin. The analysis of the reactive center on a PCDI with the crystal structure of digestive cathepsin D from the Colorado potato beetle explained the mechanism of their interaction. Sphingolipids were identified as the first endogenous inhibitors of human...
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