National Repository of Grey Literature 102 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Structure and interactions of selected forkhead transcription factors
Kohoutová, Klára ; Obšil, Tomáš (advisor) ; Hrabal, Richard (referee)
This diploma thesis is a part of a project aiming to develop and study specific inhibitors of FOXO3 transcriptional activity. FOXO3 belongs together with FOXO1, FOXO4 and FOXO6 to FOXO subfamily of forkhead family transcription factors. FOXO transcription factors are evolutionary conserved proteins playing important roles in numerous cellular processes, such as apoptosis, cell cycle regulation and metabolism. Due to their ability to induce apoptosis and to block the cell cycle they are considered tumor suppresors. However, it has been shown that increased activity of FOXO proteins is connected with many kinds of cancer. In such cases FOXO proteins function to maintain cell homeostasis. They promote tumor resistance against chemotherapy as well as they speed up its growth. The aim of this project is to develop specific inhibitors able to bind to FOXO3 DNA-binding domain (DBD, residues 156-269) and to block its interaction with target DNA. Development of specific inhibitors of FOXO3 transcriptional programme requires knowledge of solution structure of all FOXO DBDs and detailed insight into their interaction with target DNA. So far crystal structures of complexes of FOXO1, FOXO3 and FOXO4 with target DNA and solution NMR structures of apo DBDs of FOXO3 and FOXO4 have been solved. One of the goals of...
Substrate specificity of histone deacetylases
Ustinova, Kseniya ; Bařinka, Cyril (advisor) ; Bumba, Ladislav (referee) ; Obšil, Tomáš (referee)
In the cell, tubulin undergoes post-translational modifications that create functionally distinct microtubules and mark them for specialized functions. Acetylation of Lys40 of α-tubulin is one of such post-translational modifications controlled by the activity of histone deacetylase 6 (HDAC6). The Lys40 acetylation is a hallmark of stable microtubules, it protects them from mechanical aging, influences cell motility as well as axonal branching and maintenance of neuronal processes. Tubulin stands out as the most prominent physiological substrate for HDAC6. Being a multidomain cytosolic protein, HDAC6 is involved in the myriad of cellular processes and is a promising target for the treatment of cancer and neurodegenerative diseases. The understanding of the mechanisms of HDAC6 interactions with its substrates, especially with tubulin, can open avenues for the development of new treatment strategies exploiting highly selective HDAC6 inhibitors. In this thesis, we have investigated the molecular basis of tubulin recognition by HDAC6. We provided a detailed kinetic analysis showing the HDAC6 deacetylation rate of free tubulin is 1500-fold faster than microtubules. Additionally, we have shown that amino acids of the flexible Lys40 loop (except P1 and P-1) make a minor contribution to the substrate...
Study of interactions of forkhead box O (FOXO) transcription factors with DNA
Hofmanová, Adéla ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
This work studies the "O" subgroup of FOX transcription factors, which consists of four members (FOXO1, FOXO3, FOXO4 and FOXO6). They are important regulatory molecules that play a critical role in a number of physiological and pathological processes such as cell cycle control, the body's response to stress, differentiation and apoptosis. Due to their ability to induce cell death, they are generally considered to be tumor suppressors. However, recent studies have shown that they can also induce an opposite effect, i.e. to promote tumor progression or induce resistance to drugs used in the therapy of certain types of tumors. Despite intensive research, a number of questions regarding the function of FOXO proteins still remain unanswered. One question is whether the small structural differences observed in the highly conserved DNA-binding domains (DBD) of FOXO transcription factors affect their DNA- binding affinities. Furthermore, it is unclear whether the recently described protein-protein interaction of FOXO-DBD with the transcription factor p53 affects their DNA-binding affinity. Moreover, the role of the binding site for Mg2+ ion which was found in the crystal structure of FOXO4-DBD:DNA, is also still not understood. To clarify these questions, the DNA-binding domains of the human transcription...
Structural study of the complex between the 14-3-3 protein, CaMKK1 and CaMKK1:Ca2+/CaM
Mikulů, Martina ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
The Ca2+ -signaling pathway is an important mechanism of cell signaling. Ca2+ /Cal- modulin (CaM)-dependent protein kinases (CaMKs) are members of Ser/Thr protein kinase family. CaMKs are regulated by Ca2+ /CaM binding in response to increase in intracellular level of Ca2+ . An important member of this protein family is Ca2+ /CaM- dependent protein kinase kinase (CaMKK), which is an upstream activator of CaMKI and CaMKIV. There are two isoforms of CaMKK, CaMKK1 and CaMKK2. CaMKK1 is regulated not only by Ca2+ /CaM-binding, but also by phosphorylation by cAMP-dependent protein kinase A (PKA). PKA phosphorylation induces inter- action with the 14-3-3 proteins. Previous studies of interaction between CaMKK1 and 14-3-3 proteins suggested, that the interaction with 14-3-3 proteins keeps CaMKK1 in the PKA-induced inhibited state and blocks its active site. However, the exact mecha- nism of this inhibition is still unclear mainly due to the absence of structural data. Main aim of this diploma thesis was to characterize the protein complexes between CaMKK1, Ca2+ /CaM and 14-3-3γ using analytical ultracentrifugation, small angle X-ray scattering, and chemical cross-linking coupled to mass spectrometry. Analytical ultracentrifugation revealed concentration-dependent dimerization of CaMKK1, which is...
The preparation and characterisation of analogues of insulin and IGF-2 selective for both isoform of insulin receptor and IGF-1 receptor
Mlčochová, Květoslava ; Žáková, Lenka (advisor) ; Obšil, Tomáš (referee) ; Šulc, Miroslav (referee)
Insulin and insulin-like growth factor 1 (IGF-1) and 2 (IGF-2) are related protein hormones with different but overlapping biological functions. All the hormones interact with a receptor within the insulin-IGF system (insulin receptor A and B, IGF-1 receptor), however with different affinity. The different interaction with individual receptors is just one of the main tools for regulation of the system that is essential for the proper functioning of the organism. Although the residues directly interacting with receptors are mainly located in A and B domains, the C and D domains probably play a role in receptor specificity. Here, we firstly focused on the impact of D domains of IGF-1 and 2 (D1 and D2 domains) and C domain of IGF- 2 (C2 domain). To probe the impact of C and D domains, we prepared insulin analogues containing a part of or an entire domain following a pattern seen in IGFs. The receptor-binding affinities of these analogues and their receptor autophosphorylation potentials were characterised. Our results revealed that the initial part of D1 domain has a detrimental effect on IR affinity that is only slightly enhanced by the rest of the D1 domain. D2 domain has rather neutral effect on IR affinity. We further showed that the addition of amino acids derived from the C2 domain to the...
Characterizing DDI2 protein interaction by solution NMR
Staníček, Jakub ; Grantz Šašková, Klára (advisor) ; Obšil, Tomáš (referee)
Human DDI2 protein is a dimeric aspartic protease that has been recently found to play an important role in DNA damage repair and transcriptional regulation of the proteasome expression. Current insights into the mechanistic details of both functions are still quite limited. We have previously identified the human RAD23B protein to interact with the DDI2 protein. RAD23B also functions in DNA damage repair as part of the XPC complex that stimulates the nucleotide excision repair activity. Moreover, RAD23B participates as an adaptor protein in the process of protein degradation. Therefore, the interaction of DDI2 and RAD23B might have important implications for both known functions of DDI2. This work describes the DDI2 and RAD23B interaction on the structural level. Recombinant protein variants of both DDI2 and RAD23B proteins were prepared and the interaction was mapped by the affinity pull-down assay. Protein NMR titrations were further used to explore the interaction. Key words: ubiquitin-proteasome system, DNA damage repair, proteasome expression regulation, aspartyl protease, DDI2, NMR
Preparation of human Ca2+/calmodulin-dependent protein kinase kinase 2 phosphorylated at Ser100 and Ser511
Koupilová, Nicola ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
5 Abstract Ca2+ /calmodulin-dependent protein kinase kinases (CaMKK) are serine/threonine kinases involved in the calcium signaling pathway. Two CaMKK isoforms were described in mammals: CaMKK1 and CaMKK2. The increase in calcium concentrations induces Ca2+ /CaM binding to the C-terminal segment of CaMKK, thus relieving autoinhibition by disrupting the interaction between the autoinhibitory segment and the kinase domain. Active CaMKK then phosphorylate and activate their downstream kinases CaMK1 and CaMK4, and in the case of CaMKK2 also AMPK. The activity of CaMKK is also regulated by phosphorylation mediated by cAMP-dependent protein kinase A (PKA). This phosphorylation creates two binding motifs recognized by the regulatory 14-3-3 proteins. Previous studies have suggested that the 14-3-3 protein keeps phos- phorylated CaMKK1 in the inhibited state by blocking the dephosphorylation of the inhibitory phosphorylation site and it has been speculated that CaMKK2 is regulated in a similar manner. However, the role of 14-3-3 protein in the regulation of CaMKK2 is unclear. In order to study this protein complex, it is necessary to prepare recombinant CaMKK2 fully phosphorylated at both 14-3-3 binding motifs. The main aim of this bachelor thesis was to optimize the protocol for the phosphorylation of human CaMKK2...
Characterisation of recombinant mouse glutamate carboxypeptidase III
Janoušková, Karolína ; Konvalinka, Jan (advisor) ; Obšil, Tomáš (referee)
Glutamate carboxypeptidase II (GCPII, PSMA, NAALADase) is transmembrane metalopeptidase and due to cleavage of substrates β-citryl-L-glutamate (BCG), N-acetyl-L-aspartyl-L-glutamate (NAAG) and polyglutamylated folates (Pte-Glun) is being studied as potential therapeutic target. Enzymes, which could compensate for enzyme activity and functions of GCPII, are thus relevant targets of enzymology as well. One of GCPII's homologs with similar enzyme activity is mouse glutamate carboxypeptidase III (GCPIII, NAALADase II). Enzymatic cleavage has not been determined using recombinant mouse GCPIII yet. It is important to kinetically characterize mouse GCPIII so that we can compare enzyme activity with human ortolog. Then we can find out whether mouse model is comparable with human. Recombinant mouse GCPIII was kinetically characterized. Kinetic parameters (KM, kcat) for recombinant mouse GCPIII were measured for substrates NAAG and BCG using radioactive assay. Experiments with the substrate Pte-Glu2 were analyzed using HPLC method. Although human GCPIII is more effective than mouse ortolog at clearage of NAAG, both enzymes are comparable during hydrolysis of BCG. Those results can contribute to better understanding of the role of GCPIII in the most commonly used animal model.
Interaction of a surface marker of immune cells with low-molecular weight ligands and their polymer conjugates
Šimonová, Lenka ; Konvalinka, Jan (advisor) ; Obšil, Tomáš (referee)
Millions of people worldwide die of cancer every year. In the last decade, im- munotherapy offered new treatment options achieving long-lasting remissions in a number of patients. Several new immunotherapy-based drugs have been ap- proved by Food and Drug Administration. However, majority of patients either do not respond or soon relapse. Combination of therapies as well as exploring new immune checkpoints seems promising. This thesis focuses on the new immunotherapeutic target CD73. CD73 is membrane ectonucleotidase, widely expressed on the regulatory leukocytes and on cancer cells. The enzymatically active CD73 contributes to the tumour mi- croenvironment by production of immunosuppressive adenosine. This novel im- mune checkpoint is being intensively studied. This thesis aims on development of new approaches for targeting and inhibition of CD73. Soluble recombinant CD73 (rhCD73) was prepared in mammalian expression system and transfectants stably expressing membrane-bound CD73 were prepared as well. Inhibitors necessary for both of my goals have been designed based on published inhibitor of CD73. Development and evaluation of novel antibody mimetic for CD73 characteri- sation was done. The so-called iBody, HPMA polymer conjugate decorated with CD73 inhibitor for targeting, fluorophore for...
Biophysical characterization of the N-terminal part of protein kinase ASK1.
Honzejková, Karolína ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
Apoptosis signal-regulating kinase 1 (ASK1) is an apical kinase of the mitogen-activated protein kinase cascade. Its activity is triggered by various stress stimuli such as reactive oxygen species (ROS), cytokines, endoplasmic reticulum (ER) stress or osmotic stress resulting in the activation of p38 and c-Jun N-terminal kinase metabolic pathways and leading to inflammation or cell death. Dysregulation of ASK1 is linked to several pathologies such as neurodegenerative and cardiovascular diseases and cancer, which makes this protein a potential target of therapeutic intervention. The activity of ASK1 is regulated through protein-protein interactions with 14-3-3 proteins and thioredoxin1 being among the most important negative regulators and tumour necrosis factor receptor-associated factors being an example of positive regulators. Apart from that, ASK1 is also tightly regulated via oligomerization. Despite continual progress being made, the precise molecular mechanism of ASK1 regulation and the role of ASK1 oligomerization in this process still remains unclear to this day owing to the lack of structural data. Interaction of the N-terminal parts of two protomers of ASK1 dimer is one of the key steps in ASK1 activation. It was shown, that the isolated ASK1 catalytic domain (ASK1-CD) forms stable...

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