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Structural characterization of Nkr-p1f/Clrg interaction
Tůmová, Lucie ; Kavan, Daniel (advisor) ; Ptáčková, Renata (referee)
NK cells are ranked among lymphocytes, which are involved in primary immune responses to virus infected and tumour cells. They produce cytokines at the same time and are involved in the formation of secondary immune responses together with T and B lymphocytes. This diploma thesis is engaged in the study of the structure and interaction of the transmembrane receptor Nkr-p1f with its ligand Clr-g. This receptor Nkr-p1f has an activation function and is able to initiate the cytotoxic function of the NK cells. The three-dimensional structure has been solved as a Clr-g homodimer, but its interaction with the Nkr-p1f receptor remains mysterious. The aim was to prepare an expression vector coding the entire extracellular region of the receptor NKR-P1F and carry out the production of the receptor Nkr-p1f and Clr-g in prokaryotic expression system, subsequently renaturation and purification of the proteins in vitro. This way prepared proteins were analyzed by electrophoresis and mass spectrometry. Their interaction was studied with biophysical method, surface plasmon resonance (SPR). However, the interaction between them was not revealed by SPR technology. (In Czech)
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Production of interleukin 2 in fusion with monoclonal antibody S4B6
Rožová, Dominika ; Vaněk, Ondřej (advisor) ; Kavan, Daniel (referee)
Interleukin 2 is a growth factor of T cells as well as other lymphocytes, such as NK, NKT cells, dendritic and mast cells, which ensure its expression and secretion. IL-2 regulates immune cell homeostasis and is used to treat a variety of disorders including cancer and autoimmune diseases. In recent years, several cases of interleukin 2 complexed with anti-IL2 antibody have been shown to exhibit dramatically higher biological activity in vivo. These complexes have selective stimulatory activity for different IL2 receptors on target cell. This work follows up previous unsuccessful attempts to express and purify a sufficient amount of the murine IL2 immunocomplex with the S4B6 antibody linked by a 15 amino acid long glycine-serine linker. In this work, a plasmid containing the secreted fusion immunocomplex mIL2-S4B6 gene was prepared and stably transfected to the HEK293T cell line using piggyBac system. The protein was then isolated by chelation affinity chromatography and purified by gel permeation chromatography.
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Studies of NK cell receptors and other proteins using recombinant expressions and mass spectrometry
Kavan, Daniel
CD69 is considered as the marker receptor of activated lymphocytes and is expressed at sites of active immune response. Physiologically it appears in the form of covalently bound homodimer, however after examining its three- dimensional structure we suggested Q93 on one subunit and D88 with E87 on the other one to participate on the inter-subunit interactions. Even more profound intertwining was observed in case of R134 of one subunit with A136 and Y135 on the other one. Therefore Q93, R134 or both were mutated into alanines and showed the monomeric form just in case of double-mutant. This fact influenced significantly also the binding of ligands. While the Kd values for binding of GlcNAc was approximately 10-5 M in case of monomeric form, in case of dimeric form it was 10 times lower and even 100 times lower in case of the longest covalently bound dimers. Although the gel filtration retention time decrease was observed, which could indicate a change in molecular fold, the value of experimentally determined sedimentation coefficient was identical. Moreover neither the comparison of HSQC NMR spectra before and after ligand saturation revealed any significant shifts. Hydrogen deuterium exchange is a chemical process in which a covalently bonded hydrogen atom is replaced by deuterium or vice versa. As...
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Monitoring of leukemic cell line amino acid metabolism changes after Quambalarine B treatement
Matoušková, Zuzana ; Kavan, Daniel (advisor) ; Prošková, Veronika (referee)
Leukemia is the most common cancer of children, moreover it is also not uncommon of elderly patients. Research has focused on the development of specific antileukemic drugs in recent years. Abnormalities in tumor cell metabolism that can be targeted during treatment appear to be the key. Natural 1,4-naphthoquinones, including quambalarin B produced as a secondary metabolite by the basidiomycetes of Quambalaria cyanescens, are known for their therapeutic effects. Not surprisingly, Quambalarine B has also been shown to inhibit cell proliferation in some leukemic cell lines and subsequently caused cell death. In the present thesis, I tried to observe changes in amino acid metabolism by monitoring amino acid levels in the intracellular and extracellular environment of leukemic cells after treatment with Quambalarine B using amino acid analysis with fluorescence detection. The observation was performed in Jurkat, Ramos and THP-1 cell lines, each of these lines represents another type of leukemic disease. [IN CZECH] Key words Amino acid analysis, amino acid metabolism, Quambalarine B, leukemia
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The novel combinations of experimental approaches: mass spectrometry (MS) and photo-induced surface labelling, electron release (PIER), or cross-linking (PIXL)
Tuzhilkin, Roman ; Šulc, Miroslav (advisor) ; Kavan, Daniel (referee)
Countless electron transport/transfer (ET) processes occur in living organisms every day. Therefore, their study is a crucial field of modern structural and functional proteomics. In many cases model proteins like azurin from P. aeruginosa are utilised in experiments. This blue copper protein is favoured due to a characteristic absorbance maximum at 630 nm in Cu(II) redox state of the central Cu atom. During its oxidation to Cu(I) state the A630 value decreases allowing UV-Vis detection of ET reaction progress. We have introduced a structural photoinducible analogue of canonical amino acid Met - L-2-amino-5,5-azihexanoic acid (photo-Met) - into azurin structure to study oligomerization in solution via photo-induced cross-linking (PIXL). Using previously optimised protocols for recombinant expression in E. coli B834 we have inserted photo-Met into azurin moieties: wild type azurin and Az2W mutant where two adjacent W residues with confirmed role in electron hopping across protein-protein interface are present. The incorporation percentage of photo-Met in analysed samples was determined after SDS-PAGE and in-gel protease digestion via MALDI-TOF MS. PIXL was employed to study azurin-azurin interaction and oligomerization under different total concentrations of protein (in range of 15-300 µM). The...
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Production of interleukin 2 in fusion with monoclonal antibody S4B6
Rožová, Dominika ; Vaněk, Ondřej (advisor) ; Kavan, Daniel (referee)
Interleukin 2 is a growth factor of T cells as well as other lymphocytes, such as NK, NKT cells, dendritic and mast cells, which ensure its expression and secretion. IL-2 regulates immune cell homeostasis and is used to treat a variety of disorders including cancer and autoimmune diseases. In recent years, several cases of interleukin 2 complexed with anti-IL2 antibody have been shown to exhibit dramatically higher biological activity in vivo. These complexes have selective stimulatory activity for different IL2 receptors on target cell. This work follows up previous unsuccessful attempts to express and purify a sufficient amount of the murine IL2 immunocomplex with the S4B6 antibody linked by a 15 amino acid long glycine-serine linker. In this work, a plasmid containing the secreted fusion immunocomplex mIL2-S4B6 gene was prepared and stably transfected to the HEK293T cell line using piggyBac system. The protein was then isolated by chelation affinity chromatography and purified by gel permeation chromatography.
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Backbone Resonance Assignment of the mouse protein Nkrp1c
Nelic, Dominik ; Chmelík, Josef (advisor) ; Kavan, Daniel (referee)
The protein Nkrp1c is a receptor on the surface of murine natural killer cells belonging to the C-lectin receptor family. These cells create congenital immunity against tumors or pathogens before the formation of antibodies. Determining the 3D protein structure is often the key to understanding the function of the protein at the molecular level. One way to determine the structure of proteins at the atomic level is nuclear magnetic resonance. The aim of this bachelor thesis was to evaluate several already measured spectra and to assign the resonance frequencies of the peptide backbone atoms needed to obtain data for the secondary structure prediction for Nkrp1c protein, which was prepared by recombinant expression. The Sparky program was used to evaluate the measured spectra. The prediction of the secondary structure of the Nkrp1c protein itself was performed by programs Talos+ and PSIPRED. The obtained results were compared with the already published homologous model of the Nkrp1c protein receptor. Keywords: protein NMR, Nkrp1c
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Study of mechanism of signal transduction in case of two model heme-containing sensor proteins
Mihalčin, Peter ; Martínková, Markéta (advisor) ; Kavan, Daniel (referee)
Heme-based gas sensing proteins belong to a group of proteins that are present in signalling pathways of bacteria. A precise regulation of physiological functions, such as intercellular communication or biofilm production, is essential for the survival of these bacteria and their adaptation to the changing surrounding conditions. Heme-based gas sensors are able to detect the concentration of gas molecules in the local environment via their sensory domain (which contains a heme molecule as the intrinsic detection site) and transmit the signal to the functional domain helping to regulate the adaptation of many processes. These, often pathogenic, processes contribute to extended resistance of bacteria against antibiotics. Heme-based sensors are thus potentially a new therapeutic object of interest in antimicrobial treatment. In order to provide this type of treatment, it is crucial to understand the exact mechanism of intramolecular signal transduction facilitated by heme-based sensors. One of the approaches to unravel these mechanisms is further study of model sensory proteins. This thesis focuses on the analysis of a signal transduction performed by two model globin-coupled heme-based oxygen sensors.
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