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Proteins as a source of nitrogen for tobacco plants grown in vitro
Bělonožníková, Kateřina ; Ryšlavá, Helena (advisor) ; Entlicher, Gustav (referee)
Nitrogen (N) belongs among necessary elements for plant growth and development. In the past attention was paid mostly to the inorganic forms - nitrate and ammonium. In soil N is also present in organic forms, including proteins, for which plants could compete with soil microorganisms. Recently two ways have been considered - the hydrolysis of proteins by secreted proteases and endocytosis of native proteins, possibly their confluence. Tobacco plants were grown in vitro under sterile conditions in modified Murashige-Skoog medium with casein as the only source of N (CAS), decreased concentration of inorganic forms of N (AD) or in complete Murashige-Skoog medium as control plants (MS). After the 12 weeks growth, the standard growth parameters were measured. The CAS plants were able to grow without inorganic N, and protein content in the leaves was higher than in other experimental plants. Proteomic analysis documented differences in protein expression in plant roots in the dependence on the form of N. In total 185 proteins were identified, 75% of proteins were less and 14% more abundant in the CAS plants. The uptake of casein conjugated with fluorescein was followed and the proteolytic activity was analyzed by confocal microscopy. Among proteins secreted from roots to the medium aspartic protease...
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Conformational states of the opiod receptors
Provazníková, Adéla ; Hudeček, Jiří (advisor) ; Entlicher, Gustav (referee)
This Thesis elucidates the relationships between structure and function of opioid receptors. The mechanism of opioid receptor function could be better understood on the basis of the recent knowledge of their three-dimensional structure. In the first part of the Thesis, methods for membrane protein crystallization and X-ray structural analysis are reviewed with a special focus on in meso crystallization. Next, the three opioid receptor subtype crystal structures are described and analysed, starting with their general architecture and proceeding to the detailed description including the binding pocket for opioid ligands with the help of visualization with the PyMol software. In its third part, this Thesis re-examines the structure-function correlations predicted on the basis of site-directed mutagenesis (Décaillot F.M. et al, Nature Structural Biology 10, 629, 2003) in the light of now available crystal structure. This analysis is pointing to the potentially important contacts of aspartate D128, suggesting that ligand binding and receptor activation might involve changes in its interaction with tyrosine Y308.
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Effects of valproic acid and its combinations with cytostatic agents on tumor cells in vitro
Hinďoš Hřebačková, Jana ; Dyr, Jan (advisor) ; Vávrová, Jiřina (referee) ; Entlicher, Gustav (referee)
Cancer is one of the most challenging problems the modern medicine is facing today. An increasing incidence and a great variability of tumor cells are the main reasons those drive the research to develop better diagnostics and therapeutic protocols. Histone deacetylase inhibitors, a group of epigenetic chemotherapeutics, are able to improve the performance of currently used anticancer agents. Vaplroic acid that is commonly used as antiepileptic drug exhibits a remarkable anticancer activity by itself as well as it is capable of therapy potentiation based on other therapeutic agents. Its effect to inhibit growth of tumor cells and induce apoptotic cell death seems to be even greater under hypoxic conditions (<1% O2). This study is focused on effect of valproic acid on neuroblastoma cell lines in vitro under normoxic and hypoxic conditions. We observed significantly greater efficacy of valproic acid in hypoxia compared to normoxia. The mechanism of induction of apoptotic cell death is based on disruption of the balance between pro- and antiapoptoic proteins. Intrinsic apoptotic pathway is probably initiated by the action of 19 kDa variant of proapoptotic protein Bax on mitochondrial membrane. Moreover, we examined the efficiency of a combined treatment of neuroblastoma cells with valproic acid and...
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Theoretical study of enzymes related to carcinogenesis: DNA polymerase β and cytochromes P450
Jeřábek, Petr ; Martínek, Václav (advisor) ; Entlicher, Gustav (referee) ; Ettrich, Rüdiger (referee)
Present doctoral thesis contributed to understanding of mechanistic principles of two enzymes participating in the process of carcinogenesis; DNA polymerase (pol ) and cytochromes P450 (CYP). Pol is part of the DNA base-excision repair mechanism (BER). The primary role of pol in, the BER mechanism, is inserting a new nucleotide into a DNA strand according to Watson-Crick base pairing rules. Pol plays an important role in the process of carcinogenesis, approximately 30 % of human tumors express pol mutants. The ability of pol to discriminate between "right" and "wrong" nucleotide during the insertion process is called fidelity. We employed computational methods to elucidate molecular basis of the fidelity of pol . First, the relative free energy calculation method LRA was employed to compare differences in free energies between the "right" and "wrong" nucleotide during its insertion into DNA. The results indicated a better stabilization of transition-state of the nucleophilic substitution catalyzed by pol in the case of the "right" versus "wrong" nucleotide. This difference resulted in an 80-fold contribution to its fidelity. Further, computational methods FEP and LIE were used to examine how mutations effect fidelity of pol . Results were than correlated with experimental data...
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