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Structural characterization of interaction between transcription factors and DNA
Filandrová, Růžena ; Novák, Petr (advisor) ; Vondrášek, Jiří (referee) ; Wimmerová, Michaela (referee)
Structural characterization of interaction between transcription factors and DNA Mgr. Růžena Filandrová Abstract Transcription factors are proteins that mediate gene expression regulation through interactions with DNA and other factors. They allow a cell to respond to various stimuli and play a crucial role in many biological processes such as control of cell cycle progression, differentiation of cells during development or immune response. To understand these processes, the knowledge of the transcription factors 3D structure together with the mechanism of their interaction with DNA is essential. However, some of the typical features of transcription factors, such as is for example the presence of intrinsically unstructured regions, make the 3D structure determination by the commonly used high resolution methods challenging. Therefore, utilization of complementary methods like structural mass spectrometry (MS), which was used in this thesis, might prove to be beneficial to explore the structural basis of the transcription factor-DNA interaction. In first part of this work, a set of structural mass spectrometry methods with the main focus on hydrogen/deuterium exchange mass spectrometry (HDX-MS) was optimized and tested on two transcription factor-DNA complexes and their DNA binding motifs and proved to be...
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Human Membrane-bound Carbonyl Reductases
Štambergová, Hana ; Wsól, Vladimír (advisor) ; Wimmerová, Michaela (referee) ; Šebela, Marek (referee)
ABSTRACT Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biochemical Sciences Candidate Mgr. Hana ŠTAMBERGOVÁ Supervisor prof. Ing. Vladimír WSÓL, Ph.D. Title of Doctoral Thesis Human membrane-bound carbonyl reductases Human membrane bound enzymes involved in the metabolism of carbonyl containing compounds consitute a highly interesting group of enzymes. Despite the great effort of scientists over the world most of them still remain uncharacterized, mainly those from the large short-chain dehydrogenases/reductases superfamily (SDR). At present, 75 SDR members have been indentified in the human genome whereas only 20 % of them is considered to be well characterized. On the other hand 30 % SDRs remain completly uncharacterized. SDR enzymes are involved in the metabolism of steroids, saccharides, retinoids or prostaglandins and therefore play a crucial role in a number of physiological pathways as well as several serious diseases (e.g. hormon dependent cancer, metabolic syndrome, diabetes mellitus). Moreover, SDR proteins contribute to the biotransformation of some xenobiotic compounds. Several SDR enzymes have been identified to be involved in the phase I metabolism of drugs such as doxorubicin, dolasetron, benfluron, metyrapone or ketoprofen, but so far only one...
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α-N-Acetylgalactosaminidase as a tools in the synthesis of complex oligosaccharide immune stimulators
Mrázek, Hynek ; Bezouška, Karel (advisor) ; Macek, Tomáš (referee) ; Wimmerová, Michaela (referee)
1 Charles University in Prague Faculty of Science Department of Biochemistry α-N-Acetylgalactosaminidase as a tools in the synthesis of complex oligosaccharide immune stimulators Summary of Ph. D. Thesis Mgr. Hynek Mrázek Supervisor: Prof. RNDr. Karel Bezouška, Dsc. Prague 2011 2 Introduction Glycoproteins Glycoproteins consist of proteins to which carbohydrate are covalently linked. The distinction between proteoglycans and glycoproteins residues is in the level and types of carbohydrate modification. Carbohydrates are linked to the protein component through either O-glycosidic or N-glycosidic bonds. The N-glycosidic linkage is through the amide group of asparagine. The O- glycosidic linkage is to the hydroxyl of serine, threonine or hydroxylysine. The predominant carbohydrate attachment in glycoproteins of mammalian cells is via N-glycosidic linkage. The site of carbohydrate attachment to N- linked glycoproteins is found within a consensus sequence of amino acids, N-X- S(T), where X is any amino acid except proline. While the N-glycosylation is governed by the above rules, no exact rules were found for glycosylation of O- type. This process is the step-wise addition of the sugar residues directly onto the polypeptide chain. Biosynthesis of glycoproteins occurs via protein glycosylation (the addition of...
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