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Structural characterization of materials for energy applications using NMR spectroscopy
Mahun, Andrii ; Kobera, Libor (advisor) ; Hrabal, Richard (referee) ; Lebl, Tomas (referee)
Development of new, safe, highly efficient, and environmentally friendly energy storage and conversion devices is demanded in today's world. This includes the synthesis, characterization, and application of new advanced materials. Promising materials such as polymer electrolytes, conductive polymers, and perovskites have drawn the great attention of scientists worldwide and are under intensive investigation. These substances are believed to be capable of solving some issues and improving the existing energy storage and conversion technologies. The presented thesis is dedicated to the investigation of above-mentioned materials for energy applications. The research was focused on the elucidation of structure-properties relation in the compounds of interest and optimization of their composition to get better properties in terms of potential application in the energy field. Among all experimental techniques used within the thesis, NMR spectroscopy was comprehensively employed and chosen as the main tool for the structural characterization of the investigated samples. Various liquid-state as well as solid-state NMR techniques were used, and some of them were optimized for specific purposes of the research. During the investigation of polymer electrolyte systems, NMR spectroscopy was utilized to study...
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Design, preparation and structural studies of biologically relevant protein variants of cancer-related Carbonic Anhydrase IX
Fejfarová, Adéla ; Maloy Řezáčová, Pavlína (advisor) ; Novotný, Marian (referee)
3 Abstract Carbonic anhydrase IX (CA IX) represents an attractive target for the development of anticancer drugs as it is overexpressed in various types of solid tumors. By its catalytic activity, CA IX assists the cancer cells to maintain the optimal intracellular pH and to acidify the extracellular milieu promoting tumor development. There are twelve enzymatically active carbonic anhydrases (CAs) present in human body, all sharing a high sequence identity and a typical β-sheet structural fold of the well-studied catalytic domain. Although, the activity of CAs is efficiently inhibited by sulfonamide-containing compounds, the design of inhibitor selective to the cancer-related CA IX has been hampered by the high sequence conservation. CA IX has several unique features compared to other members of the family, which investigation may help in the development of selective drug compounds. Namely, it is a type I transmembrane dimeric protein with unique N-terminal proteoglycan-like (PG) domain, extracellular catalytic domain, and short cytoplasmic C-terminal segment. The above denoted traits make CA IX subject of structure-based drug design efforts. However, the expression and purification in high yield as well as crystallization experiments has been challenging. Therefore, protein variant bearing six amino acid...
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Noncovalent Interactions of Biologically Active Compounds
Osifová, Zuzana ; Dračínský, Martin (advisor) ; Lyčka, Antonín (referee) ; Sýkora, Jan (referee)
This thesis deals with the employment of nuclear magnetic resonance (NMR) spectroscopy in the studies of non-covalent interactions of biologically active compounds. The introduction serves as a brief overview of the literature, pointing out the milestones in determining and studying the most common non-covalent interactions - hydrogen bonding, π-π stacking and halogen bonding - by NMR spectroscopy. This part also includes the basics of this method to ensure that the results presented and the principles used will also be understandable for readers outside the field. Similarly, the employment and limitations of theoretical calculations are shortly discussed. The thesis aimed to determine the role of non-covalent interactions in biologically active compounds, including hydrogen bonding of modified nucleobases, interactions influencing ketoenol-diketo tautomerism of pharmacologically active curcuminoids, and the role of hydrogen bonding and amino acid sequence in the adoption of secondary structure in short peptides. Methylation and oxidation are nucleobases' most common natural modifications, causing changes in their hydrogen bonding pattern and preferences. We found that N-methylation of adenine residue stabilises its hydrogen-bonded base pairs with thymine and that these base pairs tend to adopt...
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Unravelling molecular mechanisms of the abasic crosslink DNA repair
Hušková, Andrea ; Šilhán, Jan (advisor) ; Bařinka, Cyril (referee) ; Pavlíček, Jiří (referee)
4 Abstract DNA as the primary carrier of genetic information guarantees organisms to live, grow, develop and reproduce. However, this most vital molecule in the cell is subject to various damages every moment. If it is not repaired, the cell and the organism will eventually succumb to inevitable destruction. One of the most serious damages is abasic site interstrand crosslink (Ap-ICL). Ap-ICL is formed spontaneously when an abasic site covalently pairs with an adenine on the opposite strand. The lack of information on repair mechanisms, the influence of the local sequence and its stability leads to questions about the fate, toxicity and occurrence of these lesions in cells. During evolution, several mechanisms have evolved to repair these and other damages to ensure the organism's survival. A recently discovered pathway known to repair Ap-ICL is named after the DNA glycosylase responsible for removing Ap-ICL. NEIL3 DNA glycosylase is recruited to Ap-ICL by ubiquitylation of DNA helicase, which is part of the DNA replication complex. NEIL3 glycosylase contains several zinc-finger domains, that bind to the damaged DNA and ensure its catalytic function. The molecular mechanism of the NEIL3 glycosylase repair process is currently not known. In order to answer the aforementioned unknowns, the rate of formation,...
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Methods for prediction of secondary structure in proteins
Hoštáková, Nina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The examination of protein structure is crucial in determining protein function in organism. This work deals with the issue of 1D, 2D and 3D structures, into which are proteins organized in space. Emphasis is placed on secondary structure, which can be predicted directly from the amino acid sequences and then used for the estimation of spatial structure. On this procedure are focused computational methods, using algorithms that convert the order of amino acids into the order of preferences for secondary structures. To direct determination of the structure by creating structural models is devoted chapter Experimental Methods (NMR spectroscopy, RTG crystallography). The main aim of this work is practical realization of protein secondary structure prediction method. The created program is supplemented by graphical user interface. In the final part the results of the program based on Chou- Fasman method are compared to the outputs of freely available softwares from the Internet.
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Methodology for identification of pollution sources using PMF for strategic decision making in air protection - update 2023
Horník, Štěpán ; Sýkora, Jan ; Pokorná, Petra
The presented methodology proposes utilizatíon of the spectroscopy of nuclear magnetic resonance (NMR) as another analytical technique for the identification of compounds in atmospheric aerosols. This technique makes significantly increases the number of deterined substances and thus a number of possible markers, which can be subsequently used together with other methods to identify sources of air pollution using advanced statistical\nanalysis. Among the markers determined by NMR spectroscopy there are several organic and sulfonic acids or carbohydrates, wich are characteristic for relevant sources of air pollution. The updated methodology also shows the identification of a biogenic source that previous methodologies were not able to determine.
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Study of the role of the B-chain N-terminus conformation of insulin in binding to the insulin receptor
Kosinová, Lucie ; Žáková, Lenka (advisor) ; Obšil, Tomáš (referee)
According to the International Diabetes Federation (IDF), there were 371 million people in the age from 20 to 79 years worldwide affected by diabetes in 2012. This means diabetes has become a global epidemic disease and, therefore, the importace of insulin research still grows. Insulin is a protein hormone that plays a key role in regulating blood glucose level which has a widespread impact on whole metabolism. Insulin acts through binding of its monomeric form to the insulin receptor. It is clear that insulin monomer has to undergo structural changes upon binding to the insulin receptor as the residues which are crucial for the interaction are burried within the native form. According to studies of highly active hormone analogs and the new information about the insulin-insulin receptor complex, there is a strong evidence that the C-terminal part of the B-chain is a dynamic element in insulin activation and receptor binding. Probably, there is also a great importance of the B-chain N- terminus and the transition between T and R conformations of insulin. However, the exact significance of the T and R states of insulin still remains unclear. In this work, several new insulin analogs AibB3-insulin, AibB5-insulin, AibB8- insulin, N-MeAlaB8-insulin and D-ProB8-insulin were prepared for the purpose of...
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Development of an alternative synthesis of Sm-pdta, a chiral NMR shift reagent for amino acids analysis
Hrubá, Lucie ; Vaněk, Václav (advisor) ; Pohl, Radek (referee)
This bachelor thesis deals with the preparation of chiral shift reagents sodium [(R)- and (S)-1,2-diaminopropane-N,N,N',N'-tetraacetate]samarate, for short Sm-(R)-pdta and Sm-(S)-pdta. These reagents have the ability to differentiate NMR signals of enantiomers of amino acids in an aqueous environment. The main aim of this work was to develop a new, efficient and cheap method of the preparation of these reagents which would enable their routine use in laboratory practice, because these reagents are commercially available only in limited quantities and at high price. This work describes simplifield method of separation of racemic 1,2-diaminopropane to its enantiomers from easily available starting substances, L-tartaric acid and racemic 1,2-diaminopropane. We also developed and optimized a new process of synthesis of the key intermediate, (R)- and (S)-1,2-diaminopropane-N,N,N',N'-tetraacetic acid from (R)- and (S)-1,2-diaminopropane dihydrochloride, with a new synthetic step involving tetrabenzylester of this acid and its deprotection by hydrogenolysis without contamination by extraneous ions. This process affords very pure anhydrous acid in high yield. Finally, the target complexes Sm-(R)-pdta and Sm-(S)-pdta were successfully prepared from (R)- and (S)-1,2-diaminopropane-N,N,N',N'-tetraacetic acid...
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Synthesis and characterization of ABA triblock copolymers modified with glucose via thiol - ene click reaction
Hašpl, Adam ; Uchman, Mariusz Marcin (advisor) ; Štěpánek, Miroslav (referee)
The bachelor thesis is focused on method of postpolymerisation modification of two poly(ethylene oxid-b-1,2-butadiene-b-ethylene oxide) amphiphilic block copolymer samples with high content of 1,2-isomer units in inner polybutadiene block by thiolene click. The implemented modification agent was 1-thio-β-D-glucose tetraacetate. The thesis is further focused on methods of copolymer sample characterization before and after modification reaction. Structure and degree of functionalization of vinylic units in polybutadiene block after modification was determined by nuclear magnetic resonance spectroscopy. The dimensions of prepared polymeric particles were studied by static and dynamic light scattering methods. Keywords: ABA triblock copolymers, self-assembly, click reaction, NMR spectroscopy, light scattering
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