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Non-covalent interactions of tryptophan in protein structure
Sokol, Albert ; Fišer, Radovan (advisor) ; Jurkiewicz, Piotr (referee)
A thorough knowledge of non-covalent amino acid interactions within a protein structure is essential for a complete understanding of its conformation, stability and function. Among all the amino acids that usually make up a protein, tryptophan is distinguished both by its rarity and size of its side chain formed by an indole group. It is able to provide various types of indispensable interactions within the protein and between different polypeptide chains, but also between the protein and a biological membrane. In addition, it is the most commonly used natural fluorophore. Databases of solved protein structures are commonly used to study amino acid interactions and allow more or less complex analyzes of the issue. Thus many non-covalent interactions that may occur between tryptophan and other amino acids have been found. However, most of these analyzes focus on specific interactions and do not follow up the tryptophan's environment as a whole, where all amino acids interact. Some newly developed methods have been used in this Thesis, specifically the occurrence profiles of the individual amino acids around the indole group of tryptophan and the results were compared with an available literature. The amino acid that has the greatest preference for tryptophan turned out to be tryptophan again, and...
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Non-covalent interactions of tryptophan in protein structure
Sokol, Albert ; Fišer, Radovan (advisor) ; Jurkiewicz, Piotr (referee)
A thorough knowledge of non-covalent amino acid interactions within a protein structure is essential for a complete understanding of its conformation, stability and function. Among all the amino acids that usually make up a protein, tryptophan is distinguished both by its rarity and size of its side chain formed by an indole group. It is able to provide various types of indispensable interactions within the protein and between different polypeptide chains, but also between the protein and a biological membrane. In addition, it is the most commonly used natural fluorophore. Databases of solved protein structures are commonly used to study amino acid interactions and allow more or less complex analyzes of the issue. Thus many non-covalent interactions that may occur between tryptophan and other amino acids have been found. However, most of these analyzes focus on specific interactions and do not follow up the tryptophan's environment as a whole, where all amino acids interact. Some newly developed methods have been used in this Thesis, specifically the occurrence profiles of the individual amino acids around the indole group of tryptophan and the results were compared with an available literature. The amino acid that has the greatest preference for tryptophan turned out to be tryptophan again, and...
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The effects of ions and oxidation on hydration and mobility of model lipid membranes.
Vojtíšková, Alžběta ; Jurkiewicz, Piotr (advisor) ; Michl, Martin (referee)
The presented thesis is a continuation of the bachelor work, in which the effects of monovalent ions on neutral model lipid membranes were characterized. Herein physical properties of physiologically relevant anionic membranes in the presence of monovalent cations and oxidized lipids were studied. Hydration and mobility of the lipid bilayer at glycerol level were investigated using fluorescent solvent relaxation technique. In the first part of this work the interactions of cations (Na+ , K+ , Cs+ ) with negatively charged POPC/POPS lipid mixture, which is a good model of inner leaflet of cellular membrane, were studied. The presence of cations resulted in dehydration and substantial hinderence of mobility of hydrated lipids at the glycerol level probed by Laurdan. Clear specificity of those effects, which correlated with Hofmeister series have been observed. In the second part of the work truncated oxidized phospholipids, oxPLs (PazePC, PoxnoPC, PGPC, POVPC), which are known to be important in pathophysiology of numerous diseases, were investigated. 10 mol% of each oxPL was incorporated into neutral and anionic lipid bilayers, the hydration and mobility of which were measured in water or in KCl solution. The results reveal complex interactions between oxPLs, negatively charged lipids, and K+ . In...
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