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Major structural protein of Polyomaviruses: Interactions with host cell structures
Mrkáček, Michal ; Horníková, Lenka (advisor) ; Němečková, Šárka (referee)
The main structural protein VP1 is the product of late polyomaviral genes and it is the largest and the most abundant protein of the whole polyomaviral capsid. Because of the low coding capacity of the polyomaviral genomes, it is considered that in addition to its structural role the VP1 protein might have some additional functions in the late phase of the infectious cycle. This diploma thesis is exactly on these additional functions. In the case of the VP1 protein of mouse polyomavirus, it was observed that the protein is capable of binding to the structure of cellular microtubules. The first objective of this work was to test whether pentamers of the VP1 protein are able of this binding without the participation of other cellular (or viral) proteins. Based on an in vitro experiment, we showed that protein VP1 binds to the structure of microtubules very inefficiently. The second objective of this work was to prepare a detection system that would allow an identification of potential interaction partners of BK polyomavirus VP1 protein. Therefore, expression plasmids producing the N and C-terminally tagged VP1 protein were prepared. These tagged proteins had the property of being biotinylated whilst being produced in the transfected cells. By using affinity chromatography, the entire protein complexes...
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Bioinformatic methods of detection of protein coevolution
Pařízková, Hana ; Schneider, Bohdan (advisor) ; Hampl, Vladimír (referee)
The term coevolution describes the situation when two or more species or biomole- cules reciprocally affect each others' evolution. On the protein level, it is thought to be the main mechanism ensuring correct folding, interactions and function of a protein, and it can be observed both on the level of interacting protein families and individual amino acid residues. Coevolution studies have been proved to be a powerful tool for prediction of protein structure, function, interaction partners, etc. In this thesis, different algorithms used for detection of protein coevolution are described, as well as their applications and limitations. Keywords: coevolution, protein family, protein structure prediction, interac- tion partners, correlated mutations, mirrortree, mutual information, direct cou- pling analysis
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ERK1/2 MAP kinase - Structure and Interaction Partners
Přibyl, Miroslav ; Vopálenský, Václav (advisor) ; Žíla, Vojtěch (referee)
Extracellular signal molecules are recognized by membrane receptors on the surface of eukaryotic cells. Receptors transmit the signal into the intracellular space where activation of the concrete enzymes occurs. Activated enzymes may be protein kinases that phosphorylate the substrate proteins corresponding to the requirements for specific recognition by a protein kinase. Substrate proteins may be structural proteins and enzymes, which in turn transmit the signal or directly affect the physiological processes of the cell. The protein kinase family accounts for ERK1 and ERK2 (Extracellular signal-regulated kinase 1 and 2), enzymes which affect cell growth, cell cycle and numerous other physiological processes of the cell. Protein kinases are dynamic molecules, which undergo a series of conformational changes during their catalytic cycle and whose stability and function are affected by conformational changes. Conserved amino acid residues carry out the function of protein kinases. These factors are also involved in interactions with protein substrates and regulatory proteins, and are responsible for specific function of protein kinase.
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