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Bioinformatics Tool for Prediction of Protein Solubility
Čermák, Jiří ; Hon, Jiří (referee) ; Martínek, Tomáš (advisor)
To achieve cheaper and more efficient protein production, we must be able to predict protein solubility. In this thesis, we describe creation of bioinformatic data sets based on Target Track and eSol databases, we test the features used in existing protein solubility prediction tools and create a new predictor. Even though we fail to create an effective prediction tool we find out that in most cases the old features tested on the new data do not correlate with protein solubility as strongly as others repot in older and smaller datasets.
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The characteristics of stress granules in yeast Saccharomyces cerevisiae
Slabá, Renata ; Hašek, Jiří (advisor) ; Binarová, Pavla (referee)
9 ABSTRACT For proper function proteins should have a native conformation. If their conformation is impaired due to environmental stress or genetic mutation, proteins become prone to aggregation. There exist various types of protein aggregates. Stable non-membraneous inclusions can form which can serve for clearance of aberrant proteins from place where they can interfere with essential cellular processes. Another type of aggregates can serve as transient deposits of proteins thus protecting them from stress conditions. Stress granules (SG) are a such example of transient granules. Their formation is induced by heat shock for example. SGs contain mRNA, components of translation machinery, and other proteins. One of these proteins is Mmi1, small highly conserved protein with unknown function. Association of Mmi1 with stress granules and partial co-localization with chaperon Cdc48 and proteasom indicates Mmi1 can mediate heat stress damaged protein degradation. We have uncovered that yeast prion protein Sup35 is a component of stress granules as well. With regard to its aggregation capability there existed an assumption that prion domain of Sup35 could serve as scaffold for SG assembly. However as we show deletion of prion domain of Sup35 protein does not affect stress granules formation dynamics. Yeast...
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Investigation and inhibition of α-synuclein aggregation
Afitska, Kseniia ; Yushchenko, Dmytro (advisor) ; Žídek, Lukáš (referee) ; Bařinka, Cyril (referee)
α-Synuclein (AS) is a small intrinsically disordered protein expressed in neurons and abundantly present in synapses where it is involved in regulation of synaptic vesicle-mediated protein trafficking. Misfolding of AS into amyloid fibrils is a key process in progression of Parkinson's disease (PD), the second most common neurodegenerative disorder which has no cure to date. Inhibition of AS aggregation and blocking of cell-to-cell spreading of AS fibrils is a promising strategy for PD treatment. However, rational design of inhibitors of this type remains complicated due to the lack of thorough knowledge about the mechanisms of aggregation. Therefore, the aim of this thesis was to gain deeper knowledge about AS aggregation and to apply it for developing inhibitors of AS fibrillization. In my work on the mechanisms of AS aggregation, I first determined that the concentration of AS that enables the fibril growth is an order of magnitude lower than the concentration of AS required for initial fibril formation from monomers. I explored fibril disaggregation at AS concentrations below its Kd value, and characterized AS aggregation at low micromolar concentrations. I then investigated how different modifications of AS C-terminus (namely, extensions of various sizes and charges) affect fibril growth and...
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Bioinformatics Tool for Prediction of Protein Solubility
Čermák, Jiří ; Hon, Jiří (referee) ; Martínek, Tomáš (advisor)
To achieve cheaper and more efficient protein production, we must be able to predict protein solubility. In this thesis, we describe creation of bioinformatic data sets based on Target Track and eSol databases, we test the features used in existing protein solubility prediction tools and create a new predictor. Even though we fail to create an effective prediction tool we find out that in most cases the old features tested on the new data do not correlate with protein solubility as strongly as others repot in older and smaller datasets.
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The characteristics of stress granules in yeast Saccharomyces cerevisiae
Slabá, Renata ; Hašek, Jiří (advisor) ; Binarová, Pavla (referee)
9 ABSTRACT For proper function proteins should have a native conformation. If their conformation is impaired due to environmental stress or genetic mutation, proteins become prone to aggregation. There exist various types of protein aggregates. Stable non-membraneous inclusions can form which can serve for clearance of aberrant proteins from place where they can interfere with essential cellular processes. Another type of aggregates can serve as transient deposits of proteins thus protecting them from stress conditions. Stress granules (SG) are a such example of transient granules. Their formation is induced by heat shock for example. SGs contain mRNA, components of translation machinery, and other proteins. One of these proteins is Mmi1, small highly conserved protein with unknown function. Association of Mmi1 with stress granules and partial co-localization with chaperon Cdc48 and proteasom indicates Mmi1 can mediate heat stress damaged protein degradation. We have uncovered that yeast prion protein Sup35 is a component of stress granules as well. With regard to its aggregation capability there existed an assumption that prion domain of Sup35 could serve as scaffold for SG assembly. However as we show deletion of prion domain of Sup35 protein does not affect stress granules formation dynamics. Yeast...
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