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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Study of single stranded DNA by biophysical techniques
Svoboda, Jakub ; Schneider, Bohdan (advisor) ; Novák, Petr (referee)
DNA is the fundamental functional molecule of all domains of life. One of its characteristics is the ability to self-associate to form a double stranded helix. Nevertheless, even single stranded DNA can form non-canonical structures such as hairpins, triplexes or tetraplexes. One of the interesting single stranded sequences are REP elements. These sequences form a part of bacterial transposable elements, so-called insertion sequences, which can be found in a great number of copies in wide range of bacterial species. This thesis studies structure and properties of selected REP sequences. It presents the results of spectral measurements by technique of circular dichroism, melting curves from differential scanning calorimetry, and monocrystal diffraction data. Key words Single-stranded DNA, crystallography, circular dichroism, calorimetry, transpozone, REP elements, insertion sequences.
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Krystalizační studie nově izolované halogenalkandehalogenasy DgaA z \kur{Glacieocola agarilytica} NO2
BERKOVÁ, Ivana
This bachelors thesis is focused on crystalization study of newly prepared halogenalkanedehalogenase DgaA from bacteria Glaciecola agarylitica NO2. Main target of this work is getting acquianted with methods of protein crystalization and usage of those methods for preparation of suitable DgaA protein crystals of that will be used for X-ray structural analysis. Results from difraction analysis of DgaA crystals will be starting point for further research focused on structure determination and and description of protein function.
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Statistics of directional data with an application in crystallography
Karafiátová, Iva ; Šedivý, Ondřej (advisor) ; Hlubinka, Daniel (referee)
The main purpose of this thesis is to derive methods used to estimate the mean orientation of a grain in polycrystalline material. The estimation is highly impor- tant in crystallography. However, it is often expressed by only one representative value regardless of its variability within the grain. In this thesis we present the basic concepts of crystallography, including the principle of the Electron Backs- catter Diffraction, which is used to explore the microstructure of a polycrystalline materials. Subsequently, we present six of the most commonly used descriptors of three-dimensional orientation of a crystal lattice. This overview is completed by the summary of the particular relationships between those descriptors. In the practical part of this thesis we apply derived methods on real data within the scope of research of microstructure of an aluminum alloy. 1
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Bioinformatic analysis of protein/DNA interactions
Božíková, Paulína ; Schneider, Bohdan (advisor) ; Hašek, Jindřich (referee)
In this thesis, we focused on local structural features of the DNA backbone in protein-complexed DNA and non-complexed (naked) DNA, and its dependence on types of a base pairing in DNA, and on the base sequence. To reach this goal we analyzed about 1,400 crystal structures of DNA in complexes with proteins and more than 400 crystal structures of naked DNA. DNA local conformations were structurally classified into 38 dinucleotide conformers ntCs, which were described previously (Svozil et al. Nucleic Acids Res. 2008). The ntC were further clustered into 16 structural alphabet classes ntA to reduce the number of analyzed variables. We assembled base-paired dinucleotides from double helical DNA structures accord- ing to their assigned structural alphabet classes into so called Association matrices. Three basic Association matrices were analyzed; two compare ntA/ntA associations between dinucleotides forming only Watson-Crick base pairs in protein/DNA com- plexes and in naked DNA, respectively; the third one ntA/ntA associations between dinucleotides base-paired also by non-Watson-Crick pairs. We also analyzed As- sociation matrices of dinucleotides as a function of their sequences. The analyzes revealed differences in structural behavior of various ntA and their dependence on dinucleotide sequences.
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Bioinformatics Tool for Protein Structure Prediction
Plaga, Michal ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The goal of this thesis is test and comparation of the offline tools for prediction of protein structure and creation of metaprediktor, which allows the user to select the appropriate tool, according to given parameters. Testing tool is based on a dataset of proteins, which is based on the SCOP database and it is trying to be as balanced as possible to include proteins from different families and thus could best evaluate individual tools. The results of this thesis are requirements of metaprediktor and also which data and settings can be allowed and processed and how it will be implemented.
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Geometry of protein moleculs
Novotný, Jan ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
Objective of this work was to study the spatial arrangement of protein molecules, with their extraction, notations and variables used in the course descriptions. Prediction of protein structures is very important for determining the future function of proteins. Another objective was to create a function in MATLAB that will graphically represent the spatial arrangement of the backbone structure of the protein by form Ramachandran plot. Along with this function create another function to render the side-chains of amino acids and function to calculate the stereochemical quality. Finally, create a program for a complete assessment of the spatial arrangement of the protein molecules and calculating the stereochemical quality of and test program for protein structures from public databases RSCB PDB.
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Analysis of x-ray diphractograms of organic crystalline solids
Stejkora, Jakub ; Žídek, Jan (referee) ; Salyk, Ota (advisor)
Derivates of diketopyrrolopyrrole are colored pigments with potential use in field of organic semiconductor structures. Their electrical attributes such as conductivity, photocon¬¬ductivity and electroluminescence relate to their crystal structures that determine charge transport path through the compound. For crystallographic structure determination from RTG diffractometry it is needed to grow a measurable single crystal. Growing crystals of derivates of diketopyrrolopyrrols is very difficult due to their poor solubility in all solvents. Several relatively suitable – perhaps even measurable – samples were obtained throughout the testing of series of methods. One of these samples was measured with RTG diffractometry and on the ground of this measurement it was possible to find and solve the crystallographic structure.
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