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RNA secondary structure conservation identification module for rPredictor
Pešek, Jan ; Hoksza, David (advisor) ; Škoda, Petr (referee)
The issue of comparing ribosomal RNA secondary structures is currently an open research problem. Goal of this work is to design and implement program comparing so called mutual conservancy of a group of rRNA secondary structures. This program is included as a new module of an existing system called rPredictor consisting of the structure database and an algorithm that predicts these structures. This thesis covers an introduction into the problem of secondary structures conservancy identification and summarizes known approaches towards the problem. The result of this work is a stand alone program for the secondary structure comparison and also a new analytic module of the rPredictor system, where the secondary structure comparison program can be used for comparison of the structures from the rPredictor database. Powered by TCPDF (www.tcpdf.org)
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Domain and structural characterization of tyrosine phosphorylation sites in cancer cells
Vávra, Dan ; Novotný, Marian (advisor) ; Brábek, Jan (referee)
Phosphorylation is an important mechanism for regulation of protein function and aktivity. Tyrosine phosphorylation plays a critical role in signaling pathways. Aberrant tyrosine phosphorylation was observed in many cancer types. My work follows patological details of tyrosine phosphorylation sites of lung and colorectal cancers. Point of view includes aminoacid sequence, secondary structure, domain localization, expression, model organism ortholog occurrence. The project is based on analysis of literary informations and data from protein databases. There are no new phosphorylation sites in observed cancer types. Regular secondary structures, α-helices and β-sheets, are significantly phosphorylated in compare with loops. Annexin and Kinase domains are the most phosphorylated. Gene expression change of phosphorylated proteins occurs in observed cancer cells. Powered by TCPDF (www.tcpdf.org)
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Analysis of selected secondary structures of nucleic acids
Skružný, Petr ; Mokrejš, Martin (advisor) ; Drda Morávková, Alena (referee)
This work introduces a database of experimentally verified structures of nucleic acids which were collected from published scientific literature. The database is annotated and the structures are analysed from the perspective of quality and it was found that the experimentally obtained data are not always sufficient - their supporting evidence is often limited and their quality is not convincing. This work also discusses some of the problems, that can be encountered when the structures are experimentally probed. Contents of the database were compared to the RFAM database and despite of its small range it contains 80 new structures. The complete database of 166 structures can be possibly used to optimise software used to predict derived structures of nucleic acids. Furthermore, the work presents several possible ways of improvement of the quality of contained structures.
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Measuring of conformational properties of nucleic acids
Hrazdilová, Ivana ; Renčiuk,, Daniel (referee) ; Maděránková, Denisa (advisor)
This thesis gives a brief characteristic of the most important conformations of nucleic acids. It describes alternative conformations that are different from canonical B-DNA helix, such as A-DNA, Z-DNA, triplex structures, or guanine and cytozin quadruplex structures. In the next part it presents most common methods used for determing secondary structure of nucleic acids, which are nuclear magnetic resonance (NMR), measurement of circular dichroism (CD), X-ray diffraction, computational methods, measurements of ultraviolet absorbance and its utilization for analysis of thermal melting curves. In MATLAB was created algorithm with graphical user interface, which analyze melting curves and graphically computes thermodynamic parameters, which are melting temperature and transition enthalpy, which defines stability of examined sample.
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Quadruplex Detection in DNA Sequences
Sečka, Martin ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This master's thesis focuses on search for sequences potentially forming quadruplexes in DNA sequences, their visualization and filtration. For this purpose a web application was created in cooperation with the Institute of biophysics of Academy of science of Czech republic. This application uses a newly created algorithm able to find all possible formations of quadruplex within given input sequence. Design and implementation of this algorithm are also part of this thesis.
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Web Server for Protein Secondary Structure Prediction
Villem, Lukáš ; Očenášek, Pavel (referee) ; Burgetová, Ivana (advisor)
This master’s thesis deals with protein secondary structure prediction. There is a theoretical introduction followed by study of available tools, proposal and implementation of web application, which combines functionality of several web tools used to predict secondary structure. User is asked to choose prediction methods and insert input sequence as plain text or upload a file. Results collected from selected tools serve to convert data into common format, show the result and create new type of prediction. Finally, the testing is applied and influences of tools are adjusted in order to increase percentage of prediction. The output of application is a result of prediction also available as plain text or as a file.
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Prediction of Quadruplex Structure
Mikula, Adrian ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This master's thesis focuses on search and structure prediction of quadruplexes in DNA sequences. Thesis also explains related terms that are important for understanding the function, properties and geometry of quadruplexes. Thesis describe physico-chemical and computational current methods, which possible to discover and structure prediction. This paper also explain the principle of molecular modelling, which was used in the final application. Design and implementation of the final algorithm are also part of this thesis.
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Biodegradation of environmental pollutans - Crystallization haloalkan dehalogenase DpcA of Psychrobacter cryohalolentis K5
JUNG, Jakub
Knowledge of protein structures is necessary to clarify their structure-function relationships. Haloalkane dehalogenases are microbial enzymes that catalyze the hydrolysis of carbon-halogen in the halogenated hydrocarbons. Based on their properties these enzymes are able to degrade halogenated compounds. As the environment is burdened by a lot of different pollutants, biodegradation is a necessary step to improve the quality of environment. Haloalkane dehalogenases can be used as biosensors since they can detect contamination by halogenated compounds. This thesis is focused on crystallization of the model protein lysozyme and haloalkane dehalogenase DpcA isolated from the organism Psychrobacter cryohalolentis K5. The aim of this work was to prepare crystals suitable for X-ray diffraction analysis. After verification of protein?s purity, both proteins were crystallized by the use of basic and advanced crystallization methods. Single crystals of suitable size and quality for X-ray diffraction analysis were obtained and diffraction data were used to solve the 3D atomic structure of the DpcA. Since haloalkane dehalogenases have a low activity for halogenated substrates, the main aim of protein engineering is to increase their activity so thus further research is focused on modification of substrate specificity.
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