Common crystallization procedures, X-ray diffraction method and crystallographic software to determine and refine the structure of haloalkane dehalogenase enzyme were used in this thesis.

The aim of the thesis was to compare the haloalkane dehalogenase DhaA106 with other studied protein mutant variants. For diffraction analysis, it was necessary to growappropriate crystals of DhaA106 protein. Crystallization experiments were performed by standard sitting drop method. Obtained rod crystals were used for diffraction analysis. During diffraction measurement completeset of 500 diffraction images were obtained, from which the electron density map was formed and the spatial model of the molecular structure of DhaA106 dehalogenase was created. Alternative conformation of amino acids, water molecules, parts of precipitating solution and chloride ion inthe active sitewere subsequently added into the model structure. The final structure of the moleculewas refined and validated. Subsequently, the amino acids pentade in the active site and whole protein structure were analyzed . Values of validation and refining and interatomic distances in the active site were compared with several variants mutant dehalogenase DhaA, as well as the precipitating solutions used for crystallization and diffraction data collection. In the last step of the work interactions of the selected substrate with the protein surface in the vicinity of the tunnel connecting the active site of the surfacewere studied. Mentioned interaction study was based on the principle of combination of the Monte-Carlo methods with protein structure prediction algorithms.

A nearly stoichiometric, (1×1) Cr₂O₃ (101̲2) surface was prepared from a single crystal of α-Cr₂O₃. The five-coordinate cations exposed at the stoichiometric surface dissociatively adsorb molecular oxygen to form a (1×1), terminating chromyl (Cr=O) layer that is stable to >1100 K. TDS and AES were used to investigate the reactivity of the halo-alkanes CFCl₂CH₂Cl, CF₂ClCH₂Cl, CF₃CH₂Cl, and CF₂CH₂F, in addition to the halo-alkenes CFCl=CH₂ and CF₂=CH₂. The halo-alkanes CFCl₂CH₂Cl, CF₂ClCH₂Cl, and CF₃CH₂Cl undergo 1,2-dihalo elimination similar to the Zn-catalyzed dehalogenation of vicinal dihalides to form alkenes. Some acetylene is also formed. The halo-alkenes CFCl=CH₂ and CF₂=CH₂ decompose to yield acetylene. Halogen removed from the molecules remains bound to the surface following TDS experiments and eventually terminates the surface chemistry due to site blocking of the cations. Reactivity is directly related to the chlorine content of the molecules investigated. Only CFCl₂CH₂Cl was reactive on a chromyl-terminated surface. / Ph. D.

This thesis describes the problems of storage and management of biological data, particularly of Haloalkane Dehalogenase enzymes. Furthermore, the thesis aims at project HADES (HAloalkane DEhalogenase databaSe) initiated by protein engineering group of Loschmidt Laboratories, Masaryk University in Brno. This is a project whose main goal is simply to store, preserve and display a wide variety of proteins data. The result of this work is a flexible database system allowing easy extensibility and maintainability, which is built on technologies Apache, PostgreSQL and PHP using the Zend Framework.

This thesis presents specification and implementation of a system for detection of enzymes in metagenomic data. The detection is based on a provided enzyme sequence and its goal is to search the metagenomic sample for its novel variants. In order to guarantee that found enzymes truly have the desired catalytic function, the system employs a number of catalytic function verification methods. Their specification, implementation and evaluation is one of the main contributions of this thesis. Experiments have shown, that proposed methods reach sensitivity as high as 89%, specificity of 95%, values of AUC metric above 0.9 and average throughput of 1,203 verifications per second on regular personal computer. Evaluation of the system also led to discovery of a partial sequence of novel haloalkane dehalogenase enzyme in a metagenomic sample from soil. The implementation is able to work on a personal computer as well as on a grid computing environment.