Tomáš Kovaľ

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X-ray structure analysis of macromolecules is an important tool used to study biological macromolecules. Here, we present a summary of crystallization and diffraction data collection methods that are applied in the process of structure determination. Then, structural characterisation of bacterial RNA polymerase, a multisubunit protein complex performing(More)
Bacterial RNA polymerase (RNAP) is an essential multisubunit protein complex required for gene expression. Here, we characterize YvgS (HelD) from Bacillus subtilis, a novel binding partner of RNAP. We show that HelD interacts with RNAP-core between the secondary channel of RNAP and the alpha subunits. Importantly, we demonstrate that HelD stimulates(More)
Interactions between C-type lectin-like NK cell receptors and their protein ligands form one of the key recognition mechanisms of the innate immune system that is involved in the elimination of cells that have been malignantly transformed, virally infected, or stressed by chemotherapy or other factors. We determined an x-ray structure for the extracellular(More)
The paper reports the structure of the small laccase from Streptomyces coelicolor determined from a crystal soaked with potassium hexacyanoferrate [K4Fe(CN)6]. The decolorization of the natively blue crystal observed upon soaking indicates the reduction of the enzyme in the crystal. The ligand binds between laccase molecules and stabilizes the crystal. The(More)
The new compound N-(3-nitrobenzoyl)-N',N''-bis(tert-butyl)phosphoric triamide was synthesized by reacting 3-nitrobenzoyl phosphoramidic dichloride and tert-butyl amine, and characterized by multinuclear ((1)H, (13)C and (31)P) NMR and FTIR spectroscopy techniques. Structural and conformational properties were analyzed using single-crystal X-ray diffraction,(More)
The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for(More)
This study focuses on the first step of interaction between DNA and the paddle-wheel dirhodium complex. The ammonia molecule was used to model the oligonucleotide sequence. The reaction was considered in neutral and acidic conditions, in gas phase, and in solvent, using the COSMO model. Molecular structures of the complexes were optimized in both models at(More)
New phosphoramidates with the formula RC(O)N(H)P(O)X(2), R = 2-NO(2)-C(6)H(4), 3-NO(2)-C(6)H(4) and 4-NO(2)-C(6)H(4), X = N(CH(2)CH(3)) (1)-(3), NC(4)H(8) (4)-(6), and NC(4)H(8)O (7)-(9) were synthesized and characterized by (1)H, (13)C, (31)P NMR and IR spectroscopy, and elemental analysis. The reaction of (9) with hydrated lanthanide(III) nitrate leads to(More)
Bifunctional nuclease TBN1 from Solanum lycopersicum-red tomato belongs to plant nuclease I group. TBN1 is a relatively small glycoprotein and shows considerable activity in cell apoptosis, tissue differentiation and vascular system development. Therefore detailed structural study of this enzyme can lead to new ways of cancer and bacterial disease(More)
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