Search Results - "Kukacka, Zdenek"

Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation by Yassaghi, Ghazaleh, Kukačka, Zdeněk, Fiala, Jan, Kavan, Daniel, Halada, Petr, Volný, Michael, Novák, Petr

“…Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical…”
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Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules by Fojtík, Lukáš, Fiala, Jan, Pompach, Petr, Chmelík, Josef, Matoušek, Václav, Beier, Petr, Kukačka, Zdeněk, Novák, Petr

“…Covalent labeling of proteins in combination with mass spectrometry has been established as a complementary technique to classical structural methods, such as…”
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Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor–dsDNA Complex by Polák, Marek, Yassaghi, Ghazaleh, Kavan, Daniel, Filandr, František, Fiala, Jan, Kukačka, Zdeněk, Halada, Petr, Loginov, Dmitry S., Novák, Petr

“…A combination of covalent labeling techniques and mass spectrometry (MS) is currently a progressive approach for deriving insights related to the mapping of…”
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Structural Characterization of Monoclonal Antibodies and Epitope Mapping by FFAP Footprinting by Fojtík, Lukáš, Kalaninová, Zuzana, Fiala, Jan, Halada, Petr, Chmelík, Josef, Man, Petr, Kukačka, Zdeněk, Novák, Petr

“…Covalent labeling in combination with mass spectrometry is a powerful approach used in structural biology to study protein structures, interactions, and…”
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LinX: A Software Tool for Uncommon Cross-Linking Chemistry by Kukačka, Zdeněk, Rosůlek, Michal, Jelínek, Jan, Slavata, Lukáš, Kavan, Daniel, Novák, Petr

“…Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze…”
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Multivalency of nucleosome recognition by LEDGF by Koutná, Eliška, Lux, Vanda, Kouba, Tomáš, Škerlová, Jana, Nováček, Jiří, Srb, Pavel, Hexnerová, Rozálie, Šváchová, Hana, Kukačka, Zdeněk, Novák, Petr, Fábry, Milan, Poepsel, Simon, Veverka, Václav

“…Abstract Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on…”
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Epitope and affinity determination of recombinant Mycobacterium tuberculosis Ag85B antigen towards anti-Ag85 antibodies using proteolytic affinity-mass spectrometry and biosensor analysis by Rinaldi, Francesca, Lupu, Loredana, Rusche, Hendrik, Kukačka, Zdeněk, Tengattini, Sara, Bernardini, Roberta, Piubelli, Luciano, Bavaro, Teodora, Maeser, Stefan, Pollegioni, Loredano, Calleri, Enrica, Przybylski, Michael, Temporini, Caterina

“…Tuberculosis (TB) is the first cause of death from infectious diseases worldwide. Only a single anti-TB vaccine is currently available for clinical use, but…”
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Reductant‐Induced Free Radical Fluoroalkylation of Nitrogen Heterocycles and Innate Aromatic Amino Acid Residues in Peptides and Proteins by Rahimidashaghoul, Kheironnesae, Klimánková, Iveta, Hubálek, Martin, Korecký, Michal, Chvojka, Matúš, Pokorný, Daniel, Matoušek, Václav, Fojtík, Lukáš, Kavan, Daniel, Kukačka, Zdeněk, Novák, Petr, Beier, Petr

“…A series of fluoroalkylated cyclic λ3‐iodanes and their hydrochloride salts was prepared and used in a combination with sodium ascorbate in buffer or aqueous…”
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SAP domain forms a flexible part of DNA aperture in Ku70/80 by Hnízda, Aleš, Tesina, Petr, Nguyen, Thanh‐Binh, Kukačka, Zdeněk, Kater, Lukas, Chaplin, Amanda K., Beckmann, Roland, Ascher, David B., Novák, Petr, Blundell, Tom L.

“…Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double‐strand DNA breaks to maintain genomic integrity during the entire cell cycle…”
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Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes by Zeman, Jakub, Itoh, Yuzuru, Kukačka, Zdeněk, Rosůlek, Michal, Kavan, Daniel, Kouba, Tomáš, Jansen, Myrte E, Mohammad, Mahabub P, Novák, Petr, Valášek, Leoš S

“…Abstract eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their…”
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Molecular Mechanism of LEDGF/p75 Dimerization by Lux, Vanda, Brouns, Tine, Čermáková, Kateřina, Srb, Pavel, Fábry, Milan, Mádlíková, Marcela, Hořejší, Magdalena, Kukačka, Zdeněk, Novák, Petr, Kugler, Michael, Brynda, Jiří, DeRijck, Jan, Christ, Frauke, Debyser, Zeger, Veverka, Václav

“…Dimerization of many eukaryotic transcription regulatory factors is critical for their function. Regulatory role of an epigenetic reader lens…”
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Crystal structure of native β‐N‐acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide by Škerlová, Jana, Bláha, Jan, Pachl, Petr, Hofbauerová, Kateřina, Kukačka, Zdeněk, Man, Petr, Pompach, Petr, Novák, Petr, Otwinowski, Zbyszek, Brynda, Jiří, Vaněk, Ondřej, Řezáčová, Pavlína

“…β‐N‐acetylhexosaminidase from the fungus Aspergillus oryzae is a secreted extracellular enzyme that cleaves chitobiose into constituent monosaccharides. It…”
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Role of the EF-hand-like Motif in the 14-3-3 Protein-mediated Activation of Yeast Neutral Trehalase Nth1 by Kopecka, Miroslava, Kosek, Dalibor, Kukacka, Zdenek, Rezabkova, Lenka, Man, Petr, Novak, Petr, Obsil, Tomas, Obsilova, Veronika

“…Trehalases hydrolyze the non-reducing disaccharide trehalose amassed by cells as a universal protectant and storage carbohydrate. Recently, it has been shown…”
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Structural basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1 by Macakova, Eva, Kopecka, Miroslava, Kukacka, Zdenek, Veisova, Dana, Novak, Petr, Man, Petr, Obsil, Tomas, Obsilova, Veronika

“…Trehalases are highly conserved enzymes catalyzing the hydrolysis of trehalose in a wide range of organisms. The activity of yeast neutral trehalase Nth1 is…”
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The C-type lectin-like receptor Nkrp1b: Structural proteomics reveals features affecting protein conformation and interactions by Hernychová, Lucie, Rosůlek, Michal, Kádek, Alan, Mareška, Václav, Chmelík, Josef, Adámková, Ljubina, Grobárová, Valéria, Šebesta, Ondřej, Kukačka, Zdeněk, Skála, Kristián, Spiwok, Vojtěch, Černý, Jan, Novák, Petr

“…The cytotoxicity of mouse natural killer (NK) cells in response to pathological changes in target cells is regulated via the Nkrp1b receptor. Here, we…”
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Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal β-N-acetylhexosaminidase by Ryšlavá, Helena, Kalendová, Alžběta, Doubnerová, Veronika, Skočdopol, Přemysl, Kumar, Vinay, Kukačka, Zdeněk, Pompach, Petr, Vaněk, Ondřej, Slámová, Kristýna, Bojarová, Pavla, Kulik, Natallia, Ettrich, Rudiger, Křen, Vladimír, Bezouška, Karel

“…Fungal β-N-acetylhexosaminidases are inducible extracellular enzymes with many biotechnological applications. The enzyme from Penicillium oxalicum has unique…”
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Data-Independent Acquisition Represents a Promising Alternative for Fast Photochemical Oxidation of Proteins (FPOP) Samples Analysis by Zakopcanik, Marek, Kavan, Daniel, Kukacka, Zdenek, Novak, Petr, Loginov, Dmitry S.

“…Fast Photochemical Oxidation of Proteins (FPOP) is a protein footprinting method utilizing hydroxyl radicals to provide valuable information on the…”
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Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae by Vaněk, Ondřej, Brynda, Jiří, Hofbauerová, Kateřina, Kukačka, Zdeněk, Pachl, Petr, Bezouška, Karel, Řezáčová, Pavlína

“…Fungal β‐N‐acetylhexosaminidases are enzymes that are used in the chemoenzymatic synthesis of biologically interesting oligosaccharides. The enzyme from…”
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Mapping protein structural changes by quantitative cross-linking by Kukacka, Zdenek, Rosulek, Michal, Strohalm, Martin, Kavan, Daniel, Novak, Petr

“…[Display omitted] •Quantification of calmodulin conformational changes with isotope-labeled cross-linkers.•Incomplete protein proteolysis hampers mass…”
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Structural Insight into the 14-3-3 Protein-dependent Inhibition of Protein Kinase ASK1 (Apoptosis Signal-regulating kinase 1) by Petrvalska, Olivia, Kosek, Dalibor, Kukacka, Zdenek, Tosner, Zdenek, Man, Petr, Vecer, Jaroslav, Herman, Petr, Obsilova, Veronika, Obsil, Tomas

“…Apoptosis signal-regulating kinase 1 (ASK1, also known as MAP3K5), a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family, regulates…”
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