Publication Records

KADEŘÁVEK, Pavel, Vojtěch ZAPLETAL, Nicola SALVI, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK, Martin BLACKLEDGE and Fabien FERRAGE. Detailed insight into dynamics of C-terminal domain of δ subunit of RNA polymerase from Bacillus subtilis using high-resolution relaxometry. Online. In IDP Community F2F/hybrid meeting

ZAPLETAL, Vojtěch, Nicola SALVI, Andrea FLAMM, Zuzana JASEŇÁKOVÁ, Dennis KURZBACH, Mateos BORJA, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Jozef HRITZ, Robert KONRAT, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE and Pavel KADEŘÁVEK. Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry. Online

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK and Pavel KADEŘÁVEK. Domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis beyond its major state conformation. Online. In Inaugural Biochemistry Symposium Puzzles of (Bio)molecular Structure and Dynamics: NMR spectroscopy and complementary approaches.

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK and Pavel KADEŘÁVEK. Characterisation of invisible conformation of domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis. Online. In 19th European Magnetic Resonance Congress, EUROMAR 2023

TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžbeta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK and Pavel KADEŘÁVEK. Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis. Online. Proteins: Structure, Function and Bioinformatics. Wiley, vol. 91, No 9, p. 1276-1287. ISSN 0887-3585. Available from: https://dx.doi.org/10.1002/prot.26531

TUŽINČIN, Dávid, Nicola SALVI, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Hana ŠANDEROVÁ, Alžběta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE and Pavel KADEŘÁVEK. Study of the Dynamics of Flexible Subunits of RNA Polymerase from Bacillus subtilis. Online

SALVI, Nicola, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE and Pavel KADEŘÁVEK. Convergent views on disordered protein dynamics from NMR and computational approaches. Online. BIOPHYSICAL JOURNAL. UNITED STATES: CELL PRESS, vol. 121, No 20, p. 3785-3794. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2022.09.016

TUŽINČIN, Dávid, Pavel KADEŘÁVEK, Petr PADRTA and Lukáš ŽÍDEK. Seeing the invisible – Study of transiently formed protein conformation found in domain 1.1 of bacterial transcription factor. Online. In XVIII Discussions in Structural Molecular Biology and 5th User Meeting of CIISB (Czech Infrastructure for Integrative Structural Biology)

JASEŇÁKOVÁ, Zuzana, Vojtěch ZAPLETAL, Petr PADRTA, Milan ZACHRDLA, N. BOLIK-COULON, T. MARQUARDSEN, J.M. TYBURN, Lukáš ŽÍDEK, F. FERRAGE and Pavel KADEŘÁVEK. Boosting the resolution of low-field 15N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. Online. Journal of biomolecular NMR. Dordrecht: Springer, vol. 74, 2-3, p. 139-145. ISSN 0925-2738. Available from: https://dx.doi.org/10.1007/s10858-019-00298-6

KUBÁŇ, Vojtěch, Pavel SRB, Hana ŠTÉGNEROVÁ, Petr PADRTA, Milan ZACHRDLA, Zuzana JASEŇÁKOVÁ, H. SANDEROVA, D. VITOVSKA, L. KRASNY, T. KOVAL, J. DOHNALEK, J. ZIEMSKA-LEGIECKA, M. GRYNBERG, P. JARNOT, A. GRUCA, M.R. JENSEN, M. BLACKLEDGE and Lukáš ŽÍDEK. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. Online. Journal of the American Chemical Society. Washington: American Chemical Society, vol. 141, No 42, p. 16817-16828. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/jacs.9b07837

OTRUSINOVÁ, Olga, Gabriel DEMO, Petr PADRTA, Zuzana JASEŇÁKOVÁ, Blanka PEKÁROVÁ, Zuzana GELOVÁ, Agnieszka SZMITKOWSKA, Pavel KADEŘÁVEK, Séverine JANSEN, Milan ZACHRDLA, Tomáš KLUMPLER, Jaromír MAREK, Jozef HRITZ, Lubomír JANDA, Hideo IWAI, Michaela WIMMEROVÁ, Jan HEJÁTKO and Lukáš ŽÍDEK. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. Online. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., vol. 292, No 42, p. 17525-17540. ISSN 0021-9258. Available from: https://dx.doi.org/10.1074/jbc.M117.790212

ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK, Libor KRASNY and Lukáš ŽÍDEK. Solution structure of domain 1.1 of the sigma(A) factor from Bacillus subtilis is preformed for binding to the RNA polymerase core. Online. Journal of Biological Chemistry. Bethesda: Amer. Soc. Biochem. Mol. Biol., vol. 292, No 28, p. 11610-11617. ISSN 0021-9258. Available from: https://dx.doi.org/10.1074/jbc.M117.784074

KADEŘÁVEK, Pavel, Vojtěch ZAPLETAL, Radovan FIALA, Pavel SRB, Petr PADRTA, Jana PAVLÍKOVÁ PŘECECHTĚLOVÁ, Mária ŠOLTÉSOVÁ, Jozef KOWALEWSKI, Göran WIDMALM, Josef CHMELÍK, Vladimír SKLENÁŘ and Lukáš ŽÍDEK. Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies. Online. Journal of Magnetic Resonance. San Diego: Academic Press Inc. Elsevier Science, vol. 266, May, p. 23-40. ISSN 1090-7807. Available from: https://dx.doi.org/10.1016/j.jmr.2016.02.016

KADEŘÁVEK, Pavel, Carl DIEHL, Veronika PAPOUŠKOVÁ, Hana ŠANDEROVÁ, Petr PADRTA, Lukáš ŽÍDEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ and Mikael AKKE. Complementation of 3D structure of delta subunit of RNA polymerase from Bacillus subtilis with description of internal motions in terms of reduced spectral density mapping. Online. MATERIALS STRUCTURE. vol. 18, No 1, p. 3-5. ISSN 1211-5894

PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Jiří NOVÁČEK, Petr PADRTA, Šanderová HANA, Rabatinová ALŽBĚTA, Zawadzka-Kazimierczuk ANNA, Kazimierczuk KRZYSZTOF, Lukáš ŽÍDEK, Kozminski WIKTOR, Krásný LIBOR and Vladimír SKLENÁŘ. Study of RNA polymerase delta subunit unique for gram-positive bacteria. Online. In 9th Discussions in Structural Molecular Biology Nove Hrady. ISSN 1211-5894

MOTÁČKOVÁ, Veronika, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Jiří NOVÁČEK, Petr PADRTA, Alžběta ŠVENKOVÁ, Jana KORELUSOVÁ, Jiří JONÁK, Libor KRÁSNÝ and Vladimír SKLENÁŘ. Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs. Online. Proteins: Structure, Function, and Bioinformatics. USA: John Wiley and Sons, vol. 78, No 7, p. 1807-1810. ISSN 0887-3585

MOTÁČKOVÁ, Veronika, Pavel KADEŘÁVEK, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Petr PADRTA, Jiří NOVÁČEK, Alžběta ŠVENKOVÁ, Jana KORELUSOVÁ, Anna ZAWADZKA-KAZIMIERCZUK, Krzysztof KAZIMIERCZUK, Wiktor KOŹMIŃSKI, Libor KRÁSNÝ and Vladimír SKLENÁŘ. Structure and dynamics of an RNA polymerase subunit unique for gram-positive bacteria. Online. In Joint EUROMAR 2010 and 17th ISMAR Conference

KADEŘÁVEK, Pavel, Veronika MOTÁČKOVÁ, Petr PADRTA, Carl DIEHL, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ and Mikael AKKE. Structure and dynamics of delta subunit of RNA polymerase from Bacillus subtilis. Online. In International school of biological magnetic resonance, 10th Course, Biophysics and Structure to Counter Threats and Challenges, Erice 2010

NOVÁK, Petr, Lukáš ŽÍDEK, Veronika MOTÁČKOVÁ, Petr PADRTA, Alžbeta ŠVENKOVÁ, Jean Marc NUZILLARD, Libor KRÁSNÝ and Vladimír SKLENÁŘ. S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments. Online. Journal of Biomolecular NMR. Dordrecht: Springer Netherlands, vol. 46, No 2, p. 191-197. ISSN 0925-2738

MACEK, Pavel, Josef CHMELÍK, Ivana KŘÍŽOVÁ, Pavel KADEŘÁVEK, Petr PADRTA, Lukáš ŽÍDEK, Marcela WILDOVÁ, Romana HADRAVOVÁ, Radka CHALOUPKOVÁ, Iva PICHOVÁ, Tomáš RUML, Michaela RUMLOVÁ and Vladimír SKLENÁŘ. NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason-Pfizer Monkey Virus. Online. Journal of Molecular Biology. vol. 392, No 1, p. 100-114. ISSN 0022-2836

PRECECHTELOVA, Jana, Petr PADRTA, Marketa L MUNZAROVA and Vladimir SKLENAR. P-31 chemical shift tensors for canonical and non-canonical conformations of nucleic acids: A DFT study and NMR implications. Online. Journal of Physical Chemistry B. USA: ACS Publications, vol. 112, No 11, p. 3470-3478. ISSN 1089-5647. Available from: https://dx.doi.org/10.1021/jp076073n

PRECECHTELOVA, Jana, Petr PADRTA, Marketa MUNZAROVA and Vladimír SKLENÁŘ. P-31 Chemical Shift Tensors in Nucleic Acids from the Quantum Chemistry Point of View. Online. In 23rd NMR Valtice. 2008th ed. Brno: Masaryk University. p. 7. ISBN 978-80-86441-39-9

PŘECECHTĚLOVÁ, Jana, Petr PADRTA, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ. 31P Chemical Shift Tensors for Canonical and Non-Canonical Nucleic Acid Conformations: DFT Calculations and NMR Implications. Online. Journal of Physical Chemistry B. American Chemical Society, vol. 112, No 11, p. 3470-3478. ISSN 1520-6106

NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA and Vladimír SKLENÁŘ. Program for Analysis of Internal Motion in Molecular Dynamics Simulation. Online. In Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul". Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta. 1 pp

PŘECECHTĚLOVÁ, Jana, Petr PADRTA, Markéta MUNZAROVÁ and Vladimír SKLENÁŘ. P-31 Chemical Shift Tensors in RNA and DNA Backbone. A DFT Study of Conformational Dependence and Its Implications for NMR Studies. Online. In 43rd Symposium on Theoretical Chemistry: Large, Non-Biological Systems

JANSEN, Séverine, Josef CHMELÍK, Lukáš ŽÍDEK, Petr PADRTA, Petr NOVÁK, Zbyněk ZDRÁHAL, Jean-François PICIMBON, Christer LÖFSTEDT and Vladimír SKLENÁŘ. Structure of Bombyx mori chemosensory protein 1 in solution. Online. Archives of Insect Biochemistry and Physiology. Wiley, vol. 66, No 3, p. 135-145. ISSN 0739-4462

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. NMR Distance Restraints At Low Temperatures: Application To DNA Hairpin. Online. In International school on High field NMR spectroscopy for solids and liquids. Les Houches, France: Physics Centre, Les Houches. p. 45-45

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. Analysis of NMR Distance Restraints - An Application To DNA and RNA Hairpins. Online. In Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul". Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta. p. 11-11

NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA and Vladimír SKLENÁŘ. NEW TOOLS FOR AN ANALYSIS OF EXPERIMENTAL (NMR) AND THEORETICAL (MD) DATA. Online. In Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul". Brno: Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta. 1 pp

MATEJKOVÁ, Michaela, Petr NOVÁK, Radovan FIALA, Petr PADRTA and Vladimír SKLENÁŘ. NMR Distance Restraints At Low temperatures : An Application To DNA Hairpin. Online. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., vol. 12, No 1, p. 33-33. ISSN 1211-5894

MATEJKOVÁ, Michaela, Petr PADRTA, Radovan FIALA and Vladimír SKLENÁŘ. NMR Distance Restraints At Low Temperatures : An Application to DNA Hairpin. Online. In 19th NMR Valtice : Central European NMR Discussion Groups. Brno: Masarykova univerzita. p. 29-29. ISBN 80-210-3352-5

NOVÁK, Petr, Lukáš ŽÍDEK, Petr PADRTA and Vladimír SKLENÁŘ. Refinement of Trypanosoma U6 RNA Stem-Loop Structure Using 1- and 2-Bond Residual Dipolar Couplings. Online. In 19th NMR Valtice. Brno: Masarykova universita v Brně. p. 30-30. ISBN 80-210-3352-5

ŽÍDEK, Lukáš, Petr PADRTA, Josef CHMELÍK and Vladimír SKLENÁŘ. Internal Consistency of NMR Data Obtained in Partially Aligned Biomacromolecules. Online. Journal of Magnetic Resonance. San Diego: Academic Press, vol. 162, No 1, p. 385-395. ISSN 1090-7807

PADRTA, Petr and Vladimír SKLENÁŘ. Program MULDER - A tool for extracting torsion angles from NMR data. Online. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, vol. 24, No 4, p. 339-349. ISSN 0925-2738

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. Online. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, vol. 24, No 1, p. 1-14. ISSN 0925-2738