prof. Mgr. Lukáš Žídek, Ph.D.

Curriculum vitae

Lukáš Žídek

• born in Náchod, Czech Republic on June 13, 1968.

Position

• Professor

Education

• 2016: Professor of Biomolecular Chemistry, Masaryk University, Brno, Czech Republic
• 2009: Assoc. Professor of Biomolecular Chemistry, Masaryk University, Brno, Czech Republic
• 1999: Ph.D. in Biochemistry, Indiana University, Bloomington, IN, USA
• 1991: M.S. in Biochemistry, Masaryk University, Brno, Czech Republic

Employment Summary

• since 2016: Professor of Biomolecular Chemistry, Masaryk University, Brno, Czech Republic
• 2009-2016: Assoc. Professor of Biomolecular Chemistry, Masaryk University, Brno, Czech Republic
• 1999-2009: Research worker, Masaryk University, Brno, Czech Republic
• 1999: Postdoctoral fellow, Masaryk University, Brno, Czech Republic

Teaching

• C5320 - Theoretical Concepts of Nuclear Magnetic Resonance
• C5321 - Theoretical Concepts of Nuclear Magnetic Resonance (seminar)
• C9530 - Structure of biomacromolecules
• C9531 - Structure of biomacromolecules (seminar)
• C6670 - NMR Spectroscopy of Biomolecules
• PhD students: Veronika Papoušková née Motáčková (defended 2012), Jiří Nováček (defended 2013), Vojtěch Kubáň (defended 2019), Milan Zachrdla (defended 2017), Zuzana Jaseňáková (defended 2020), Kateřina Melková (defended 2019), Vojtěch Zapletal (defended 2020), Subhash Narasimhan (defended 2024), Jitka Plucarová, Martin Černý, Viktor Bartošík, Róbert Šándor

Research Activities

• My long-term research interest is investigation of structure, dynamics, and biologically relevant properties of proteins, using NMR spectroscopy and other high-resolution approaches. Currently, my group is mostly interested in studies of molecular motions using NMR relaxation and relaxation dispersion; in studies of protein disorder using NMR approaches providing sufficient resolution (usually based on non-uniformly sampled high-dimensional spectra); and in studies of interactions of intrinsically disordered proteins with their binding partners and close to their physiological conditions (using NMR, cryo-EM, and biophysical methods). The systems currently studied in the laboratory include bacterial RNA polymerases, microtubule associated proteins, and proteins involved in plant hormone signalling.
• Microtubule associated proteins: We previously implemented and further developed NMR methodology providing sufficient resolution for studies of large intrinsically disordered proteins. We recently performed atomic-resolution conformational analysis of MAP2c (consisting of 466 amino acids) and compared the results with homologous protein tau. The analysis revealed presence of multiple functionally important pre-structured motifs, highly correlated with regions of known or proposed functions. This result documents clear evidence of structure-function relationship in intrinsically disordered proteins. We further characterized pattern and kinetics of MAP2c phosphorylation by several kinases and described its interactions with several protein partners. We are currently studying MAP2c close to its native conditions by in-cell NMR.
• Bacterial RNA polymerases: We determined structure and dynamics of well-ordered domains of subunit delta and of sigmaA-1.1 factor of RNA polymerase from B. subtilis, implemented and further developed NMR methodology providing sufficient resolution for studies of disordered proteins with extremely narrow chemical shift dispersion, characterized structural features and dynamics of disordered C-terminal domain of the subunit delta and studied importance of electrostatic interactions for structural properties and biological function of the protein. Currently we extend our interest to RNA polymerase of Staphylococcus aureus and of Mycobacteria.
• Proteins involved in plant hormone signalling: We explained effects of Mg(2+) binding and pseudo-phosphorylation on structural ensembles and dynamics of receiver domain of CKI1 sensory histidine kinase and described differences between receiver domains of CKI1 and ETR1.
• Czech Science Foundation grants: 204-09-0583 (2009-2012), P206-11-0758 (2011-2013), P305-11-0756 (2011-2014), 13-16842S (2013-2017), 15-14974S (2015-2017), 19-12956S (2019-2021), 20-12669S (2020-2022), 22-12023S (2022-2024)
• INTEREXCELLENCE INTERCOST grant LTC17078 (2017-2019)
• SCIEX grant: 12.251 (2013-2014, home mentor)

Academic Activities

• since 2021: head of Doctoral board, program Biomolecular chemistry and bioinformatics

Other Scientific Activities:

• 2005-2008: Grant Agency of the Academy of Sciences of the Czech Republic
• 2010-2014: Czech Science Foundation - panel member
• 2013-2014: Czech Science Foundation - head of the panel
• since 2010: member of Czech Society for Structural Biology
• since 2018: member of The American Society for Biochemistry and Molecular Biology
• 2015-2019: Management Committee of COST Action BM1405 (Non-globular proteins from sequence to structure, function and application in molecular physiopathology)

Awards and Invited Lectures

• Henry Mahler Memorial Award (1996)
• Lubrizol Scholarship (1996-1997)
• Indiana University COAS Scholarship (1997)
• Award of the J. M. Marci Spectroscopic Society (2002)
• Petr Sedmera award (corresponding author of the awarded publication, 2013)
• Petr Sedmera award (corresponding author of the awarded publication, 2020)
• International BaCaTeC Summer School, Bayreuth, Germany, Oct. 3-8, 2004 "Nuclear Overhauser Effect (NOE): Theory, Experiments, and Limits" "Study of a DNA Hairpin"
• EAST-NMR Workshop, Eötvös Loránd University, Budapest, Hungary, Aug. 30-31, 2011: "Data Evaluation and Interpretation In Protein Dynamics Studies: Spectral Density Mapping"
• Meeting in honor of Attila Szabó organized by Hungarian NMR Discussion Group, June 14, 2014: "NMR analysis of motions of intrinsically disordered proteins - delta subunit of RNA polymerase of B subtilis as a case study"
• Seminar of Max F. Perutz Laboratories, Department of Structural and Computational Biology, Vienna, Austria, Oct. 20, 2016: “Structural Biology without Unique Structure? Intrinsically disordered proteins”
• Magnetic Moments in Central Europe, Budapest, Hungary, March 8-12, 2017: "Structural features and dynamics of disordered proteins"
• Satellite Meeting of the 42nd FEBS Congress "Integrated Methodologies for Studying Intrinsically Disordered Proteins", Jerusalem, Israel, Sep. 14-15, 2017: "NMR methods for studies of structural features and dynamics of intrinsically disordered proteins"
• Magnetic Moments in Central Europe, Prague, Czech Republic, Feb. 27-March 3, 2019: "NMR as a window to the dynamic microcosmos of (disordered) proteins"
• 2nd Workshop on Intrinsically Disordered Proteins in Core Data Resources, Prague, Czech Republic, March 13-14, 2019: "From NMR data to IDP conformation and back"
• 8th School of the European Federation of EPR Groups on Advanced EPR, Brno, Czech Republic, Nov. 18-25, 2019: "Introduction to NMR"
• 17th EUROMAR, Portorož, Slovenia, July 4-8, 2021 "NMR reveals structure-function relationship in disordered proteins: MAP2c as an example"
• Central European NMR Symposium & Bruker users meeting, Warsaw, Poland, Sep. 21-23, 2022: "Intrinsically disordered Microtubule Associated Protein 2c (MAP2c): Function and regulation probed by NMR"
• 1st ML4NGP Training School "Protein aggregation, intrinsic disorder and phase separation in the era of machine learning", Porto, Portugal, Apr. 19-21, 2023: "NMR as a tool to study disordered proteins at atomic resolution"

Selected Publications

• BARTOŠÍK, Viktor, Jitka PLUCAROVÁ, Alice LANÍKOVÁ, Zuzana JANÁČKOVÁ, Petr PADRTA, Séverine JANSEN, Tobias GRUBER, Vojtěch VAŘEČKA, Stephan M FELLER a Lukáš ŽÍDEK. Structural basis of binding the unique N-terminal domain of microtubule-associated protein 2c to proteins regulating kinases of signaling pathways. International Journal of Biological Chemistry. AMSTERDAM: ANSInet, 2024, roč. 300, č. 8, s. 1-22. ISSN 1819-155X. Dostupné z: https://dx.doi.org/10.1016/j.jbc.2024.107551. URL info
• TUŽINČIN, Dávid, Petr PADRTA, Hana ŠANDEROVÁ, Alžbeta RABATINOVÁ, Kateřina BENDOVÁ, Libor KRÁSNÝ, Lukáš ŽÍDEK a 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. Proteins: Structure, Function and Bioinformatics. Wiley, 2023, roč. 91, č. 9, s. 1276-1287. ISSN 0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.26531. URL info
• CAMACHO-ZARCO, Aldo R., Vincent SCHNAPKA, Serafima GUSEVA, Anton ABYZOV, Wiktor ADAMSKI, Sigrid MILLES, Malene Ringkjøbing JENSEN, Lukáš ŽÍDEK, Nicola SALVI a Martin BLACKLEDGE. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. CHEMICAL REVIEWS. UNITED STATES: AMER CHEMICAL SOC, 2022, roč. 122, č. 10, s. 9331-9356. ISSN 0009-2665. Dostupné z: https://dx.doi.org/10.1021/acs.chemrev.1c01023. URL info
• PLUCAROVÁ, Jitka, Séverine JANSEN, Subhash NARASIMHAN, Alice LANÍKOVÁ, Marc LEWITZKY, M. Stephan FELLER a Lukáš ŽÍDEK. Specific phosphorylation of microtubule-associated protein 2c by extracellular signal–regulated kinase reduces interactions at its Pro-rich regions. JOURNAL OF BIOLOGICAL CHEMISTRY. UNITED STATES: ELSEVIER, 2022, roč. 298, č. 10, s. 102384-102399. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1016/j.jbc.2022.102384. URL info
• SALVI, Nicola, Vojtěch ZAPLETAL, Zuzana JASEŇÁKOVÁ, Milan ZACHRDLA, Petr PADRTA, Subhash NARASIMHAN, Thorsten MARQUARDSEN, Jean-Max TYBURN, Lukáš ŽÍDEK, Martin BLACKLEDGE, Fabien FERRAGE a Pavel KADEŘÁVEK. Convergent views on disordered protein dynamics from NMR and computational approaches. BIOPHYSICAL JOURNAL. UNITED STATES: CELL PRESS, 2022, roč. 121, č. 20, s. 3785-3794. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2022.09.016. URL info
• TAYLOR, C., N. SCHONBERGER, Alice LANÍKOVÁ, M. PATZSCHKE, B. DROBOT, Lukáš ŽÍDEK a F. LEDERER. Investigation of the structure and dynamics of gallium binding to high-affinity peptides elucidated by multi-scale simulation, quantum chemistry, NMR and ITC dagger. Physical Chemistry Chemical Physics. CAMBRIDGE: Royal Society of Chemistry, 2021, roč. 23, č. 14, s. 8618-8632. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/d1cp00356a. URL info
• ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Kateřina BENDOVÁ, Petr LOUŠA, Erik NOMILNER, Zuzana JASEŇÁKOVÁ, Vojtěch KUBÁŇ, Markéta MAKOVICKÁ, Alice LANÍKOVÁ, Lukáš ŽÍDEK a Jozef HRITZ. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophysical Journal. Bethesda, USA: Biophysical Society, 2020, roč. 118, č. 7, s. 1621-1633. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2020.02.019. URL info
• JASEŇÁKOVÁ, Zuzana, Vojtěch ZAPLETAL, Petr PADRTA, Milan ZACHRDLA, N. BOLIK-COULON, T. MARQUARDSEN, J.M. TYBURN, Lukáš ŽÍDEK, F. FERRAGE a Pavel KADEŘÁVEK. Boosting the resolution of low-field 15N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. Journal of biomolecular NMR. Dordrecht: Springer, 2020, roč. 74, 2-3, s. 139-145. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-019-00298-6. URL info
• KUBÁŇ, Vojtěch, P. MACEK, Jozef HRITZ, K. NECHVATALOVA, K. NEDBALCOVA, M. FALDYNA, Peter ŠEBO, Lukáš ŽÍDEK a L. BUMBA. Structural Basis of Ca2+-Dependent Self-Processing Activity of Repeat-in-Toxin Proteins. MBIO. Washington, D.C.: American Society for Microbiology, 2020, roč. 11, č. 2, s. 1-18. ISSN 2150-7511. Dostupné z: https://dx.doi.org/10.1128/mBio.00226-20. URL info
• MELKOVÁ, Kateřina, Vojtěch ZAPLETAL, Subhash NARASIMHAN, Séverine JANSEN, Jozef HRITZ, R. SKRABANA, M. ZWECKSTETTER, M. RINGKJOBING JENSEN, M. BLACKLEDGE a Lukáš ŽÍDEK. Structure and Functions of Microtubule Associated Proteins Tau and MAP2c: Similarities and Differences. Biomolecules. Basel, Switzerland: MDPI AG, 2019, roč. 9, č. 3, s. 105-136. ISSN 2218-273X. Dostupné z: https://dx.doi.org/10.3390/biom9030105. URL info
• 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 a Lukáš ŽÍDEK. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. Journal of the American Chemical Society. Washington: American Chemical Society, 2019, roč. 141, č. 42, s. 16817-16828. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.9b07837. URL info
• BENEŠÍK, Martin, Jiří NOVÁČEK, Lubomír JANDA, Radka DOPITOVÁ, Markéta PERNISOVÁ, Kateřina MELKOVÁ, Lenka TISAKOVA, Jiří DOŠKAŘ, Lukáš ŽÍDEK, Jan HEJÁTKO a Roman PANTŮČEK. Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity. Virus Genes. DORDRECHT: Springer US, 2018, roč. 54, č. 1, s. 130-139. ISSN 0920-8569. Dostupné z: https://dx.doi.org/10.1007/s11262-017-1507-2. URL info
• MELKOVÁ, Kateřina, Vojtěch ZAPLETAL, Séverine JANSEN, Erik NOMILNER, Milan ZACHRDLA, Jozef HRITZ, Jiří NOVÁČEK, M. ZWECKSTETTER, M.R. JENSEN, M. BLACKLEDGE a Lukáš ŽÍDEK. Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2018, roč. 293, č. 34, s. 13297-13309. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.RA118.001769. URL info
• ZACHRDLA, Milan, Zuzana JASEŇÁKOVÁ a Lukáš ŽÍDEK. Nuclear Magnetic Resonance. Online. In Jan Hejátko, Toshio Hakoshima. Plant Structural Biology: Hormonal Regulations. 1. vyd. CHAM: SPRINGER INT PUBLISHING AG, 2018, s. 223-221, 25 s. n/a. ISBN 978-3-319-91352-0. Dostupné z: https://dx.doi.org/10.1007/978-3-319-91352-0_12. URL info
• ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA, Pavel SRB, Milan ZACHRDLA, Lukáš ŽÍDEK a Jiří KOZELKA. Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Physical Chemistry Chemical Physics. CAMBRIDGE: Royal Society of Chemistry, 2018, roč. 20, č. 18, s. 12664-12677. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c7cp08623g. URL info
• JANSEN, Séverine, Kateřina MELKOVÁ, Zuzana TROŠANOVÁ, Kateřina HANÁKOVÁ, Milan ZACHRDLA, Jiří NOVÁČEK, Erik ŽUPA, Zbyněk ZDRÁHAL, Jozef HRITZ a Lukáš ŽÍDEK. Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3 zeta-binding sites reveals key differences between MAP2c and its homolog Tau. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2017, roč. 292, č. 16, s. 6715-6727. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M116.771097. URL info
• ZACHRDLA, Milan, Petr PADRTA, Alzbeta RABATINOVA, Hana SANDEROVA, Ivan BARVIK, Libor KRASNY a 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. Journal of Biological Chemistry. Bethesda: Amer. Soc. Biochem. Mol. Biol., 2017, roč. 292, č. 28, s. 11610-11617. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M117.784074. URL info
• 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 a Lukáš ŽÍDEK. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2017, roč. 292, č. 42, s. 17525-17540. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M117.790212. URL info
• ŽÍDEK, Lukáš a Eva MEIROVITCH. Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2017, roč. 121, č. 37, s. 8684-8692. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.7b06049. URL info
• SRB, Pavel, Jiří NOVÁČEK, Pavel KADEŘÁVEK, A. RABATINOVA, L. KRÁSNÝ, J. ŽÍDKOVÁ, J. BOBÁĽOVÁ, Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. Journal of Biomolecular NMR. Dordrecht: Springer, 2017, roč. 69, č. 3, s. 133-146. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-017-0138-1. URL info
• VÍCHA, Jan, Martin BABINSKÝ, Gabriel DEMO, Olga OTRUSINOVÁ, Séverine JANSEN, Blanka PEKÁROVÁ, Lukáš ŽÍDEK a Markéta MUNZAROVÁ. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins: Structure, Function, and Bioinformatics. 2016, roč. 84, č. 5, s. 686-699. ISSN 0887-3585. Dostupné z: https://dx.doi.org/10.1002/prot.25019. info
• KADEŘÁVEK, Pavel, Vojtěch ZAPLETAL, Radovan FIALA, Pavel SRB, Petr PADRTA, Jana PAVLÍKOVÁ PŘECECHTĚLOVÁ, Mária ŠOLTÉSOVÁ, Jozef KOWALEWSKI, Göran WIDMALM, Josef CHMELÍK, Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies. Journal of Magnetic Resonance. San Diego: Academic Press Inc. Elsevier Science, 2016, roč. 266, May, s. 23-40. ISSN 1090-7807. Dostupné z: https://dx.doi.org/10.1016/j.jmr.2016.02.016. URL info
• PEKÁROVÁ, Blanka, Agnieszka SZMITKOWSKA, Radka DOPITOVÁ, Oksana DEGTJARIK, Lukáš ŽÍDEK a Jan HEJÁTKO. Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants. Molecular Plant. Cambridge (USA): Cell Press, 2016, roč. 9, č. 1, s. 71-85. ISSN 1674-2052. Dostupné z: https://dx.doi.org/10.1016/j.molp.2015.11.008. URL info
• MACRAILD, Christopher A., Milan ZACHRDLA, Dean ANDREW, Bankala KRISHNARJUNA, Jiří NOVÁČEK, Lukáš ŽÍDEK, Vladimír SKLENÁŘ, Jack S. RICHARDS, James G. BEESON, Robin F. ANDERS a Raymond S. NORTON. Conformational dynamics and antigenicity in the disordered malaria antigen merozoite surface protein 2. PLOS ONE. San Francisco: Public Library Science, 2015, roč. 10, č. 3, s. "nestránkováno", 18 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0119899. URL info
• KUBÁŇ, Vojtěch, Jiří NOVÁČEK, Ladislav BUMBA a Lukáš ŽÍDEK. NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. Biomolecular NMR Assignments. Dordrecht (Netherlands): Springer Netherlands, 2015, roč. 9, č. 2, s. 435-440. ISSN 1874-2718. Dostupné z: https://dx.doi.org/10.1007/s12104-015-9625-z. URL info
• KADEŘÁVEK, Pavel, Sarina GRUTSCH, Nicola SALVI, Martin TOLLINGER, Lukáš ŽÍDEK, Geoffrey BODENHAUSEN a Fabien FERRAGE. Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins. Journal of Biomolecular NMR. Dordrecht: Springer, 2015, roč. 63, č. 4, s. 353-365. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-015-9994-8. Full Text info
• KADEŘÁVEK, Pavel, Vojtěch ZAPLETAL, Alžběta RABATINOVÁ, Libor KRÁSNÝ, Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Spectral density mapping protocols for analysis of molecular motions in disordered proteins. Journal of Biomolecular NMR. Dordrecht: Springer, 2014, roč. 58, č. 3, s. 193-207. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-014-9816-4. URL info
• NOVÁČEK, Jiří, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Toward optimal-resolution NMR of intrinsically disordered proteins. Journal of Magnetic Resonance. San Diego: Academic Press Inc Elsevier Science, 2014, roč. 241, April, s. 41-52. ISSN 1090-7807. Dostupné z: https://dx.doi.org/10.1016/j.jmr.2013.12.008. URL info
• DEMO, Gabriel, Veronika PAPOUŠKOVÁ, Jan KOMÁREK, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ, Pavel SRB, Alzbeta RABATINOVA, Libor KRÁSNÝ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Michaela WIMMEROVÁ. X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase. Journal of Structural Biology. San Diego: Academic Press, 2014, roč. 187, č. 2, s. 174-186. ISSN 1047-8477. Dostupné z: https://dx.doi.org/10.1016/j.jsb.2014.06.001. URL info
• OBR, Martin, Romana HADRAVOVÁ, Michal DOLEŽAL, Ivana KŘÍŽOVÁ, Veronika PAPOUŠKOVÁ, Lukáš ŽÍDEK, Richard HRABAL, Tomáš RUML a Michaela RUMLOVÁ. Stabilization of the beta-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity. Retrovirology. London: Biomed Central LTD, 2014, roč. 11, October 2014, s. "nestránkováno", 14 s. ISSN 1742-4690. Dostupné z: https://dx.doi.org/10.1186/s12977-014-0094-8. URL info
• VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Jiří VONDRÁŠEK. Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition. PROTEIN ENGINEERING DESIGN & SELECTION. OXFORD: OXFORD UNIV PRESS, 2014, roč. 27, č. 12, s. 463-472. ISSN 1741-0126. Dostupné z: https://dx.doi.org/10.1093/protein/gzu046. URL info
• NYARKO, Afua, Yujuan SONG, Jiří NOVÁČEK, Lukáš ŽÍDEK a Elisar BARBAR. Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159-Dyn2 Assembly. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2013, roč. 288, č. 4, s. 2614-2622. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M112.432831. URL info
• RABATINOVÁ, Alžbeta, Hana ŠANDEROVÁ, Jitka JIRÁT MATĚJČKOVÁ, Jana KORELUSOVÁ, Luděk SOJKA, Ivan BARVÍK, Veronika PAPOUŠKOVÁ, Vladimír SKLENÁŘ, Lukáš ŽÍDEK a Libor KRÁSNÝ. The Delta Subunit of RNA Polymerase Is Required for Rapid Changes in Gene Expression and Competitive Fitness of the Cell. Journal of Bacteriology. Washington: American Society for Microbiology, 2013, roč. 195, č. 11, s. 2603-2611. ISSN 0021-9193. Dostupné z: https://dx.doi.org/10.1128/JB.00188-13. URL info
• PAPOUŠKOVÁ, Veronika, Pavel KADEŘÁVEK, Olga OTRUSINOVÁ, Alžběta RABATINOVÁ, Hana ŠANDEROVÁ, Jiří NOVÁČEK, Libor KRÁSNÝ, Vladimír SKLENÁŘ a Lukáš ŽÍDEK. Structural Study of the Partially Disordered Full-Length delta Subunit of RNA Polymerase from Bacillus subtilis. ChemBioChem. WEINHEIM: WILEY-VCH Verlag, 2013, roč. 14, č. 14, s. 1772-1779. ISSN 1439-4227. Dostupné z: https://dx.doi.org/10.1002/cbic.201300226. URL info
• HABA, Noam Y, Renana GROSS, Jiří NOVÁČEK, Hadassa SHAKED, Lukáš ŽÍDEK, Mira BARDA-SAAD a Jordan H CHILL. NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein. Biophysical Journal. CAMBRIDGE: CELL PRESS, 2013, roč. 105, č. 2, s. 481-493. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2013.05.046. URL info
• NOVÁČEK, Jiří, Lubomír JANDA, Radka DOPITOVÁ, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. Journal of Biomolecular NMR. Dordrecht: Springer, 2013, roč. 56, č. 4, s. 291-301. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-013-9761-7. URL info
• NOVÁČEK, Jiří, Noam Y HABA, Jordan H CHILL, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. 4D Non-uniformly sampled HCBCACON and (1) J(NC alpha)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins. Journal of Biomolecular NMR. Dordrecht: Springer Netherlands, 2012, roč. 53, č. 2, s. 139-148. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-012-9631-8. URL info
• NOVÁČEK, Jiří, Anna ZAWADZKA-KAZIMIERCZUK, Veronika PAPOUŠKOVÁ, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Libor KRÁSNÝ, Wiktor KOZMINSKI a Vladimír SKLENÁŘ. 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. Journal of Biomolecular NMR. Dordrecht: Springer Netherlands, 2011, roč. 50, č. 1, s. 1-11. ISSN 0925-2738. Dostupné z: https://dx.doi.org/10.1007/s10858-011-9496-2. info
• PEKÁROVÁ, Blanka, Tomáš KLUMPLER, Olga TŘÍSKOVÁ, Jakub HORÁK, Séverine JANSEN, Radka DOPITOVÁ, Petra BORKOVCOVÁ, Veronika PAPOUŠKOVÁ, Eliška NEJEDLÁ, Vladimír SKLENÁŘ, Jaromír MAREK, Lukáš ŽÍDEK, Jan HEJÁTKO a Lubomír JANDA. Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana. The Plant Journal. England: BLACKWELL PUBLISHING, 2011, roč. 67, č. 5, s. 827-839. ISSN 0960-7412. Dostupné z: https://dx.doi.org/10.1111/j.1365-313X.2011.04637.x. URL info
• NOVÁK, Petr, Lukáš ŽÍDEK, Veronika MOTÁČKOVÁ, Petr PADRTA, Alžbeta ŠVENKOVÁ, Jean Marc NUZILLARD, Libor KRÁSNÝ a Vladimír SKLENÁŘ. S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments. Journal of Biomolecular NMR. Dordrecht: Springer Netherlands, 2010, roč. 46, č. 2, s. 191-197. ISSN 0925-2738. URL info
• MOTÁČKOVÁ, Veronika, Hana ŠANDEROVÁ, Lukáš ŽÍDEK, Jiří NOVÁČEK, Petr PADRTA, Alžběta ŠVENKOVÁ, Jana KORELUSOVÁ, Jiří JONÁK, Libor KRÁSNÝ a Vladimír SKLENÁŘ. Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs. Proteins: Structure, Function, and Bioinformatics. USA: John Wiley and Sons, 2010, roč. 78, č. 7, s. 1807-1810. ISSN 0887-3585. info
• MOTÁČKOVÁ, Veronika, Jiří NOVÁČEK, Anna ZAWADZKA-KAZIMIERCZUK, Krzysztof KAZIMIERCZUK, Lukáš ŽÍDEK, Hana ŠANDEROVÁ, Libor KRÁSNÝ, Wiktor KOZMINSKI a Vladimír SKLENÁŘ. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. Journal of Biomolecular NMR. Netherlands: Springer Netherlands, 2010, roč. 48, č. 3, s. 169-177. ISSN 0925-2738. URL info
• MACEK, Pavel, Josef CHMELÍK, Ivana KŘÍŽOVÁ, Pavel KADEŘÁVEK, Petr PADRTA, Lukáš ŽÍDEK, Marcela WILDOVÁ, Romana HADRAVOVÁ, Radka CHALOUPKOVÁ, Iva PICHOVÁ, Tomáš RUML, Michaela RUMLOVÁ a Vladimír SKLENÁŘ. NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason-Pfizer Monkey Virus. Journal of Molecular Biology. 2009, roč. 392, č. 1, s. 100-114. ISSN 0022-2836. info
• MATEJKOVÁ, Michaela, Jitka ŽÍDKOVÁ, Lukáš ŽÍDEK, Michaela WIMMEROVÁ, Josef CHMELÍK a Vladimír SKLENÁŘ. Investigation of Thermal Denaturation of Barley Nonspecific Lipid Transfer Protein 1 (ns-LTP1b) by Nuclear Magnetic Resonance and Differential Scanning Calorimetry. Journal of Agricultural and Food Chemistry. WASHINGTON: AMER CHEMICAL SOC, 2009, roč. 57, č. 18, s. 8444-8452. ISSN 0021-8561. info
• MOTÁČKOVÁ, Veronika, Monika KUBÍČKOVÁ, Milan KOŽÍŠEK, Klára GRANTZ ŠAŠKOVÁ, Martin ŠVEC, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Backbone 1H, 13C, and 15N NMR assignment for the inactive form of the retroviral protease of the murine intracisternal A-type particle, inMIA-14 PR. Biomolecular NMR Assignments. Netherlands: Springer Netherlands, 2009, roč. 3, č. 2, s. 261-264. ISSN 1874-2718. info
• MACEK, Pavel, Lukáš ŽÍDEK, Michaela RUMLOVÁ, Ivana PÍCHOVÁ a Vladimír SKLENÁŘ. 1H, 13C, and 15N Resonance Assignment of the N-terminal Domain of Mason-Pfizer Monkey Virus Capsid Protein, CA1-140. Biomolecular NMr Assignments. Netherlands: Springer Netherlands, 2008, roč. 2, č. 1, s. 43-45. ISSN 1874-2718. info
• VANĚK, Ondřej, Monika KUBÍČKOVÁ, Daniel KAVAN, Ivana BOROVIČKOVÁ, Petr POMPACH, Petr NOVÁK, Vinay KUMAR, Luca VANNUCCI, Jiří HUDEČEK, Kateřina HOFBAUEROVÁ, Vladimír, Jr KOPECKÝ, Jiří BRYNDA, Petr KOLENO, Jan DOHNÁLEK, Pavel KADEŘÁVEK, Josef CHMELÍK, Lukáš GORČÍK, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Karel BEZOUŠKA. Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemicsl stability display prolonged circulation and remain intact in the blood of mice. the FEBS Journal. 2008, roč. 2008, č. 275, s. 5589-5606. ISSN 1742-464X. info
• ŠMAJS, David, Magda DOLEŽALOVÁ, Pavel MACEK a Lukáš ŽÍDEK. Inactivation of colicin Y by intramembrane helix helix interaction with its immunity protein. FEBS Journal. 2008, roč. 275, č. 21, s. 5325 - 5331. ISSN 1742-464X. info
• MACEK, Pavel, Petr NOVÁK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2007, roč. 111, č. 20, s. 5731-5739. ISSN 1089-5639. info
• JANSEN, Séverine, Josef CHMELÍK, Lukáš ŽÍDEK, Petr PADRTA, Petr NOVÁK, Zbyněk ZDRÁHAL, Jean-François PICIMBON, Christer LÖFSTEDT a Vladimír SKLENÁŘ. Structure of Bombyx mori chemosensory protein 1 in solution. Archives of Insect Biochemistry and Physiology. Wiley, 2007, roč. 66, č. 3, s. 135-145. ISSN 0739-4462. info
• MACEK, Pavel, Petr NOVÁK, Hana KŘÍŽOVÁ, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Molecular dynamics study of major urinary protein-pheromone interactions: A structural model for ligand-induced flexibility increase. FEBS Letters. Amsterdam: Elsevier Science B.V., 2006, roč. 580, č. 1, s. 682-684. ISSN 0014-5793. URL info
• JANSEN, Séverine, Lukáš ŽÍDEK, Christer LÖFSTEDT, Jean-Francois PICIMBON a Vladimír SKLENÁŘ. 1H, 13C, and 15N resonance assignment of Bombyx mori chemosensory protein 1 (BmorCSP1). Journal of Biomolecular NMR. ESCOM Science Publishers B.V., 2006, roč. 36, č. 5, s. 47-47. ISSN 0925-2738. info
• KŘÍŽOVÁ, Hana, Lukáš ŽÍDEK, Martin J. STONE, Milos V. NOVOTNY a Vladimír SKLENÁŘ. Temperature Dependent Spectral Density Analysis Applied to Monitoring Backbone Dynamics of Major Urinary Protein-I Complexed with the Pheromone 2-sec-Butyl-4,5-dihydrothiazole. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2004, roč. 28, č. 4, s. 369-384. ISSN 0925-2738. info
• SYCHROVSKÝ, Vladimír, Bohdan SCHNEIDER, Pavel HOBZA, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. The effect of water on NMR spin-spin couplings in DNA: Improvement of calculated values by application of two solvent models. Physical Chemistry Chemical Physics. Great Britain: ROYAL SOC CHEMISTRY, 2003, roč. 5, č. 4, s. 734-739. ISSN 1463-9076. info
• ŽÍDEK, Lukáš, Petr PADRTA, Josef CHMELÍK a Vladimír SKLENÁŘ. Internal Consistency of NMR Data Obtained in Partially Aligned Biomacromolecules. Journal of Magnetic Resonance. San Diego: Academic Press, 2003, roč. 162, č. 1, s. 385-395. ISSN 1090-7807. info
• SYCHROVSKÝ, Vladimír, Jaroslav VACEK, Pavel HOBZA, Lukáš ŽÍDEK, Vladimír SKLENÁŘ a Dieter CREMER. Exploring the Structure of a DNA Hairpin with the Help of NMR Spin-spin Coupling Constants: An Experimental and Quantum Chemical Investigation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2002, roč. 106, č. 29, s. 10242-10250. ISSN 1089-5639. info
• PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2002, roč. 24, č. 1, s. 1-14. ISSN 0925-2738. info
• SHARROW, Scott D., Jeffrey L. VAUGHN, Lukáš ŽÍDEK, Milos V. NOVOTNY a Martin J STONE. Pheromone binding by polymorphic mouse major urinary proteins. Protein Science. Plainview: Cold Spring Harbor Lab. Press, 2002, roč. 11, č. 11, s. 2247-2256. ISSN 0961-8368. info
• TIMM, David E., L. J. BAKER, H MUELLER, Lukáš ŽÍDEK a Milos NOVOTNY. Structural basis of pheromone binding to mouse major urinary protein (MUP-I). Protein Science. Plainview: Cold Spring Harbor Lab. Press, 2001, roč. 10, č. 5, s. 997-1005. ISSN 0961-8368. info
• ŽÍDEK, Lukáš, Richard ŠTEFL a Vladimír SKLENÁŘ. NMR methodology for the study of nucleic acids. Current Opinion in Structural Biology. London: Elsevier Science Ltd., 2001, roč. 11, č. 3, s. 275-281. ISSN 0959-440X. info
• ŽÍDEK, Lukáš, Haihong WU, Juli FEIGON a Vladimír SKLENÁŘ. Measurement of small scalar and resiudal dipolar couplings in purine and pyrimidine bases. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2001, roč. 21, č. 2, s. 153-159. ISSN 0925-2738. info
• MECHREF, Yehiya, Lukáš ŽÍDEK, Weidong MA a Milos NOVOTNY. Glycosylated major urinary protein of the house mouse: characterization of its N-linked oligosaccharides. Glycobiology. Oxford: Oxford University Press, 2000, roč. 10, č. 3, s. 231-235. ISSN 0959-6658. info
• ŽÍDEK, Lukáš, Martin J STONE, Susan M LATO, Mark D PAGEL, Zhongshan MIAO, Andrew D ELLINGTON a Milos V NOVOTNY. NMR mapping of the recombinant mouse major urinary protein I binding site occupied by the pheromone 2-sec-butyl-4,5-dihydrothiazole. Biochemistry. Washington: Amer. Chemical Soc., 1999, roč. 38, č. 31, s. 9850-9861. ISSN 0006-2960. info
• NOVOTNY, Milos, Weidong MA, Don WIESLER a Lukáš ŽÍDEK. Positive identification of the puberty-accelerating pheromone of the house mouse: the volatile ligands associating with the major urinary protein. Proceedings of the Royal Society of London, Series B - Biological Sciences. London: Royal Soc. London, 1999, roč. 266, č. 1432, s. 2017-2022. ISSN 0962-8452. info
• ŽÍDEK, Lukáš, Milos NOVOTNY a Martin J STONE. Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nature Structural Biology. New York: Nature America Inc., 1999, roč. 6, č. 12, s. 1118-1121. ISSN 1072-8368. info
• NOVOTNY, Milos V., Weidong MA, Lukáš ŽÍDEK a Evgenij DAEV. Recent biochemical insights into puberty acceleration, estrus induction and puberty delay in the house mouse. editors. In JOHNSTON, Robert E., Dietland MULLER-SCHWARTZE a Peter W. SORENSEN. Chemical Signals in Vertebrates 8. New York: Kluwer Academic / Plenum Publishers, 1999, s. 99-116. ISBN 0306461145. info
• BAKER, Andrew, Lukáš ŽÍDEK, Don WIESLER a Milos NOVOTNY. Reaction of N-Acetylglycyllysine Methyl Ester with 2-Alkenals: An Alternative Model for Covalent Modification of Proteins. Chemical Research in Toxicology. Washington, DC (USA): American Chemical Society, 1998, roč. 11, č. 7, s. 730-740. ISSN 08993228X. info
• ŽÍDEK, Lukáš, Petr DOLEŽEL, Josef CHMELÍK, Andrew G BAKER a Milos NOVOTNY. Modification of horse heart cytochrome c with trans-2-hexenal. Chemical Research in Toxicology. Washington, DC (USA): American Chemical Society, 1997, roč. 10, č. 6, s. 702-710. ISSN 08993228X. info
• ŽÍDEK, Lukáš a Michaela WIMMEROVÁ. Osnova paradigmat biochemie? Chemické listy. Praha: Česká společnost chemická, 1993, roč. 87, č. 1, s. 122-125. ISSN 0009-2770. info
• ŽÍDEK, Lukáš a Miroslav ŘEZÁČ. Kinetics of inhibition of horse liver alcohol-dehydrogenase by p-methylbenzyl hydroperoxide. Journal of Enzyme Inhibition. Reading: Harwood Acad. Publ. GmbH, 1993, roč. 7, č. 3, s. 191-197. ISSN 8755-5093. info
• SKURSKÝ, Ladislav, Miroslav ŘEZÁČ, Allah N KHAN, Lukáš ŽÍDEK a Jaroslav ROČEK. Hydroperoxidic inhibitor of horse liver alcohol-dehydrogenase activity, tightly bound to the enzyme-NAD+ complex, characteristically degrades the coenzyme. Journal of Enzyme Inhibition. Reading: Harwood Acad. Publ. GmbH, 1992, roč. 6, č. 3, s. 211-222. ISSN 8755-5093. info
• ŽÍDEK, Lukáš, Miroslav MACHALA a Ladislav SKURSKÝ. Interactions of Organic Hydroperoxides with Heme Proteins. Drug Metabolism and Drug Interactions. Tel Aviv: Freund Publishing House, Ltd., 1991, roč. 9, 3-4, s. 209-234. ISSN 0792-5077. info

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