Prof. Lukáš Žídek, Ph.D.

Publications that are part of the Web of Science database, possibly also other publications chosen by authors.

2021

• Corey, T; Schonberger, N; Lanikova, A; Patzschke, M; Drobot, B; Zidek, L; Lederer, F, 2021: 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 23(14), p. 8618 - 8632, doi: 10.1039/d1cp00356a

2020

• Kuban, V; Macek, P; Hritz, J; Nechvatalova, K; Nedbalcova, K; Faldyna, M; Sebo, P; Zidek, L; Bumba, L, 2020: Structural Basis of Ca2+-Dependent Self-Processing Activity of Repeat-in-Toxin Proteins. MBIO 11(2), doi: 10.1128/mBio.00226-20
• Zapletal, V; Mladek, A; Melkova, K; Lousa, P; Nomilner, E; Jasenakova, Z; Kuban, V; Makovicka, M; Lanikova, A; Zidek, L; Hritz, J, 2020: Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. BIOPHYSICAL JOURNAL 118(7), p. 1621 - 1633, doi: 10.1016/j.bpj.2020.02.019
• Jasenakova, Z; Zapletal, V; Padrta, P; Zachrdla, M; Bolik-Coulon, N; Marquardsen, T; Tyburn, JM; Zidek, L; Ferrage, F; Kaderavek, P, 2020: Boosting the resolution of low-field 15N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. JOURNAL OF BIOMOLECULAR NMR 74(2020-03-02T00:00:00.000), p. 139 - 145, doi: 10.1007/s10858-019-00298-6

2019

• Kuban, V; Srb, P; Stegnerova, H; Padrta, P; Zachrdla, M; Jasenakova, Z; Sanderova, H; Vitovska, D; Krasny, L; Koval, T; Dohnalek, J; Ziemska-Legiecka, J; Grynberg, M; Jarnot, P; Gruca, A; Jensen, MR; Blackledge, M; Zidek, L, 2019: 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 141(42), p. 16817 - 16828, doi: 10.1021/jacs.9b07837
• Melkova, K; Zapletal, V; Narasimhan, S; Jansen, S; Hritz, J; Skrabana, R; Zweckstetter, M; Ringkjobing Jensen, M; Blackledge, M; Zidek, L, 2019: Structure and Functions of Microtubule Associated Proteins Tau and MAP2c: Similarities and Differences. BIOMOLECULES 9(3), doi: 10.3390/biom9030105

2018

• Benesik, M; Novacek, J; Janda, L; Dopitova, R; Pernisova, M; Melkova, K; Tisakova, L; Doskar, J; Zidek, L; Hejatko, J; Pantucek, R, 2018: Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity. VIRUS GENES 54(1), p. 130 - 139, doi: 10.1007/s11262-017-1507-2
• Zapletal, V; Melkova, K; Jansen, S; Nomilner, E; Jensen, MR; Blackledge, M; Zidek, L, 2018: Conformation and dynamics of intrinsically disordered microtubule associated protein 2c. FEBS OPEN BIO 8, p. 399 - 399
• Melkova, K; Zapletal, V; Jansen, S; Nomilner, E; Zachrdla, M; Hritz, J; Novacek, J; Zweckstetter, M; Jensen, MR; Blackledge, M; Zidek, L, 2018: Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics. JOURNAL OF BIOLOGICAL CHEMISTRY 293(34), p. 13297 - 13309, doi: 10.1074/jbc.RA118.001769
• Spackova, N; Trosanova, Z; Sebesta, F; Jansen, S; Burda, JV; Srb, P; Zachrdla, M; Zidek, L; Kozelka, J, 2018: Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 20(18), p. 12664 - 12677, doi: 10.1039/c7cp08623g

2017

• Zachrdla, M; Padrta, P; Rabatinova, A; Sanderova, H; Barvik, I; Krasny, L; Zidek, L, 2017: 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 292(28), p. 11610 - 11617, doi: 10.1074/jbc.M117.784074
• Srb, P; Novacek, J; Kaderavek, P; Rabatinova, A; Krasny, L; Zidkova, J; Bobalova, J; Sklenar, V; Zidek, L, 2017: Triple resonance NMR relaxation experiments for studies of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 69(3), p. 133 - 146, doi: 10.1007/s10858-017-0138-1
• Otrusinova, O; Demo, G; Padrta, P; Jasenakova, Z; Pekarova, B; Gelova, Z; Szmitkowska, A; Kaderavek, P; Jansen, S; Zachrdla, M; Klumpler, T; Marek, J; Hritz, J; Janda, L; Iwai, H; Wimmerova, M; Hejatko, J; Zidek, L, 2017: 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 292(42), p. 17525 - 17540, doi: 10.1074/jbc.M117.790212
• Zapletal, V; Mladek, A; Hritz, J; Zidek, L, 2017: Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions. FEBS JOURNAL 284, p. 321 - 321
• Zidek, L; Meirovitch, E, 2017: 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 121(37), p. 8684 - 8692, doi: 10.1021/acs.jpcb.7b06049
• Melkova, K; Jansen, S; Hritz, J; Zidek, L, 2017: NMR characterization of intrinsically disordered microtubule associated protein 2c. FEBS JOURNAL 284, p. 321 - 322
• Jansen, S; Melkova, K; Trosanova, Z; Hanakova, K; Zachrdla, M; Novacek, J; Zupa, E; Zdrahal, Z; Hritz, J; Zidek, L, 2017: 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 292(16), p. 6715 - 6727, doi: 10.1074/jbc.M116.771097

2016

• Pekarova, B; Szmitkowska, A; Dopitova, R; Degtjarik, O; Zidek, L; Hejatko, J, 2016: Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants. MOLECULAR PLANT 9(1), p. 71 - 85, doi: 10.1016/j.molp.2015.11.008
• Kaderavek, P; Zapletal, V; Fiala, R; Srb, P; Padrta, P; Precechtelova, JP; Soltesova, M; Kowalewski, J; Widmalm, G; Chmelik, J; Sklenar, V; Zidek, L, 2016: Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies. JOURNAL OF MAGNETIC RESONANCE 266, p. 23 - 40, doi: 10.1016/j.jmr.2016.02.016
• Vicha, J; Babinsky, M; Demo, G; Otrusinova, O; Jansen, S; Pekarova, B; Zidek, L; Munzarova, ML, 2016: The influence of Mg2+ coordination on C-13 and N-15 chemical shifts in CKI1(RD) protein domain from experiment and molecular dynamics/density functional theory calculations. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 84(5), p. 686 - 699, doi: 10.1002/prot.25019
• Perczel, A; Atanasov, AG; Sklenar, V; Novacek, J; Papouskova, V; Kaderavek, P; Zidek, L; Kozlowski, H; Watly, J; Hecel, A; Kolkowska, P; Koca, J; Svobodova-Varekova, R; Pravda, L; Sehnal, D; Horsky, V; Geidl, S; Enriz, RD; Matejka, P; Jenistova, A; Dendisova, M; Kokaislova, A; Weissig, V; Olsen, M; Coffey, A; Ajuebor, J; Keary, R; Sanz-Gaitero, M; Raaij, MJ; McAuliffe, O; Waltenberger, B; Mocan, A; Smejkal, K; Heis, EH; Diederich, M; Musiol, R; Kosmrlj, J; Polanski, J; Jampilek, J, 2016: The Eighth Central European Conference ´´Chemistry towards Biology´´: Snapshot. MOLECULES 21(10), doi: 10.3390/molecules21101381

2015

• Kaderavek, P; Grutsch, S; Salvi, N; Tollinger, M; Zidek, L; Bodenhausen, G; Ferrage, F, 2015: Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins. JOURNAL OF BIOMOLECULAR NMR 63(4), p. 353 - 365, doi: 10.1007/s10858-015-9994-8
• Kuban, V; Novacek, J; Bumba, L; Zidek, L, 2015: NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. BIOMOLECULAR NMR ASSIGNMENTS 9(2), p. 435 - 440, doi: 10.1007/s12104-015-9625-z
• MacRaild, CA; Zachrdla, M; Andrew, D; Krishnarjuna, B; Novacek, J; Zidek, L; Sklenar, V; Richards, JS; Beeson, JG; Anders, RF; Norton, RS, 2015: Conformational Dynamics and Antigenicity in the Disordered Malaria Antigen Merozoite Surface Protein 2. PLOS ONE 10(3), doi: 10.1371/journal.pone.0119899

2014

• Obr, M; Hadravova, R; Dolezal, M; Krizova, I; Papouskov, V; Zidek, L; Hrabal, R; Ruml, T; Rumlova, M, 2014: Stabilization of the beta-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity. RETROVIROLOGY 11, doi: 10.1186/s12977-014-0094-8
• Vymetal, J; Bathula, SR; Cerny, J; Chaloupkova, R; Zidek, L; Sklenar, V; Vondrasek, J, 2014: 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 27(12), p. 463 - 472, doi: 10.1093/protein/gzu046
• Kaderavek, P; Zapletal, V; Rabatinova, A; Krasny, L; Sklenar, V; Zidek, L, 2014: Spectral density mapping protocols for analysis of molecular motions in disordered proteins. JOURNAL OF BIOMOLECULAR NMR 58(3), p. 193 - 207, doi: 10.1007/s10858-014-9816-4

2013

• Nyarko, A; Song, YJ; Novacek, J; Zidek, L; Barbar, E, 2013: Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159-Dyn2 Assembly. JOURNAL OF BIOLOGICAL CHEMISTRY 288(4), p. 2614 - 2622, doi: 10.1074/jbc.M112.432831
• Papouskova, V; Kaderavek, P; Otrusinova, O; Rabatinova, A; Sanderova, H; Novacek, J; Krasny, L; Sklenar, V; Zidek, L, 2013: Structural Study of the Partially Disordered Full-Length delta Subunit of RNA Polymerase from Bacillus subtilis. CHEMBIOCHEM 14(14), p. 1772 - 1779, doi: 10.1002/cbic.201300226
• Papouskova, V; Novacek, J; Kaderavek, P; Sanderova, H; Rabatinova, A; Zidek, L; Krasny, L; Sklenar, V, 2013: Structural study of partially disordered delta subunit of RNA polymerase unique for gram-positive bacteria. FEBS JOURNAL 280, p. 146 - 147
• Haba, NY; Gross, R; Novacek, J; Shaked, H; Zidek, L; Barda-Saad, M; Chill, JH, 2013: NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein. BIOPHYSICAL JOURNAL 105(2), p. 481 - 493, doi: 10.1016/j.bpj.2013.05.046
• Novacek, J; Janda, L; Dopitova, R; Zidek, L; Sklenar, V, 2013: 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 56(4), p. 291 - 301, doi: 10.1007/s10858-013-9761-7
• Rabatinova, A; Sanderova, H; Matejckova, JJ; Korelusova, J; Sojka, L; Barvik, I; Papouskova, V; Sklenar, V; Zidek, L; Krasny, L, 2013: The delta Subunit of RNA Polymerase Is Required for Rapid Changes in Gene Expression and Competitive Fitness of the Cell. JOURNAL OF BACTERIOLOGY 195(11), p. 2603 - 2611, doi: 10.1128/JB.00188-13

2012

• Novacek, J; Haba, NY; Chill, JH; Zidek, L; Sklenar, V, 2012: 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 53(2), p. 139 - 148, doi: 10.1007/s10858-012-9631-8

2011

• Novacek, J; Zawadzka-Kazimierczuk, A; Papouskova, V; Zidek, L; Sanderova, H; Krasny, L; Kozminski, W; Sklenar, V, 2011: 5D C-13-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. JOURNAL OF BIOMOLECULAR NMR 50(1), p. 1 - 11, doi: 10.1007/s10858-011-9496-2
• Pekarova, B; Klumpler, T; Triskova, O; Horak, J; Jansen, S; Dopitova, R; Borkovcova, P; Papouskova, V; Nejedla, E; Sklenar, V; Marek, J; Zidek, L; Hejatko, J; Janda, L, 2011: Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana. PLANT JOURNAL 67(5), p. 827 - 839, doi: 10.1111/j.1365-313X.2011.04637.x

2010

• Motackova, V; Sanderova, H; Zidek, L; Novacek, J; Padrta, P; Svenkova, A; Korelusova, J; Jonak, J; Krasny, L; Sklenar, V, 2010: 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 78(7), p. 1807 - 1810, doi: 10.1002/prot.22708
• Kovalova, A; Ledvina, M; Saman, D; Zyka, D; Kubickova, M; Zidek, L; Sklenar, V; Pompach, P; Kavan, D; Bily, J; Vanek, O; Kubinkova, Z; Libigerova, M; Ivanova, L; Antolikova, M; Mrazek, H; Rozbesky, D; Hofbauerova, K; Kren, V; Bezouska, K, 2010: Synthetic N-Acetyl-D-glucosamine Based Fully Branched Tetrasaccharide, a Mimetic of the Endogenous Ligand for CD69, Activates CD69(+) Killer Lymphocytes upon Dimerization via a Hydrophilic Flexible Linker. JOURNAL OF MEDICINAL CHEMISTRY 53(10), p. 4050 - 4065, doi: 10.1021/jm100055b
• Motackova, V; Novacek, J; Zawadzka-Kazimierczuk, A; Kazimierczuk, K; Zidek, L; Anderova, HS; Krasny, L; Kozminski, W; Sklenar, V, 2010: Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. JOURNAL OF BIOMOLECULAR NMR 48(3), p. 169 - 177, doi: 10.1007/s10858-010-9447-3
• Novak, P; Zidek, L; Motackova, V; Padrta, P; Svenkova, A; Nuzillard, JM; Krasny, L; Sklenar, V, 2010: S3EPY: a Sparky extension for determination of small scalar couplings from spin-state-selective excitation NMR experiments. JOURNAL OF BIOMOLECULAR NMR 46(1 I), p. 191 - 197, doi: 10.1007/s10858-009-9392-1
• Kavan, D; Kubickova, M; Bily, J; Vanek, O; Hofbauerova, K; Mrazek, H; Rozbesky, D; Bojarova, P; Kren, V; Zidek, L; Sklenar, V; Bezouska, K, 2010: Cooperation between Subunits Is Essential for High-Affinity Binding of N-Acetyl-D-hexosamines to Dimeric Soluble and Dimeric Cellular Forms of Human CD69. BIOCHEMISTRY 49(19), p. 4060 - 4067

2009

• MACEK, P., CHMELIK, J., KRIZOVA, I., KADERAVEK, P., ZIDEK, L., WILDOVA, M., HADRAVOVA, R., CHALOUPKOVA, R., PICHOVA, I., RUML, T., RUMLOVA, M., SKLENAR, V., 2009: NMR structure of the N-terminal domain of capsid protein from the Mason-Pfizer monkey virus. JOURNAL OF MOLECULAR BIOLOGY 392(1), p. 100 - 114
• Matejkova, M; Zidkova, J; Zidek, L; Wimmerova, M; Chmelik, J; Sklenar, V, 2009: 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 57(18), p. 8444 - 8452

• Interactions defining physiological functions of Microtubule Associated Protein 2c at atomic resolution, Grantová agentura ČR, 2020 - 2022
• Klíčové aspekty mykobakteriální transkriprce: SigA, podjednotka RNAP rozpoznávající promotor a její nově identifikovaný vazebný partner., Grantová agentura ČR, 2019 - 2021
• CIISB - Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví (CZ.02.1.01/0.0/0.0/16_013/0001776), Ministerstvo školství, mládeže a tělovýchovy ČR, 2017 - 2021
• iNEXT - Infrastructure for NMR, EM and X-ray crystallography for translational research (653706), Evropská unie, 2015 - 2019
• Study of domain interactions of intrinsically disordered protein MAP2c (Microtubule-Associated Protein 2c) with its binding partners via computational methods and nuclear magnetic resonance (LTC17078), Ministerstvo školství, mládeže a tělovýchovy ČR, 2017 - 2019
• Efektivní výpočty volných energií a konfiguračního vzorkování protein-proteinových interakcí (I 1999-N28), Czech Science Foundation - International Projects, 2015 - 2017
• Podjednotky urcující DNA specificitu bakteriální RNA polymerázy s flexibilními doménami: funkce a dynamika (GA13-16842S), Grantová agentura ČR, 2013 - 2017
• Charakterizace proteinu MAP2c (microtubule associated protein 2c) a modifikací regulujících jeho funkci s atomovým rozlišením, Grantová agentura ČR, 2015 - 2017
• Structural determination of the human 14-3-3zeta in complex with a double phosphorylated human tyrosine hydroxylase 1 (4SGA8679), Jihomoravský kraj, 2014 - 2016
• Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci (CZ.1.07/2.3.00/30.0009), Ministerstvo školství, mládeže a tělovýchovy ČR, 2012 - 2015
• Strukturní princip specificity přenosu signálu v rostlinách: síť interakcí příjímačové domény histidinkinas u Arabidospis (GAP305/11/0756), Grantová agentura ČR, 2011 - 2014
• Infrastructure for NMR, EM, and X-ray for Translational Research, Masarykova univerzita, 2014 - 2014
• Motions in Disordered Proteins (12.251-Sciex-N-7), Nadace/fond - zahraniční, 2013 - 2014
• Vývoj metodologie s vysokým rozlišením pro NMR studie neuspořádaných proteinů s vysoce degenerovanými rezonančními frekvencemi (GAP206/11/0758), Grantová agentura ČR, 2011 - 2013
• Delta podjednotka RNA polymerázy z Gram pozitivních bakterií (GA204/09/0583), Grantová agentura ČR, 2009 - 2012
• Charakterizace MAGE proteinů: kofaktory E3 ubiquitin ligáz? (IAA501630902), Akademie věd ČR, 2009 - 2011