Embedded Files
2024
Mycobacterial HelD connects RNA polymerase recycling with transcription initiation.
Kovaľ, T., Borah, N., Sudzinová, P. et al.
Nat Commun 15, 8740 (2024). https://doi.org/10.1038/s41467-024-52891-5
PDB: 8Q3I, 8QN8, 8QU6, 8R3M, 8R2M, 8R6P, 8R6R, 8QTI
Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study
Kristýna Adámková; Mária Trundová; Tomáš Kovaľ; Blanka Husťáková; Petr Kolenko; Jarmila Dušková; Tereza Skálová; Jan Dohnalek
FEBS Journal 292 (2025), 129-152, https://doi.org/10.1111/febs.17265
PDB: 8QJL, 8QJM, 8QJN, 8QJO, 8QJP, 8QJQ, 9EMG
2023
A highly active S1-P1 nuclease from the opportunistic pathogen Stenotrophomonas maltophilia cleaves c-di-GMP
Blanka Husťáková , Mária Trundová , Kristýna Adámková , Tomáš Kovaľ , Jarmila Dušková , Jan Dohnálek
FEBS Letters (2023)
Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia
Malý, Martin; Kolenko, Petr; Stránský, Jan; Švecová, Leona; Dušková, Jarmila; Koval', Tomáš; Skálová, Tereza; Trundová, Mária; Adámková, Kristýna; Černý, Jiří; Božíková, Paulína; Dohnálek, Jan
ActaF, vol 79, 180-192, DOI: https://doi.org/10.1107/S2053230X23005381
PDB: 8AQ8
2022
The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective
substrate specificity.
Koval'ová, Terezia - Koval, Tomáš - Stránský, Jan - Kolenko, Petr - Dušková, Jarmila - Švecová, Leona - Vodickova, P. - Spiwok, V. -
Benešová, E. - Lipovová, P. - Dohnálek, Jan
FEBS Journal. Roč. 289, č. 16 (2022), paper no. 16387.
https://doi.org/10.1111/febs.16387
PDB: 6TVK
C-type lectin-(like) fold-Protein-protein interaction patterns and utilization.
Dohnálek, Jan - Skálová, Tereza
Biotechnology Advances. Roč. 58, SEP 2022 (2022), paper no. 107944.
https://doi.org/10.1016/j.biotechadv.2022.107944
Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
Blaha, J. - Skálová, Tereza - Kalousková, B. - Skořepa, O. - Cmunt, D. - Grobárová, V. - Pažický, S. - Polachova, E. - Abreu, C. -
Stránský, Jan - Koval, Tomáš - Dušková, Jarmila - Zhao, Y. - Harlos, K. - Hašek, Jindřich - Dohnálek, Jan - Vaněk, O.
Nature Communications. Roč. 13, č. 1 (2022), paper no. 5022
PDB: 5MGR, 5MGS, 5MGT
https://doi.org/10.1038/S41467-022-32577-6
Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.
Adámková, Kristýna - Koval, Tomáš - Ostergaard, L. H. - Dušková, Jarmila - Malý, Martin - Švecová, Leona - Skálová, Tereza - Kolenko,
Petr - Dohnálek, Jan
Acta Crystallographica Section D-Biological Crystallography. Roč. 78, OCT 1 2022 (2022), s. 1194-1209.
DOI: 10.1107/s2059798322008397
PDB: 7QTA, 7QTB
2021
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum
Švecová, L., Østergaard, L.H., Skálová, T., Schnorr, K.M., Koval', T., Kolenko, P., Stránský, J., Sedlák, D., Dušková, J., Trundová, M., Hašek, J., Dohnálek, J.
Acta Cryst. 2021, D77, 755-775
https://doi.org/10.1107/S2059798321003533
PDB: 6ZE2, 6ZE3, 6ZE4, 6ZE5, 6ZE6, 6ZE7, 7AA2
SHELIXIR: automation of experimental phasing procedures using SHELXC/D/E
Kolenko, P., Stránský, J., Koval', T., Malý, M., Dohnálek, J.
J. Appl. Cryst. 54 (2021)
2020
Kouba, T., Kovaľ, T., Sudzinodá, P., Pospíšil, J., Brezovská, B., Hnilicová, J., Šanderová, H., Janoušková, M., Šiková, M., Halada, P., Sýkora, M., Barvík, I., Nováček, J., Trundová, M., Dušková, J., Skálová, T., Chon, U., Murakami, K. S., Dohnálek, J., Krásný, L.
Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase
Nature communications (2020) 11:6419
https://doi.org/10.1038/s41467-020-20158-4
PDB: 6YYS, 6YXU
Natural Killer Cell Activation Receptor NKp30 Oligomerization Depends on Its N-Glycosylation
Skořepa, O.; Pazicky, S.; Kalousková, B.; Bláha, J.; Abreu, C.; Ječmen, T.; Rosůlek, M.; Fish, A.; Sedivy, A.; Harlos, K.; Dohnálek, J.; Skálová, T.; Vaněk, O.
Cancers 2020, 12, 1998.
https://doi.org/10.3390/cancers12071998
PDB: 6YJP, SBGrid Data Bank: 753
Paired refinement under the control of PAIREF
Martin Malý, Kay Diederichs, Jan Dohnálek, Petr Kolenko
IUCrJ 7, 681-692.
doi: 10.1107/S2052252520005916.
https://pairef.fjfi.cvut.cz/
Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction
Tereza Skalova, Alzbeta Lengalova, Jan Dohnalek, Karl Harlos, Peter Mihalcin, Petr Kolenko, Martin Stranava, Jan Blaha, Toru Shimizu and Markéta Martínková
J. Biol. Chem.(2020) 295(6) 1587–1597
https://www.jbc.org/content/295/6/1587
PDB: 6OTD, SBGrid Data Bank: 715
2019
Trp–His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer
Tomáš Koval, Leona Švecová, Lars H. Østergaard, Tereza Skalova, Jarmila Dušková, Jindřich Hašek, Petr Kolenko, Karla Fejfarová, Jan Stránský, Mária Trundová & Jan Dohnálek
Scientific Reports, in press
https://doi.org/10.1038/s41598-019-50105-3
open access
Domain structure of HelD, an interaction partner of Bacillus subtilis RNA polymerase
Tomas Koval’, Petra Sudzinova, Terezia Perhacova,Maria Trundova, Tereza Skalova, Karla Fejfarova, Hana Sanderova, Libor Krasny, Jarmila Duskova and Jan Dohnalek
FEBS letters, 593 (2019) 996–1005
doi:10.1002/1873-3468.13385
2018
Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus. Terézia Kovaľová Tomáš Kovaľ Eva Benešová Patricie Vodičková Vojtěch Spiwok Petra Lipovová Jan Dohnálek.
Glycobiology, (2019), 29 (1), 59–73
https://doi.org/10.1093/glycob/cwy078.
PDB: 6GN6
Mária Trundová, Tomáš Kovaľ, Raymond J. Owens, Karla Fejfarová, Jarmila Dušková, Petr Kolenko and Jan Dohnálek
Highly stable single-strand-specific 3′-nuclease/nucleotidase from Legionella pneumophila
International Journal of Biological Macromolecules 114 (2018), 776-787
Int. J. Biol. Macromol.
doi: 10.1016/j.ijbiomac.2018.03.113
T. Kovaľ, J. Dohnálek
Characteristics and application of S1–P1 nucleases in biotechnology and medicine
Biotechnology Advances 36 (2018), 603-612
DOI: 10.1016/j.biotechadv.2017.12.007
Tomáš Podzimek, Tereza Přerovská, Jiří Šantrůček, Tomáš Kovaľ, Jan Dohnálek, Jaroslav Matoušek, Petra Lipovová
N-glycosylation of tomato nuclease TBN1 produced in N. benthamiana and its effect on the enzyme activity
Plant Science 276 (2018), 152-161
2017
Stranava, M., Man, P., Skalova, T., Kolenko, P., Blaha, J. ,Fojtikova, V. ,Martinek, V. ,Dohnalek, J. ,Lengalova, A. ,Rosulek, M. ,Shimizu, T. ,Martinkova, M. Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. J. Biol. Chem. (2017), 292(51), 20921-20935
doi: 10.1074/jbc.M117.817023
PDB: 5OHE, 5OHF, SBGrid Data Bank: 776 and 777
2016
T. Kovaľ, L.H. Oestergaard, J. Lehmbeck, A. Noergaard, P. Lipovová, J. Dušková, T. Skálová, M. Trundová, P. Kolenko, K. Fejfarová, J. Stránský, L. Švecová, J. Hašek, J. Dohnálek. (2016). Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity , and Inhibition. PLoS ONE, 11 (12), e0168832.
P. Mikulecký, J. Zahradník, P. Kolenko, J. Černý, T. Charnavets, L. Kolářová, I. Nečasová, P. N. Pham and B. Schneider.
Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity. Acta Cryst. (2016). D 72, 1017-1025. doi: 10.1107/S2059798316012237
PDB: 5eh1
Fejfarova, K., Kadek, A., Mrazek, H., Hausner, J., Tretyachenko, V., Koval, T., Man, P., Hasek, J., Dohnalek, J. Crystallization of nepenthesin I using a low-pH crystallization screen. Acta Cryst. F72, 24-28, 2016. doi:10.1107/S2053230X15022323.
Agirre, J., Ariza, A., Offen, W.A., Turkenburg, J.P., Roberts, S.M., McNicholas, S., Harris, P.V., McBrayer, B., Dohnalek, J., Cowtan, K.D., Davies, G.J., Wilson, K.S. 3-D structures of two heavily N-glycosylated Aspergillus sp. family GH3 beta-D-glucosidases. Acta Cryst. D72, 2059-7983, 2016
Dohnalek, J., McAuley, K. E., Brzozowski, A. M., Ostergaard, P. R., Svendsen, A., Wilson, K. S. Stabilization of Enzymes by Metal Binding: Structures of Two Alkalophilic Bacillus Subtilases and Analysis of the Second Metal-Binding Site of the Subtilase Family. Chapter in Understanding enzymes: Function, Design, Engineering and Analysis, Pan Stanford Publishing, ed. A. Svendsen, 203-266, 2016. doi: 10.4032/9789814669337. ISBN 789814669320.
2015
J. Stransky, T. Koval', T. Podzimek, A. Tycova, P. Lipovova, J. Matousek, P. Kolenko, K. Fejfarova, J. Duskova, T. Skalova, J. Hasek and J. Dohnalek The structure of a mutant of tomato multifunctional nuclease TBN1 with phosphate ion bound in the active centre explains the stabilization of the conserved crystal-packing motif of molecular superhelices.
Acta Cryst. (2015). F71, 1408-1415 [http://dx.doi.org/10.1107/S2053230X15018324]
PDB: 4jdg
T. Skálová, J. Bláha, K. Harlos, J. Dušková, T. Koval', J. Stránský, J. Hašek, O. Vaněk and J. Dohnálek
Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states
Acta Cryst. (2015). D71, 578-591 [ doi:10.1107/S1399004714027928 ]
Open Access
Acta Crystallographica Section D: Biological Crystallography, 2015, Volume D71, pages 578-591
http://creativecommons.org/licenses/by/2.0/uk/legalcode licence
PDB: 4qkg (monomeric LLT1), 4qkh and 4qki (dimeric LLT1), 4qkj (hexameric LLT1), SBGrid Data Bank: 722, 723, 724 and 726
2014
Koval', T.;Stransky, J.; Lipovova, P. ;Podzimek, T. ;Matousek, J. ; Duskova, J. ;Skalova, T.; Hasek, J. ;Fejfarova, K. ;Kolenko, P.; Dohnalek, J.
Structure features of TBN1, a P1/S1-like nuclease
FEBS JOURNAL, Volume: 281, Pages: 601-601, Supplement: 1, Special Issue: SI, Meeting Abstract: TUE-508, 2014
Wiedermannová J, Sudzinová P, Kovaľ T, Rabatinová A, Šanderova H, Ramaniuk O, Rittich Š, Dohnálek J, Fu Z, Halada P, Lewis P, Krásny L. Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res. (2014);42(8):5151-63.
2013
Andrea Štěpánková, Jarmila Dušková, Tereza Skálová, Jindřich Hašek, Tomáš Koval', Lars Henrik Ostergaard and Jan Dohnálek
Organophosphorous acid anhydrolase from Alteromonas macleodii - a structural study and functional relationship to prolidases
Acta Cryst. (2013) F69, 346-354.
PDB: 3RVA
Tomáš Koval’, Petra Lipovová, Tomáš Podzimek, Jaroslav Matoušek, Jarmila Dušková, Tereza Skálová, Andrea Štěpánková, Jindřich Hašek and Jan Dohnálek
Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis
Acta Cryst. (2013). D69, 213–226
PDB: TBN1, wild type, 3sng; N211D mutant, 4dj4
2012
Tereza Skalova, Kristyna Kotynkova, Jarmila Duskova, Jindrich Hasek, Tomas Koval, Petr Kolenko, Petr Novak, Petr Man, Pavel Hanc, Ondrej Vanek, Karel Bezouska, and Jan Dohnalek
Mouse Clr-g, a Ligand for NK Cell Activation Receptor NKR-P1F: Crystal Structure and Biophysical Properties
J. of Immunology, 2012, 189 (10), 4881-4889
cover page www.jimmunol.org/content/189/10/local/front-matter.pdf
mClrg in PDB: 3RS1, SBGrid Data Bank: 713
http://www.jimmunol.org/content/189/10/4881.abstract.html
doi: 10.4049/jimmunol.1200880
Natasza E. Ziółkowska, Anna Bujacz, Ramnarayan S. Randad, John W. Erickson, Tereza Skálová, Jindřich Hašek and Grzegorz Bujacz
New Active HIV-1 Protease Inhibitors Derived from 3-Hexanol. Conformation Study of the Free Inhibitors in Crystalline State and in Complex with the Enzyme
Chem. Biol. Drug Des. 2012, 79, 798-809
DOI: 10.1111/j.1747-0285.2012.01328.x
2011
J. Hasek, J. Labsky, T. Skalova, P. Kolenko, J. Dohnalek, J. Duskova, A. Stepankova und T. Koval
Polymer structure database and protein-polymer interactions
Z. Kristallogr. Proc. 1 (2011) 475-480 / DOI 10.1524/zkpr.2011.0072
http://www.oldenbourg-link.com/toc/zkpr/2011/1
(nema impakt faktor)
Sample preparation in separation of the extracellular chitinolytic enzymes of the human intestinal bacterium Clostridium paraputrificum J4 from the culture fluids
Tishchenko Galina; Simunek Jiri; Bartonova Hana; et al.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES, 879 (22), 2175-2178, 2011
DOI: 10.1016/j.jchromb.2011.05.043
P. Kolenko, D. Rozbeský, O. Vanek, K. Bezouska, J. Hasek and J. Dohnálek
Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution
Acta Cryst. (2011). F67, 1519-1523 [ doi:10.1107/S1744309111046203 ]
PDB : 3t3a
Petr Kolenko, Daniel Rozbesky, Ondrej Vanek, Vladimir Kopecky, Jr.; Katerina Hofbauerova, Petr Novak, Petr Pompach, Jindrich Hasek, Tereza Skalova, Karel Bezouska, Jan Dohnalek
Molecular architecture of mouse activating NKR-P1 receptors
JOURNAL OF STRUCTURAL BIOLOGY, 2011, 175 (3), 434-441
DOI: 10.1016/j.jsb.2011.05.001
PDB: 3M9Z
Jarmila Dušková, Galina Tishchenko, Evgenia Ponomareva, Jiří Šimůnek, Ingrid Koppová, Tereza Skálová, Andrea Štěpánková, Jindřich Hašek and Jan Dohnálek
Chitinolytic enzymes from bacterium inhabiting human gastrointestinal tract - critical parameters of protein isolation from anaerobic culture
Acta Biochimica Polonica, Vol. 58, No. 2/2011, 261–263
http://www.actabp.pl/pdf/2_2011/261.pdf
Koval', T; Lipovová, P; Podzimek, T; Matousek, J; Duskova, J; Skalova, T; Stepankova, A; Hasek and J Dohnálek, J.
Crystallization of recombinant bifunctional nuclease TBN1 from tomato
Acta Cryst. (2011). F67, 124-128
http://dx.doi.org/10.1107/S1744309110048177
pdf below on this page
Skalova, T; Duskova, J; Hasek, J; Stepankova, A; Koval, T; Ostergaard L.H. and Dohnalek, J.
Structure of laccase from Streptomyces coelicolor after soaking with potassium hexacyanoferrate and at an improved resolution of 2.3 A
Acta Cryst. (2011). F67, 27-32.
http://dx.doi.org/10.1107/S1744309110046099
PDB: 3KW8, SBGrid Data Bank: 717
pdf below on this page
2010
Tishchenko, G.; Koppova, I.;, Simunek, J.; Dohnalek, J.
Extracellular Complex of Chitinolytic Enzymes of Clostridium paraputrificum Strain J4 Separated by Membrane Ultrafiltration
FOLIA MICROBIOLOGICA Volume: 55 Issue: 4 Pages: 386-389 Published: 2010
A. Stsiapanava, J. Dohnalek, J. A. Gavira, M. Kuty, T. Koudelakova, J. Damborsky and I. Kuta Smatanova
Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels
Acta Cryst. (2010). D66, 962-969
PDB: 3fbw, 3g9x and 3fwh
Skalova, T; Duskova, J; Hasek, J; Kolenko, P; Stepankova, A; Dohnalek, J.
Alternative polymer precipitants for protein crystallization
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2010, 43, 737-742.
2009
Kolenko, P; Skalova, T; Vanek, O; Stepankova, A; Duskova, J; Hasek, J; Bezouska, K; Dohnalek, J
The high-resolution structure of the extracellular domain of human CD69 using a novel polymer
ACTA CRYSTALLOGRAPHICA, 2009, F65, 1258-1260.
PDB: 3HUP
pdf below on this page
Duskova, J; Dohnalek, J; Skalova, T; Oestergaard, LH; Fuglsang, CC; Kolenko, P; Stepankova, A; Hasek, J
Crystallization of carbohydrate oxidase from Microdochium nivale
ACTA CRYSTALLOGRAPHICA, 2009, F65, 638-640.
PDB: 3RJ8, SBGrid Data Bank: 796
Skalova, T; Dohnalek, J; Ostergaard, LH; Ostergaard, PR; Kolenko, P; Duskova, J; Stepankova, A; Hasek, J
The structure of the small laccase from Streptomyces coelicolor reveals a link between laccases and nitrite reductases
JOURNAL OF MOLECULAR BIOLOGY, 2009, 385, 1165-1178.
PDB: 3CG8, SBGrid Data Bank: 718
Kraus, J. P.; Hašek, J.; Kožich, V.; Collard, R.; Venezia, S.; Janošíková, B.; Wang, J.; Stabler, S. P.; Allen, R. H.; Jakobs, C.; Finn, C. T.; Chien, Y. H.; Hwu, W. L.; Hegele, R. A.; Mudd, S. H.
Cystathionine gamma-lyase: Clinical, metabolic, genetic, and structural studies.
Molecular Genetics and Metabolism, 2009, 97, 250-259.
Hašek, J; Makrlík, E; Dušek, M; Císařová, I; Dohnálek, J; Dušková, J; Skálová, T
Structure of valinomycin and its complexes.
MATERIALS STRUCTURE IN CHEMISTRY, BIOLOGY, PHYSICS, AND TECHNOLOGY, 2009, 16, 30-31.
2008
Kolenko, P; Dohnalek, J; Duskova, J; Skalova, T; Collard, R; Hasek, J
New insights into intra- and intermolecular interactions of immunoglobulins; Crystal structure of mouse IgG2b-Fc at 2.1 Å resolution
IMMUNOLOGY, 2008, 126, 378-385.
PDB: 2RGS
Vanek, O; Nalezkova, M; Kavan, D; Borovickova, I; Pompach, P; Novak, P; Kumar, V; Vannucci, L; Hudecek, J; Brynda, J; Kolenko, P; Dohnalek, J; Kaderavek, P; Chmelik, J; Gorcik, L; Zidek, L; Sklenar, V; Bezouska, K
Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemical stability display prolonged circulation and remain intact in the blood of mice
FEBS Journal, 2008, 275, 5589-5606.
Kolenko, P; Skalova, T; Dohnalek, J; Hasek, J
L-Fucose in crystal structures of IgG-Fc: Reinterpretation of experimental data
COLLECT. CZECH. CHEM. COMMUN., 2008, 73, 608-615.
http://cccc.uochb.cas.cz/73/5/0608/
2007
Spiwok, V; Lipovova, P; Skalova, T; Duskova, J; Dohnalek, J; Hasek, J; Russell, NJ; Kralova, B
Cold-active enzymes studied by comparative molecular dynamics simulation
J MOL MODEL, 2007, 13, 485-497.
Skalova, T; Dohnalek, J; Oestergaard, L.H.; Oestergaard, P.R.; Kolenko, P.; Duskova, J.; Hasek, J.
Crystallization and preliminary X-ray diffraction analysis of the small laccase from Streptomyces coelicolor
ACTA CRYSTALLOGRAPHICA, 2007, F63, 1077-1079.
pdf below on this page
2006
Duskova, J; Dohnalek, J; Skalova, T; Petrokova, H; Vondrackova, E; Hradilek, M; Konvalinka, J; Soucek, M; Brynda, J; Fabry, M; Sedlacek, J; Hasek, J
On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 angstrom resolution
ACTA CRYSTALLOGRAPHICA, 2006, D62(5), 489-497
PDB: 1ZSF, 1ZSR, SBGrid Data Bank: 729
Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Hradilek, M; Soucek, M; Konvalinka, J; Hasek, J
HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site
JOURNAL OF MEDICINAL CHEMISTRY, 2006, 49(19), 5777-5784
PDB: 1ZJ7, 1ZLF, SBGrid Data Bank: 725 and 721
Duskova, J; Labsky, J; Cisarova, I; Skalova, T; Dohnalek, J; Hasek, J
4-Acetamido-3,3,5,5-[H-2(4)]-2,2,6,6-tetra([H-2(3)]methyl)piperidin-1-yl oxyl 0.33-hydrate
ACTA CRYSTALLOGRAPHICA, 2006, C62(9), O563- O566
Duskova, J; Labsky, J; Dusek, M; Hasek, J
The 3,3,5,5[H-2(4)]-4-methacrylamido-2,2,6,6-tetra([H-2(3)]methyl)piperidin-1-yloxyl radical
ACTA CRYSTALLOGRAPHICA, 2006, E62(2), O811-O813
Hasek, J.
Poly(ethylene glycol) interactions with proteins
Z.Kristallogr.Suppl., 2006, 23, 613-618.
2005
Spiwok, V; Lipovova, P; Skalova, T; Vondrackova, E; Dohnalek, J; Hasek, J; Kralova, B
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2005, 19(12), 887-901
Skalova, T; Dohnalek, J; Spiwok, V; Lipovova, P; Vondrackova, E; Petrokova, H; Duskova, J; Strnad, H; Kralova, B; Hasek, J
Cold-active beta-galactosidase from Arthrobacter sp C2-2 forms compact 660 kDa hexamers: Crystal structure at 1.9 angstrom resolution
JOURNAL OF MOLECULAR BIOLOGY, 2005, 353(2), 282-294
PDB: 1YQ2
Petrokova, H; Vondrackova, E; Skalova, T; Dohnalek, J; Lipovova, P; Spiwok, V; Strnad, H; Kralova, B; Hasek, J
Crystallization and preliminary X-ray diffraction analysis of cold-active beta-galactosidase from Arthrobacter sp C2-2
COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, 2005, 70(1), 124-132
http://cccc.uochb.cas.cz/70/1/0124/
2004
Petrokova, H; Duskova, J; Dohnalek, J; Skalova, T; Vondrackova-Buchtelova, E; Soucek, M; Konvalinka, J; Brynda, J; Fabry, M; Sedlacek, J; Hasek, J
Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors
EUROPEAN JOURNAL OF BIOCHEMISTRY, 2004, 271(22), 4451-4461
PDB: 1M0B, SBGrid Data Bank: 730
Spiwok, V; Lipovova, P; Skalova, T; Buchtelova, E; Hasek, J; Kralova, B
Role of CH/pi interactions in substrate binding by Escherichia coli beta-galactosidase
CARBOHYDRATE RESEARCH, 2004, 339(13), 2275-2280
2003
Skalova, T; Hasek, J; Dohnalek, J; Petrokova, H; Buchtelova, E; Duskova, J; Soucek, M; Majer, P; Uhlikova, T; Konvalinka, J
An ethylenamine inhibitor binds tightly to both wild type and mutant HIV-1 proteases. Structure and energy study
JOURNAL OF MEDICINAL CHEMISTRY, 2003, 46(9), 1636-1644
PDB: 1LZQ, SBGrid Data Bank: 720
2002
Dohnalek, J; Hasek, J; Duskova, J; Petrokova, H; Hradilek, M; Soucek, M; Konvalinka, J; Brynda, J; Sedlacek, J; Fabry, M
Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a peptidomimetic inhibitor
JOURNAL OF MEDICINAL CHEMISTRY, 2002, 45(7), 1432-1438
PDB: 1IIQ, SBGrid Data Bank: 728
Skalova, T; Hasek, J; Dohnalek, J; Petrokova, H; Buchtelova, E;
Mutant HIV-1 protease complexed with tetrapeptide inhibitor - Preliminary report
ACTA PHYSICA POLONICA A, 2002, 101(5), 659-663
2001
Dohnalek, J; Hasek, J; Duskova, J; Petrokova, H; Hradilek, M; Soucek, M; Konvalinka, J; Brynda, J; Sedlacek, J; Fabry, M
A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease
ACTA CRYSTALLOGRAPHICA, 2001, D57(3), 472-476
PDB: 1FQX, SBGrid Data Bank: 727
Duskova, J; Labsky, J; Hasek, J; Cisarova, I
TI 3-ethoxycarbonyl-2,2,5,5-tetramethyl-1H-2,5-dihydropyrrol-1-yloxyl
ACTA CRYSTALLOGRAPHICA, 2001, E57(1), O85- O86
Not published PDBs:
Not published PDBs:
PDB: 1ZPK (Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2)
PDB: 1ZBG (Crystal structure of a complex of mutant hiv-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2)
PhD. Thesis
PhD. Thesis
Petr Kolenko
Study of macromolecular complexes of immune system: structure-function relationship (in Czech)
Czech Technical University, Dept. of Solid State Engineering, Prague, 2009
PDB: 2RGS, 3HUP
Tereza Skálová
HIV-1 protease and its interaction with inhibitors (in Czech)
Charles University, Faculty of Mathematics and Physics, Prague, 2003
PDB: 1LZQ
Jan Dohnálek
X-ray Diffraction Methods for Solving Macromolecular Structures - Application to Enzymes (in English)
CVUT, FJFI, Prague, 2000
PDB: 1FQX , 1IIQ , 1PGJ
MSc. Thesis
MSc. Thesis
Andrea Stepankova
Characterization and crystallization of bio-macromolecules for X-ray structural analysis - application on enzyme beta-galactosidase from bakterium Arthrobacter sp. C2-2 (in Czech)
CVUT, FJFI, Prague, 2007
Petr Kolenko
Structure determination of IgG2b-Fc using X-ray diffraction (in Czech)
CVUT, FJFI, Prague, 2006
Ondrej Hartman
Structure determination of mutant form of HIV protease using diffraction methods (in Czech)
CVUT, FJFI, Prague, 2004
Petr Skokan
X-ray structure analysis of the HIV-1 protease mutant with hydroxyethylamine peptidomimetic inhibitor
CVUT, FJFI, Prague, 2002
Martin Saturka
Computer modeling of conformation inhibition of HIV-1 Protease
Charles University, Faculty of Science, Prague, 2000
Bc. Thesis
Bc. Thesis
Leona Švecová
Krystalizace biologických makromolekul pro strukturní studie pomocí rentgenové difrakce
obor: Fyzikální inženýrství
zaměření: Inženýrství pevných látek
obhájena: 30.srpen 2012
Vedoucí práce: RNDr. Tereza Skálová, PhD.
Konzultant: Prof. Ing. Nikolaj Ganev, CSc.
CVUT, FJFI, Prague, 2012
Other publications
Other publications
Hasek, J; Skalova, T; Petrokova, H; Buchtelova, E; Dohnalek, J; Spiwok, V; Lipovova, P; Strnad, H; Kralova, B
Beta-galactosidase from psychrotrophic microorganism (strain Arthrobacter)
Materials Structure, 2004, 11(1), 18-19
Buchtelova, E
Neutron crystallography of biological molecules
Materials Structure, 2002, 9(1), 20-21
Hasek, J
Protein crystallography with synchrotron radiation (in Czech)
Proteinová krystalografie na zdrojích synchrotronového záření
Materials Structure, 2002, 9(1), 22-25
Selected conferences
Selected conferences
T. Skálová, J. Dušková, J. Hašek, P. Kolenko, T. Kovaľ, A. Štěpánková, J. Dohnálek
Protein crystallization with alternative polymer precipitants
Proceedings of RAMC 2011 - Recent Advances in Macromolecular Crystallization,
Le Bischenberg Conference Centre, Strasbourg, France, page 40.
(poster awarded as the best poster)
J. Dohnálek, T. Koval', P. Lipovová, T. Podzimek and J. Matousek
Structure analysis of group I plant nucleases
J. Synchrotron Rad. (2011). 18, 29-30
open access
Hasek, J.
Protein surface shielding agents in protein crystallization
J. Synchrotron Rad. (2011), 18, 50-52
open access
J. Hasek, J. Dohnálek, T. Skálová, J. Dusková, A. Stepánková and P. Kolenko
Synthetic polymers in biological environment
Acta Cryst. (2010). A66, s247-s248
open access, 26th ECM Darmstadt
http://journals.iucr.org/a/issues/2010/a1/00/issconts.html
J. Hasek, T. Skálová, J. Dusková, J. Dohnálek, P. Kolenko, T. Koval and A. Stepánková
Hydrophilic polymers as efficient protein surface-shielding agents in protein crystallization
Acta Cryst. (2009). A65, s155-s156
open access, 25th ECM Istanbul
http://journals.iucr.org/a/issues/2009/a1/00/issconts.html
Kolenko, Petr; Dohnálek, Jan; Dušková, Jarmila; Koval, Tomáš; Skálová, Tereza; Štěpánková, Andrea; Hašek, Jindřich.
Nové polymery pro krystalizaci biologických makromolekul: Aplikace na protein CD69.
Chemické listy (2009). 103, 441.
www.chemicke-listy.cz/docs/full/2009_05_427-457.pdf
Štěpánková, Andrea; Skálová, Tereza; Dohnálek, Jan; Dušková, Jarmila; Kolenko, Petr; Hašek, Jindřich; Lipovová, P.
Preferenční selekce izomeru D-galaktono-1,5-laktonu enzymem .beta.-galaktosidasou z Arthrobacter sp. C2-2 pro vazbu do aktivního místa.
Chemické listy (2009). 103, 450-451.
www.chemicke-listy.cz/docs/full/2009_05_427-457.pdf
Hasek, J; Dohnalek, J; Duskova, J; Skalova, T; Kolenko, P; Koval, T; Stepankova, A
Polymer and co-polymer surface modifying effects in the protein crystallization
Acta Cryst. (2008). A64,C233.
http://journals.iucr.org/a/issues/2008/a1/00/issconts.html
open access, 21th IUCr congress, Japan
Duskova, J; Dohnalek, J; Skalova, T; Ostergaard, LH; de Maria, L; Kolenko, P; Stepankova, A; Hasek, J
Crystallization of carbohydrate oxidase from Microdochium nivale
Acta Cryst. (2008). A64, C236.
http://journals.iucr.org/a/issues/2008/a1/00/issconts.html
open access, 21th IUCr congress, Japan
Skalova, T; Dohnalek, J; Ostergaard, LH; Ostergaard, PR; Kolenko, P; Duskova, J; Stepankova, A; Hasek, J
Structure of laccase from Streptomyces Coelicolor
Acta Cryst. (2008). A64, C351.
http://journals.iucr.org/a/issues/2008/a1/00/issconts.html
open access, 21th IUCr congress, Japan
Dohnalek, J; Koval, T; Dusek, M
Protein diffraction experiments with Atlas CCD detector
Acta Cryst. (2008). A64, C192.
http://journals.iucr.org/a/issues/2008/a1/00/issconts.html
open access, 21th IUCr congress, Japan
Skalova, T; Dohnalek, J; Stepankova, A; Lipovova, P; Spiwok, V; Duskova, J; Kolenko, P; Petrokova, H; Strnad, H; Kralova, B; Hasek, J
Structural properties and electrostatics of cold-active beta-galactosidase
Acta Cryst. (2007). A63, s125-126.
http://journals.iucr.org/a/issues/2007/a1/00/issconts.html
open access, 24th ECM Marrakech
Hasek, J; Kolenko, P; Dohnalek, J; Duskova, J; Skalova, T
Interaction of hydrophilic polymers with proteins
Acta Cryst. (2007). A63, s177.
http://journals.iucr.org/a/issues/2007/a1/00/issconts.html
open access, 24th ECM Marrakech
Dohnalek, J; Svendsen, A; Wilson, K. S.
Identity of ions in the second site of subtilisins
Acta Cryst. (2007). A63, s120.
http://journals.iucr.org/a/issues/2007/a1/00/issconts.html
open access, 24th ECM Marrakech
Hasek, J; Dohnalek, J; Skalova, T; Duskova, J; Kolenko, P; Petrokova, H; Vondráèkova, E
HIV protease inhibition seen by X-ray diffraction and molecular dynamics
PROTEIN SCIENCE, 2005, 14, 276
Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Vondrackova, E; Hasek, J
Series of HIV-1 protease nanomolar inhibitors; binding to WT and mutant protease
ACTA CRYSTALLOGRAPHICA, 2005, A61, C243
open access, 20th IUCr congress, Florence
http://journals.iucr.org/a/issues/2005/a1/00/issconts.html
Dohnalek, J; Skalova, T; Duskova, J; Petrokova, H; Vondrackova, E; Lipovova, P; Spiwok, V; Kralova, B; Hasek, J
Cage-like hexamers of cold-active -galactosidase from Arthrobacter sp. C2-2
ACTA CRYSTALLOGRAPHICA, 2005, A61, C237
open access, 20th IUCr congress, Florence
http://journals.iucr.org/a/issues/2005/a1/00/issconts.html
Hasek, J; Zimmermann, K; Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Vondrackova, E
HIV protease inhibition seen by X-ray diffraction and molecular dynamics
ACTA CRYSTALLOGRAPHICA, 2005, A61, C242-243
open access, 20th IUCr congress, Florence
http://journals.iucr.org/a/issues/2005/a1/00/issconts.html
Skalova, T; Zimmermann, K; Taly, J F; Hasek J
HIV-1 protease – process of ligand unbinding
Proceedings of Modelling interactions in biomolecules II, p. 46, 2005
Hasek, J; Skalova, T; Dohnalek, J; Duskova, J; Petrokova, H; Vondrackova, E; Zimmermann, K.,
Drug Design Based on X-ray diffraction and steered molecular dynamics
Materials Structure, 12, 208-210, 2005.
http://www.xray.cz/ms/bul2005-3/zentiva.pdf
Skalova, T; Hasek, J; Dohnalek, J; Petrokova, H
Real and virtual disorder in complexes of HIV protease
ACTA CRYSTALLOGRAPHICA 2002, A58 , C290
open access, 19th IUCr congress, Geneva
http://journals.iucr.org/a/issues/2002/s1/00/issconts.html
Petrokova, H; Dohnalek, J; Skalova, T; Duskova, J; Hasek, J
Influence of mutations of HIV-1 protease on binding of hydroxyethylamine and ethylenamine type inhibitors
ACTA CRYSTALLOGRAPHICA, 2002, A58, C290
open access, 19th IUCr congress, Geneva
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